A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.

PubMed

Muscarella, Robert; Uriarte, María; Erickson, David L; Swenson, Nathan G; Zimmerman, Jess K; Kress, W John

2014-01-01

The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning.

Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known.

PubMed

Housworth, E A; Martins, E P

2001-01-01

Statistical randomization tests in evolutionary biology often require a set of random, computer-generated trees. For example, earlier studies have shown how large numbers of computer-generated trees can be used to conduct phylogenetic comparative analyses even when the phylogeny is uncertain or unknown. These methods were limited, however, in that (in the absence of molecular sequence or other data) they allowed users to assume that no phylogenetic information was available or that all possible trees were known. Intermediate situations where only a taxonomy or other limited phylogenetic information (e.g., polytomies) are available are technically more difficult. The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information (e.g., four taxa belong together in a subclade). The procedure can be used to conduct comparative analyses when the phylogeny is only partially resolved or can be used in other randomization tests in which large numbers of possible phylogenies are needed.

Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences

PubMed Central

Hibbett, David S.; Pine, Elizabeth M.; Langer, Ewald; Langer, Gitta; Donoghue, Michael J.

1997-01-01

Homobasidiomycete fungi display many complex fruiting body morphologies, including mushrooms and puffballs, but their anatomical simplicity has confounded efforts to understand the evolution of these forms. We performed a comprehensive phylogenetic analysis of homobasidiomycetes, using sequences from nuclear and mitochondrial ribosomal DNA, with an emphasis on understanding evolutionary relationships of gilled mushrooms and puffballs. Parsimony-based optimization of character states on our phylogenetic trees suggested that strikingly similar gilled mushrooms evolved at least six times, from morphologically diverse precursors. Approximately 87% of gilled mushrooms are in a single lineage, which we call the “euagarics.” Recently discovered 90 million-year-old fossil mushrooms are probably euagarics, suggesting that (i) the origin of this clade must have occurred no later than the mid-Cretaceous and (ii) the gilled mushroom morphology has been maintained in certain lineages for tens of millions of years. Puffballs and other forms with enclosed spore-bearing structures (Gasteromycetes) evolved at least four times. Derivation of Gasteromycetes from forms with exposed spore-bearing structures (Hymenomycetes) is correlated with repeated loss of forcible spore discharge (ballistospory). Diverse fruiting body forms and spore dispersal mechanisms have evolved among Gasteromycetes. Nevertheless, it appears that Hymenomycetes have never been secondarily derived from Gasteromycetes, which suggests that the loss of ballistospory has constrained evolution in these lineages. PMID:9342352

Zooplankton and the Ocean Carbon Cycle.

PubMed

Steinberg, Deborah K; Landry, Michael R

2017-01-03

Marine zooplankton comprise a phylogenetically and functionally diverse assemblage of protistan and metazoan consumers that occupy multiple trophic levels in pelagic food webs. Within this complex network, carbon flows via alternative zooplankton pathways drive temporal and spatial variability in production-grazing coupling, nutrient cycling, export, and transfer efficiency to higher trophic levels. We explore current knowledge of the processing of zooplankton food ingestion by absorption, egestion, respiration, excretion, and growth (production) processes. On a global scale, carbon fluxes are reasonably constrained by the grazing impact of microzooplankton and the respiratory requirements of mesozooplankton but are sensitive to uncertainties in trophic structure. The relative importance, combined magnitude, and efficiency of export mechanisms (mucous feeding webs, fecal pellets, molts, carcasses, and vertical migrations) likewise reflect regional variability in community structure. Climate change is expected to broadly alter carbon cycling by zooplankton and to have direct impacts on key species.

The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation

PubMed Central

Yang, Guan-Dong; Agapow, Paul-Michael

2017-01-01

The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors. PMID:28644846

The phylogenetic structure of plant-pollinator networks increases with habitat size and isolation.

PubMed

Aizen, Marcelo A; Gleiser, Gabriela; Sabatino, Malena; Gilarranz, Luis J; Bascompte, Jordi; Verdú, Miguel

2016-01-01

Similarity among species in traits related to ecological interactions is frequently associated with common ancestry. Thus, closely related species usually interact with ecologically similar partners, which can be reinforced by diverse co-evolutionary processes. The effect of habitat fragmentation on the phylogenetic signal in interspecific interactions and correspondence between plant and animal phylogenies is, however, unknown. Here, we address to what extent phylogenetic signal and co-phylogenetic congruence of plant-animal interactions depend on habitat size and isolation by analysing the phylogenetic structure of 12 pollination webs from isolated Pampean hills. Phylogenetic signal in interspecific interactions differed among webs, being stronger for flower-visiting insects than plants. Phylogenetic signal and overall co-phylogenetic congruence increased independently with hill size and isolation. We propose that habitat fragmentation would erode the phylogenetic structure of interaction webs. A decrease in phylogenetic signal and co-phylogenetic correspondence in plant-pollinator interactions could be associated with less reliable mutualism and erratic co-evolutionary change. © 2015 John Wiley & Sons Ltd/CNRS.

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks.

PubMed

Pérez-Valera, Eduardo; Goberna, Marta; Faust, Karoline; Raes, Jeroen; García, Carlos; Verdú, Miguel

2017-01-01

Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co-occurrence networks to detect co-presence (bacteria that co-occur) or exclusion (bacteria that do not co-occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co-presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co-presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co-presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Spatial and phylogenetic variation in plant defense in a tropical moist forest canopy community

NASA Astrophysics Data System (ADS)

McManus, K. M.; Asner, G. P.; Martin, R.

2013-12-01

Plants employ physical and chemical defenses to mitigate damage caused by herbivory. Spatial patterns of plant defense may provide insight into the role of plant-herbivore interactions in the assembly of plant communities. Within plant communities, the spatial overdispersion of anti-herbivore defenses by individuals may reflect a strategy to avoid host shifts from herbivore assemblages of neighboring plants. However, variation in plant defense may also result from trade-offs between foliar investment into defense and growth, mediated by variations in abiotic nutrient availability, or constrained by phylogeny. We measured four defensive traits (leaf toughness, total phenols, condensed tannins, and hydrolysable tannins) and three growth traits (LMA, C:N, total protein) of outer canopy foliage for 345 canopy trees representing 78 species, 65 genera, and 34 families in a moist tropical rainforest on Barro Colorado Island, Panama. The outer canopy provides an important, but rarely evaluated, cross-sectional image of the tropical forest ecosystem, and observations at this scale may provide an important link between field and remote sensing based studies. We used existing data on edaphic and geological properties to investigate the relationships of abiotic nutrient variation on variation in defense. Using regression and nested random-effects variance modeling, we found strong phylogenetic association with defensive traits at the family and species level, and little evidence for a trade-off between defensive traits. Greater understanding of phylogenetic structure in trait variation may yield improved characterizations of tropical biodiversity, from functional traits to risk assessments.

Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition event.

PubMed

Schneider, Kevin; Resl, Philipp; Spribille, Toby

2016-07-01

Large, architecturally complex lichen symbioses arose only a few times in evolution, increasing thallus size by orders of magnitude over those from which they evolved. The innovations that enabled symbiotic assemblages to acquire and maintain large sizes are unknown. We mapped morphometric data against an eight-locus fungal phylogeny across one of the best-sampled thallus size transition events, the origins of the Placopsis lichen symbiosis, and used a phylogenetic comparative framework to explore the role of nitrogen-fixing cyanobacteria in size differences. Thallus thickness increased by >150% and fruiting body core volume increased ninefold on average after acquisition of cyanobacteria. Volume of cyanobacteria-containing structures (cephalodia), once acquired, correlates with thallus thickness in both phylogenetic generalized least squares and phylogenetic generalized linear mixed-effects analyses. Our results suggest that the availability of nitrogen is an important factor in the formation of large thalli. Cyanobacterial symbiosis appears to have enabled lichens to overcome size constraints in oligotrophic environments such as acidic, rain-washed rock surfaces. In the case of the Placopsis fungal symbiont, this has led to an adaptive radiation of more than 60 recognized species from related crustose members of the genus Trapelia. Our data suggest that precyanobacterial symbiotic lineages were constrained to forming a narrow range of phenotypes, so-called cryptic species, leading systematists until now to recognize only six of the 13 species clusters we identified in Trapelia. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Should I stay or should I go? Mycorrhizal plants are more likely to invest in long-distance seed dispersal than non-mycorrhizal plants.

PubMed

Correia, Marta; Heleno, Ruben; Vargas, Pablo; Rodríguez-Echeverría, Susana

2018-05-01

Seed dispersal and mycorrhizal associations are key mutualisms for the functioning and regeneration of plant communities; however, these processes have seldom been explored together. We hypothesised that obligatory mycorrhizal plants will be less likely to have long-distance dispersal (LDD) syndromes since the probability of finding suitable mycorrhizal partners is likely to decrease with distance to the mother plant. We contrasted the mycorrhizal status and LDD syndromes for 1960 European plant species, using phylogenetically corrected log-linear models. Contrary to our expectation, having specialised structures for LDD is more frequent in obligate mycorrhizal plants than in non-mycorrhizal plants, revealing that lack of compatible mutualists does not constrain investment in LDD structures in the European Flora. Ectomycorrhizal plants associated with wind-dispersing fungi are also more likely to have specialised structures for wind dispersal. Habitat specificity and narrower niche of non-mycorrhizal plants might explain the smaller investment in specialised structures for seed dispersal. © 2018 John Wiley & Sons Ltd/CNRS.

Phylogenetic comparative analysis of electric communication signals in ghost knifefishes (Gymnotiformes: Apteronotidae).

PubMed

Turner, Cameron R; Derylo, Maksymilian; de Santana, C David; Alves-Gomes, José A; Smith, G Troy

2007-12-01

Electrocommunication signals in electric fish are diverse, easily recorded and have well-characterized neural control. Two signal features, the frequency and waveform of the electric organ discharge (EOD), vary widely across species. Modulations of the EOD (i.e. chirps and gradual frequency rises) also function as active communication signals during social interactions, but they have been studied in relatively few species. We compared the electrocommunication signals of 13 species in the largest gymnotiform family, Apteronotidae. Playback stimuli were used to elicit chirps and rises. We analyzed EOD frequency and waveform and the production and structure of chirps and rises. Species diversity in these signals was characterized with discriminant function analyses, and correlations between signal parameters were tested with phylogenetic comparative methods. Signals varied markedly across species and even between congeners and populations of the same species. Chirps and EODs were particularly evolutionarily labile, whereas rises differed little across species. Although all chirp parameters contributed to species differences in these signals, chirp amplitude modulation, frequency modulation (FM) and duration were particularly diverse. Within this diversity, however, interspecific correlations between chirp parameters suggest that mechanistic trade-offs may shape some aspects of signal evolution. In particular, a consistent trade-off between FM and EOD amplitude during chirps is likely to have influenced the evolution of chirp structure. These patterns suggest that functional or mechanistic linkages between signal parameters (e.g. the inability of electromotor neurons increase their firing rates without a loss of synchrony or amplitude of action potentials) constrain the evolution of signal structure.

Disentangling environmental and spatial effects on phylogenetic structure of angiosperm tree communities in China.

PubMed

Qian, Hong; Chen, Shengbin; Zhang, Jin-Long

2017-07-17

Niche-based and neutrality-based theories are two major classes of theories explaining the assembly mechanisms of local communities. Both theories have been frequently used to explain species diversity and composition in local communities but their relative importance remains unclear. Here, we analyzed 57 assemblages of angiosperm trees in 0.1-ha forest plots across China to examine the effects of environmental heterogeneity (relevant to niche-based processes) and spatial contingency (relevant to neutrality-based processes) on phylogenetic structure of angiosperm tree assemblages distributed across a wide range of environment and space. Phylogenetic structure was quantified with six phylogenetic metrics (i.e., phylogenetic diversity, mean pairwise distance, mean nearest taxon distance, and the standardized effect sizes of these three metrics), which emphasize on different depths of evolutionary histories and account for different degrees of species richness effects. Our results showed that the variation in phylogenetic metrics explained independently by environmental variables was on average much greater than that explained independently by spatial structure, and the vast majority of the variation in phylogenetic metrics was explained by spatially structured environmental variables. We conclude that niche-based processes have played a more important role than neutrality-based processes in driving phylogenetic structure of angiosperm tree species in forest communities in China.

Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest.

PubMed

Jin, Yi; Qian, Hong; Yu, Mingjian

2015-01-01

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from seedlings to canopy trees, as well as forest gap influence on the phylogenetic structure of forest regeneration in a forest of the subtropical region in China. We investigate changes in phylogenetic relatedness (measured as NRI) of tree species from seedlings, saplings, treelets to canopy trees; we compare the phylogenetic turnover (measured as βNRI) between canopy trees and seedlings in forest understory with that between canopy trees and seedlings in forest gaps. We found that phylogenetic relatedness generally increases from seedlings through saplings and treelets up to canopy trees, and that phylogenetic relatedness does not differ between seedlings in forest understory and those in forest gaps, but phylogenetic turnover between canopy trees and seedlings in forest understory is lower than that between canopy trees and seedlings in forest gaps. We conclude that tree species tend to be more closely related from seedling to canopy layers, and that forest gaps alter the seedling phylogenetic turnover of the studied forest. It is likely that the increasing trend of phylogenetic clustering as tree stem size increases observed in this subtropical forest is primarily driven by abiotic filtering processes, which select a set of closely related evergreen broad-leaved tree species whose regeneration has adapted to the closed canopy environments of the subtropical forest developed under the regional monsoon climate.

Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest

PubMed Central

Jin, Yi; Qian, Hong; Yu, Mingjian

2015-01-01

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from seedlings to canopy trees, as well as forest gap influence on the phylogenetic structure of forest regeneration in a forest of the subtropical region in China. We investigate changes in phylogenetic relatedness (measured as NRI) of tree species from seedlings, saplings, treelets to canopy trees; we compare the phylogenetic turnover (measured as βNRI) between canopy trees and seedlings in forest understory with that between canopy trees and seedlings in forest gaps. We found that phylogenetic relatedness generally increases from seedlings through saplings and treelets up to canopy trees, and that phylogenetic relatedness does not differ between seedlings in forest understory and those in forest gaps, but phylogenetic turnover between canopy trees and seedlings in forest understory is lower than that between canopy trees and seedlings in forest gaps. We conclude that tree species tend to be more closely related from seedling to canopy layers, and that forest gaps alter the seedling phylogenetic turnover of the studied forest. It is likely that the increasing trend of phylogenetic clustering as tree stem size increases observed in this subtropical forest is primarily driven by abiotic filtering processes, which select a set of closely related evergreen broad-leaved tree species whose regeneration has adapted to the closed canopy environments of the subtropical forest developed under the regional monsoon climate. PMID:26098916

Seed plant phylogenetic diversity and species richness in conservation planning within a global biodiversity hotspot in eastern Asia.

PubMed

Li, Rong; Kraft, Nathan J B; Yu, Haiying; Li, Heng

2015-12-01

One of the main goals of conservation biology is to understand the factors shaping variation in biodiversity across the planet. This understanding is critical for conservation planners to be able to develop effective conservation strategies. Although many studies have focused on species richness and the protection of rare and endemic species, less attention has been paid to the protection of the phylogenetic dimension of biodiversity. We explored how phylogenetic diversity, species richness, and phylogenetic community structure vary in seed plant communities along an elevational gradient in a relatively understudied high mountain region, the Dulong Valley, in southeastern Tibet, China. As expected, phylogenetic diversity was well correlated with species richness among the elevational bands and among communities. At the community level, evergreen broad-leaved forests had the highest levels of species richness and phylogenetic diversity. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region. Evergreen broad-leaved forests were phylogenetically overdispersed, whereas other vegetation types tended to be phylogenetically clustered. We suggest that communities with high species richness or overdispersed phylogenetic structure should be a focus for biodiversity conservation within the Dulong Valley because these areas may help maximize the potential of this flora to respond to future global change. In biodiversity hotspots worldwide, we suggest that the phylogenetic structure of a community may serve as a useful measure of phylogenetic diversity in the context of conservation planning. © 2015 Society for Conservation Biology.

Head shape evolution in Tropidurinae lizards: does locomotion constrain diet?

PubMed

Kohlsdorf, T; Grizante, M B; Navas, C A; Herrel, A

2008-05-01

Different components of complex integrated systems may be specialized for different functions, and thus the selective pressures acting on the system as a whole may be conflicting and can ultimately constrain organismal performance and evolution. The vertebrate cranial system is one of the most striking examples of a complex system with several possible functions, being associated to activities as different as locomotion, prey capture, display and defensive behaviours. Therefore, selective pressures on the cranial system as a whole are possibly complex and may be conflicting. The present study focuses on the influence of potentially conflicting selective pressures (diet vs. locomotion) on the evolution of head shape in Tropidurinae lizards. For example, the expected adaptations leading to flat heads and bodies in species living on vertical structures may conflict with the need for improved bite performance associated with the inclusion of hard or tough prey into the diet, a common phenomenon in Tropidurinae lizards. Body size and six variables describing head shape were quantified in preserved specimens of 23 species, and information on diet and substrate usage was obtained from the literature. No phylogenetic signal was observed in the morphological data at any branch length tested, suggesting adaptive evolution of head shape in Tropidurinae. This pattern was confirmed by both factor analysis and independent contrast analysis, which suggested adaptive co-variation between the head shape and the inclusion of hard prey into the diet. In contrast to our expectations, habitat use did not constrain or drive head shape evolution in the group.

A proteomic approach for studying insect phylogeny: CAPA peptides of ancient insect taxa (Dictyoptera, Blattoptera) as a test case

PubMed Central

Roth, Steffen; Fromm, Bastian; Gäde, Gerd; Predel, Reinhard

2009-01-01

Background Neuropeptide ligands have to fit exactly into their respective receptors and thus the evolution of the coding regions of their genes is constrained and may be strongly conserved. As such, they may be suitable for the reconstruction of phylogenetic relationships within higher taxa. CAPA peptides of major lineages of cockroaches (Blaberidae, Blattellidae, Blattidae, Polyphagidae, Cryptocercidae) and of the termite Mastotermes darwiniensis were chosen to test the above hypothesis. The phylogenetic relationships within various groups of the taxon Dictyoptera (praying mantids, termites and cockroaches) are still highly disputed. Results Tandem mass spectrometry of neuropeptides from perisympathetic organs was used to obtain sequence data of CAPA peptides from single specimens; the data were analysed by Maximum Parsimony and Bayesian Interference. The resulting cladograms, taking 61 species into account, show a topology which is in general agreement with recent molecular and morphological phylogenetic analyses, including the recent phylogenetic arrangement placing termites within the cockroaches. When sequence data sets from other neuropeptides, viz. adipokinetic hormones and sulfakinins, were included, the general topology of the cladogram did not change but bootstrap values increased considerably. Conclusion This study represents the first comprehensive survey of neuropeptides of insects for solely phylogenetic purposes and concludes that sequences of short neuropeptides are suitable to complement molecular biological and morphological data for the reconstruction of phylogenetic relationships. PMID:19257902

Structural biomechanics determine spectral purity of bush-cricket calls.

PubMed

Chivers, Benedict D; Jonsson, Thorin; Soulsbury, Carl D; Montealegre-Z, Fernando

2017-11-01

Bush-crickets (Orthoptera: Tettigoniidae) generate sound using tegminal stridulation. Signalling effectiveness is affected by the widely varying acoustic parameters of temporal pattern, frequency and spectral purity (tonality). During stridulation, frequency multiplication occurs as a scraper on one wing scrapes across a file of sclerotized teeth on the other. The frequency with which these tooth-scraper interactions occur, along with radiating wing cell resonant properties, dictates both frequency and tonality in the call. Bush-cricket species produce calls ranging from resonant, tonal calls through to non-resonant, broadband signals. The differences are believed to result from differences in file tooth arrangement and wing radiators, but a systematic test of the structural causes of broadband or tonal calls is lacking. Using phylogenetically controlled structural equation models, we show that parameters of file tooth density and file length are the best-fitting predictors of tonality across 40 bush-cricket species. Features of file morphology constrain the production of spectrally pure signals, but systematic distribution of teeth alone does not explain pure-tone sound production in this family. © 2017 The Authors.

Structural biomechanics determine spectral purity of bush-cricket calls

PubMed Central

2017-01-01

Bush-crickets (Orthoptera: Tettigoniidae) generate sound using tegminal stridulation. Signalling effectiveness is affected by the widely varying acoustic parameters of temporal pattern, frequency and spectral purity (tonality). During stridulation, frequency multiplication occurs as a scraper on one wing scrapes across a file of sclerotized teeth on the other. The frequency with which these tooth–scraper interactions occur, along with radiating wing cell resonant properties, dictates both frequency and tonality in the call. Bush-cricket species produce calls ranging from resonant, tonal calls through to non-resonant, broadband signals. The differences are believed to result from differences in file tooth arrangement and wing radiators, but a systematic test of the structural causes of broadband or tonal calls is lacking. Using phylogenetically controlled structural equation models, we show that parameters of file tooth density and file length are the best-fitting predictors of tonality across 40 bush-cricket species. Features of file morphology constrain the production of spectrally pure signals, but systematic distribution of teeth alone does not explain pure-tone sound production in this family. PMID:29187608

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.

PubMed

Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

2016-01-01

Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

PubMed Central

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Discussion Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space. PMID:27761338

Patterns of co-speciation and host switching in primate malaria parasites.

PubMed

Garamszegi, László Zsolt

2009-05-22

The evolutionary history of many parasites is dependent on the evolution of their hosts, leading to an association between host and parasite phylogenies. However, frequent host switches across broad phylogenetic distances may weaken this close evolutionary link, especially when vectors are involved in parasites transmission, as is the case for malaria pathogens. Several studies suggested that the evolution of the primate-infective malaria lineages may be constrained by the phylogenetic relationships of their hosts, and that lateral switches between distantly related hosts may have been occurred. However, no systematic analysis has been quantified the degree of phylogenetic association between primates and their malaria parasites. Here phylogenetic approaches have been used to discriminate statistically between events due to co-divergence, duplication, extinction and host switches that can potentially cause historical association between Plasmodium parasites and their primate hosts. A Bayesian reconstruction of parasite phylogeny based on genetic information for six genes served as basis for the analyses, which could account for uncertainties about the evolutionary hypotheses of malaria parasites. Related lineages of primate-infective Plasmodium tend to infect hosts within the same taxonomic family. Different analyses testing for congruence between host and parasite phylogenies unanimously revealed a significant association between the corresponding evolutionary trees. The most important factor that resulted in this association was host switching, but depending on the parasite phylogeny considered, co-speciation and duplication may have also played some additional role. Sorting seemed to be a relatively infrequent event, and can occur only under extreme co-evolutionary scenarios. The concordance between host and parasite phylogenies is heterogeneous: while the evolution of some malaria pathogens is strongly dependent on the phylogenetic history of their primate hosts, the congruent evolution is less emphasized for other parasite lineages (e.g. for human malaria parasites). Estimation of ancestral states of host use along the phylogenetic tree of parasites revealed that lateral transfers across distantly related hosts were likely to occur in several cases. Parasites cannot infect all available hosts, and they should preferentially infect hosts that provide a similar environment for reproduction. Marginally significant evidence suggested that there might be a consistent variation within host ranges in terms of physiology. The evolution of primate malarias is constrained by the phylogenetic associations of their hosts. Some parasites can preserve a great flexibility to infect hosts across a large phylogenetic distance, thus host switching can be an important factor in mediating host ranges observed in nature. Due to this inherent flexibility and the potential exposure to various vectors, the emergence of new malaria disease in primates including humans cannot be predicted from the phylogeny of parasites.

Phylogenetic overdispersion of plant species in southern Brazilian savannas.

PubMed

Silva, I A; Batalha, M A

2009-08-01

Ecological communities are the result of not only present ecological processes, such as competition among species and environmental filtering, but also past and continuing evolutionary processes. Based on these assumptions, we may infer mechanisms of contemporary coexistence from the phylogenetic relationships of the species in a community. We studied the phylogenetic structure of plant communities in four cerrado sites, in southeastern Brazil. We calculated two raw phylogenetic distances among the species sampled. We estimated the phylogenetic structure by comparing the observed phylogenetic distances to the distribution of phylogenetic distances in null communities. We obtained null communities by randomizing the phylogenetic relationships of the regional pool of species. We found a phylogenetic overdispersion of the cerrado species. Phylogenetic overdispersion has several explanations, depending on the phylogenetic history of traits and contemporary ecological interactions. However, based on coexistence models between grasses and trees, density-dependent ecological forces, and the evolutionary history of the cerrado flora, we argue that the phylogenetic overdispersion of cerrado species is predominantly due to competitive interactions, herbivores and pathogen attacks, and ecological speciation. Future studies will need to include information on the phylogenetic history of plant traits.

Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids

PubMed Central

Tsuboi, Masahito; Gonzalez-Voyer, Alejandro; Kolm, Niclas

2015-01-01

Functional coupling, where a single morphological trait performs multiple functions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrooding introduces a novel function to the craniofacial system and offers an ideal opportunity to test the functional coupling hypothesis. Using a combination of geometric morphometrics and a recently developed phylogenetic comparative method, we found that head morphology evolution was 43% faster in substrate guarding species than in mouthbrooding species. Furthermore, for species in which females were solely responsible for mouthbrooding the males had a higher rate of head morphology evolution than in those with bi-parental mouthbrooding. Our results support the hypothesis that adaptations resulting in functional coupling constrain phenotypic evolution. PMID:25948565

Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids.

PubMed

Tsuboi, Masahito; Gonzalez-Voyer, Alejandro; Kolm, Niclas

2015-05-01

Functional coupling, where a single morphological trait performs multiple functions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrooding introduces a novel function to the craniofacial system and offers an ideal opportunity to test the functional coupling hypothesis. Using a combination of geometric morphometrics and a recently developed phylogenetic comparative method, we found that head morphology evolution was 43% faster in substrate guarding species than in mouthbrooding species. Furthermore, for species in which females were solely responsible for mouthbrooding the males had a higher rate of head morphology evolution than in those with bi-parental mouthbrooding. Our results support the hypothesis that adaptations resulting in functional coupling constrain phenotypic evolution.

T box transcription antitermination riboswitch: Influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element

PubMed Central

Fauzi, Hamid; Agyeman, Akwasi; Hines, Jennifer V.

2008-01-01

Many bacteria utilize riboswitch transcription regulation to monitor and appropriately respond to cellular levels of important metabolites or effector molecules. The T box transcription antitermination riboswitch responds to cognate uncharged tRNA by specifically stabilizing an antiterminator element in the 5′-untranslated mRNA leader region and precluding formation of a thermodynamically more stable terminator element. Stabilization occurs when the tRNA acceptor end base pairs with the first four nucleotides in the seven nucleotide bulge of the highly conserved antiterminator element. The significance of the conservation of the antiterminator bulge nucleotides that do not base pair with the tRNA is unknown, but they are required for optimal function. In vitro selection was used to determine if the isolated antiterminator bulge context alone dictates the mode in which the tRNA acceptor end binds the bulge nucleotides. No sequence conservation beyond complementarity was observed and the location was not constrained to the first four bases of the bulge. The results indicate that formation of a structure that recognizes the tRNA acceptor end in isolation is not the determinant driving force for the high phylogenetic sequence conservation observed within the antiterminator bulge. Additional factors or T box leader features more likely influenced the phylogenetic sequence conservation. PMID:19152843

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification.

PubMed

Badyaev, Alexander V; Morrison, Erin S; Belloni, Virginia; Sanderson, Michael J

2015-08-20

Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the evolution of carotenoid pigmentation that produces spectacular diversity in avian colors and show that basic structural properties of the underlying carotenoid metabolic network are reflected in global patterns of elaboration and diversification in color displays. Birds color themselves by consuming and metabolizing several dietary carotenoids from the environment. Such fundamental dependency on the most upstream external compounds should intrinsically constrain sustained evolutionary elongation of multi-step metabolic pathways needed for color elaboration unless the metabolic network gains robustness - the ability to synthesize the same carotenoid from an additional dietary starting point. We found that gains and losses of metabolic robustness were associated with evolutionary cycles of elaboration and stasis in expressed carotenoids in birds. Lack of metabolic robustness constrained lineage's metabolic explorations to the immediate biochemical vicinity of their ecologically distinct dietary carotenoids, whereas gains of robustness repeatedly resulted in sustained elongation of metabolic pathways on evolutionary time scales and corresponding color elaboration. The structural link between length and robustness in metabolic pathways may explain periodic convergence of phylogenetically distant and ecologically distinct species in expressed carotenoid pigmentation; account for stasis in carotenoid colors in some ecological lineages; and show how the connectivity of the underlying metabolic network provides a mechanistic link between microevolutionary elaboration and macroevolutionary diversification.

Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities

DTIC Science & Technology

2004-09-01

Science 190 and Engineering DOCTORAL DISSERTATION Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj...Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj Massachusetts Institute of Technology Cambridge, Massachusetts 02139 and Woods Hole...Phylogenetic Structure of Two Complex Marine Microbial Communities. Ph.D. Thesis. MIT/WHOI, 2004-11. Approved for publication; distribution unlimited

What Shapes the Phylogenetic Structure of Anuran Communities in a Seasonal Environment? The Influence of Determinism at Regional Scale to Stochasticity or Antagonistic Forces at Local Scale

PubMed Central

Ferreira, Vanda Lúcia; Strüssmann, Christine; Tomas, Walfrido Moraes

2015-01-01

Ecological communities are structured by both deterministic and stochastic processes. We investigated phylogenetic patterns at regional and local scales to understand the influences of seasonal processes in shaping the structure of anuran communities in the southern Pantanal wetland, Brazil. We assessed the phylogenetic structure at different scales, using the Net Relatedness Index (NRI), the Nearest Taxon Index (NTI), and phylobetadiversity indexes, as well as a permutation test, to evaluate the effect of seasonality. The anuran community was represented by a non-random set of species with a high degree of phylogenetic relatedness at the regional scale. However, at the local scale the phylogenetic structure of the community was weakly related with the seasonality of the system, indicating that oriented stochastic processes (e.g. colonization, extinction and ecological drift) and/or antagonist forces drive the structure of such communities in the southern Pantanal. PMID:26102202

What Shapes the Phylogenetic Structure of Anuran Communities in a Seasonal Environment? The Influence of Determinism at Regional Scale to Stochasticity or Antagonistic Forces at Local Scale.

PubMed

Martins, Clarissa de Araújo; Roque, Fabio de Oliveira; Santos, Bráulio A; Ferreira, Vanda Lúcia; Strüssmann, Christine; Tomas, Walfrido Moraes

2015-01-01

Ecological communities are structured by both deterministic and stochastic processes. We investigated phylogenetic patterns at regional and local scales to understand the influences of seasonal processes in shaping the structure of anuran communities in the southern Pantanal wetland, Brazil. We assessed the phylogenetic structure at different scales, using the Net Relatedness Index (NRI), the Nearest Taxon Index (NTI), and phylobetadiversity indexes, as well as a permutation test, to evaluate the effect of seasonality. The anuran community was represented by a non-random set of species with a high degree of phylogenetic relatedness at the regional scale. However, at the local scale the phylogenetic structure of the community was weakly related with the seasonality of the system, indicating that oriented stochastic processes (e.g. colonization, extinction and ecological drift) and/or antagonist forces drive the structure of such communities in the southern Pantanal.

Turnover of plant lineages shapes herbivore phylogenetic beta diversity along ecological gradients.

PubMed

Pellissier, Loïc; Ndiribe, Charlotte; Dubuis, Anne; Pradervand, Jean-Nicolas; Salamin, Nicolas; Guisan, Antoine; Rasmann, Sergio

2013-05-01

Understanding drivers of biodiversity patterns is of prime importance in this era of severe environmental crisis. More diverse plant communities have been postulated to represent a larger functional trait-space, more likely to sustain a diverse assembly of herbivore species. Here, we expand this hypothesis to integrate environmental, functional and phylogenetic variation of plant communities as factors explaining the diversity of lepidopteran assemblages along elevation gradients in the Swiss Western Alps. According to expectations, we found that the association between butterflies and their host plants is highly phylogenetically structured. Multiple regression analyses showed the combined effect of climate, functional traits and phylogenetic diversity in structuring butterfly communities. Furthermore, we provide the first evidence that plant phylogenetic beta diversity is the major driver explaining butterfly phylogenetic beta diversity. Along ecological gradients, the bottom up control of herbivore diversity is thus driven by phylogenetically structured turnover of plant traits as well as environmental variables. © 2013 Blackwell Publishing Ltd/CNRS.

Macroevolutionary developmental biology: Embryos, fossils, and phylogenies.

PubMed

Organ, Chris L; Cooper, Lisa Noelle; Hieronymus, Tobin L

2015-10-01

The field of evolutionary developmental biology is broadly focused on identifying the genetic and developmental mechanisms underlying morphological diversity. Connecting the genotype with the phenotype means that evo-devo research often considers a wide range of evidence, from genetics and morphology to fossils. In this commentary, we provide an overview and framework for integrating fossil ontogenetic data with developmental data using phylogenetic comparative methods to test macroevolutionary hypotheses. We survey the vertebrate fossil record of preserved embryos and discuss how phylogenetic comparative methods can integrate data from developmental genetics and paleontology. Fossil embryos provide limited, yet critical, developmental data from deep time. They help constrain when developmental innovations first appeared during the history of life and also reveal the order in which related morphologies evolved. Phylogenetic comparative methods provide a powerful statistical approach that allows evo-devo researchers to infer the presence of nonpreserved developmental traits in fossil species and to detect discordant evolutionary patterns and processes across levels of biological organization. © 2015 Wiley Periodicals, Inc.

Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide.

PubMed

Kissling, W Daniel; Eiserhardt, Wolf L; Baker, William J; Borchsenius, Finn; Couvreur, Thomas L P; Balslev, Henrik; Svenning, Jens-Christian

2012-05-08

Despite long-standing interest in the origin and maintenance of species diversity, little is known about historical drivers of species assemblage structure at large spatiotemporal scales. Here, we use global species distribution data, a dated genus-level phylogeny, and paleo-reconstructions of biomes and climate to examine Cenozoic imprints on the phylogenetic structure of regional species assemblages of palms (Arecaceae), a species-rich plant family characteristic of tropical ecosystems. We find a strong imprint on phylogenetic clustering due to geographic isolation and in situ diversification, especially in the Neotropics and on islands with spectacular palm radiations (e.g., Madagascar, Hawaii, and Cuba). Phylogenetic overdispersion on mainlands and islands corresponds to biotic interchange areas. Differences in the degree of phylogenetic clustering among biogeographic realms are related to differential losses of tropical rainforests during the Cenozoic, but not to the cumulative area of tropical rainforest over geological time. A largely random phylogenetic assemblage structure in Africa coincides with severe losses of rainforest area, especially after the Miocene. More recent events also appear to be influential: phylogenetic clustering increases with increasing intensity of Quaternary glacial-interglacial climatic oscillations in South America and, to a lesser extent, Africa, indicating that specific clades perform better in climatically unstable regions. Our results suggest that continental isolation (in combination with limited long-distance dispersal) and changing climate and habitat loss throughout the Cenozoic have had strong impacts on the phylogenetic structure of regional species assemblages in the tropics.

Fish species introductions provide novel insights into the patterns and drivers of phylogenetic structure in freshwaters

PubMed Central

Strecker, Angela L.; Olden, Julian D.

2014-01-01

Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. We quantify phylogenetic clustering and overdispersion of native and non-native fishes of a large river basin in the American Southwest to test for the mechanisms (environmental filtering versus competitive exclusion) and spatial scales influencing community structure. Contrary to expectations, non-native species were phylogenetically clustered and related to natural environmental conditions, whereas native species were not phylogenetically structured, likely reflecting human-related changes to the basin. The species that are most invasive (in terms of ecological impacts) tended to be the most phylogenetically divergent from natives across watersheds, but not within watersheds, supporting the hypothesis that Darwin's naturalization conundrum is driven by the spatial scale. Phylogenetic distinctiveness may facilitate non-native establishment at regional scales, but environmental filtering restricts local membership to closely related species with physiological tolerances for current environments. By contrast, native species may have been phylogenetically clustered in historical times, but species loss from contemporary populations by anthropogenic activities has likely shaped the phylogenetic signal. Our study implies that fundamental mechanisms of community assembly have changed, with fundamental consequences for the biogeography of both native and non-native species. PMID:24452027

Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure.

PubMed

Ghosh, Jayadri Sekhar; Bhattacharya, Samik; Pal, Amita

2017-06-01

The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.

The problem and promise of scale dependency in community phylogenetics.

PubMed

Swenson, Nathan G; Enquist, Brian J; Pither, Jason; Thompson, Jill; Zimmerman, Jess K

2006-10-01

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure

PubMed Central

Escobedo, Víctor M.; Rios, Rodrigo S.; Salgado-Luarte, Cristian; Stotz, Gisela C.

2017-01-01

Abstract Background and Aims Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles. Methods Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus, measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel’s lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters. Key Results The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct. Conclusions Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated. PMID:28087661

Range size heritability and diversification patterns in the liverwort genus Radula.

PubMed

Patiño, Jairo; Wang, Jian; Renner, Matt A M; Gradstein, S Robbert; Laenen, Benjamin; Devos, Nicolas; Shaw, A Jonathan; Vanderpoorten, Alain

2017-01-01

Why some species exhibit larger geographical ranges than others, and to what extent does variation in range size affect diversification rates, remains a fundamental, but largely unanswered question in ecology and evolution. Here, we implement phylogenetic comparative analyses and ancestral area estimations in Radula, a liverwort genus of Cretaceous origin, to investigate the mechanisms that explain differences in geographical range size and diversification rates among lineages. Range size was phylogenetically constrained in the two sub-genera characterized by their almost complete Australasian and Neotropical endemicity, respectively. The congruence between the divergence time of these lineages and continental split suggests that plate tectonics could have played a major role in their present distribution, suggesting that a strong imprint of vicariance can still be found in extant distribution patterns in these highly mobile organisms. Amentuloradula, Volutoradula and Metaradula species did not appear to exhibit losses of dispersal capacities in terms of dispersal life-history traits, but evidence for significant phylogenetic signal in macroecological niche traits suggests that niche conservatism accounts for their restricted geographic ranges. Despite their greatly restricted distribution to Australasia and Neotropics respectively, Amentuloradula and Volutoradula did not exhibit significantly lower diversification rates than more widespread lineages, in contrast with the hypothesis that the probability of speciation increases with range size by promoting geographic isolation and increasing the rate at which novel habitats are encountered. We suggest that stochastic long-distance dispersal events may balance allele frequencies across large spatial scales, leading to low genetic structure among geographically distant areas or even continents, ultimately decreasing the diversification rates in highly mobile, widespread lineages. Copyright © 2016 Elsevier Inc. All rights reserved.

Phylogenetic patterns and the adaptive evolution of osmoregulation in fiddler crabs (Brachyura, Uca)

PubMed Central

Faria, Samuel Coelho; Provete, Diogo Borges; Thurman, Carl Leo

2017-01-01

Salinity is the primary driver of osmoregulatory evolution in decapods, and may have influenced their diversification into different osmotic niches. In semi-terrestrial crabs, hyper-osmoregulatory ability favors sojourns into burrows and dilute media, and provides a safeguard against hemolymph dilution; hypo-osmoregulatory ability underlies emersion capability and a life more removed from water sources. However, most comparative studies have neglected the roles of the phylogenetic and environmental components of inter-specific physiological variation, hindering evaluation of phylogenetic patterns and the adaptive nature of osmoregulatory evolution. Semi-terrestrial fiddler crabs (Uca) inhabit fresh to hyper-saline waters, with species from the Americas occupying higher intertidal habitats than Indo-west Pacific species mainly found in the low intertidal zone. Here, we characterize numerous osmoregulatory traits in all ten fiddler crabs found along the Atlantic coast of Brazil, and we employ phylogenetic comparative methods using 24 species to test for: (i) similarities of osmoregulatory ability among closely related species; (ii) salinity as a driver of osmoregulatory evolution; (iii) correlation between salt uptake and secretion; and (iv) adaptive peaks in osmoregulatory ability in the high intertidal American lineages. Our findings reveal that osmoregulation in Uca exhibits strong phylogenetic patterns in salt uptake traits. Salinity does not correlate with hyper/hypo-regulatory abilities, but drives hemolymph osmolality at ambient salinities. Osmoregulatory traits have evolved towards three adaptive peaks, revealing a significant contribution of hyper/hypo-regulatory ability in the American clades. Thus, during the evolutionary history of fiddler crabs, salinity has driven some of the osmoregulatory transformations that underpin habitat diversification, although others are apparently constrained phylogenetically. PMID:28182764

Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity

PubMed Central

Bryant, Jessica A.; Lamanna, Christine; Morlon, Hélène; Kerkhoff, Andrew J.; Enquist, Brian J.; Green, Jessica L.

2008-01-01

The study of elevational diversity gradients dates back to the foundation of biogeography. Although elevational patterns of plant and animal diversity have been studied for centuries, such patterns have not been reported for microorganisms and remain poorly understood. Here, in an effort to assess the generality of elevational diversity patterns, we examined soil bacterial and plant diversity along an elevation gradient. To gain insight into the forces that structure these patterns, we adopted a multifaceted approach to incorporate information about the structure, diversity, and spatial turnover of montane communities in a phylogenetic context. We found that observed patterns of plant and bacterial diversity were fundamentally different. While bacterial taxon richness and phylogenetic diversity decreased monotonically from the lowest to highest elevations, plants followed a unimodal pattern, with a peak in richness and phylogenetic diversity at mid-elevations. At all elevations bacterial communities had a tendency to be phylogenetically clustered, containing closely related taxa. In contrast, plant communities did not exhibit a uniform phylogenetic structure across the gradient: they became more overdispersed with increasing elevation, containing distantly related taxa. Finally, a metric of phylogenetic beta-diversity showed that bacterial lineages were not randomly distributed, but rather exhibited significant spatial structure across the gradient, whereas plant lineages did not exhibit a significant phylogenetic signal. Quantifying the influence of sample scale in intertaxonomic comparisons remains a challenge. Nevertheless, our findings suggest that the forces structuring microorganism and macroorganism communities along elevational gradients differ. PMID:18695215

Change in phylogenetic community structure during succession of traditionally managed tropical rainforest in southwest China.

PubMed

Mo, Xiao-Xue; Shi, Ling-Ling; Zhang, Yong-Jiang; Zhu, Hua; Slik, J W Ferry

2013-01-01

Tropical rainforests in Southeast Asia are facing increasing and ever more intense human disturbance that often negatively affects biodiversity. The aim of this study was to determine how tree species phylogenetic diversity is affected by traditional forest management types and to understand the change in community phylogenetic structure during succession. Four types of forests with different management histories were selected for this purpose: old growth forests, understorey planted old growth forests, old secondary forests (∼200-years after slash and burn), and young secondary forests (15-50-years after slash and burn). We found that tree phylogenetic community structure changed from clustering to over-dispersion from early to late successional forests and finally became random in old-growth forest. We also found that the phylogenetic structure of the tree overstorey and understorey responded differentially to change in environmental conditions during succession. In addition, we show that slash and burn agriculture (swidden cultivation) can increase landscape level plant community evolutionary information content.

Change in Phylogenetic Community Structure during Succession of Traditionally Managed Tropical Rainforest in Southwest China

PubMed Central

Mo, Xiao-Xue; Shi, Ling-Ling; Zhang, Yong-Jiang; Zhu, Hua; Slik, J. W. Ferry

2013-01-01

Tropical rainforests in Southeast Asia are facing increasing and ever more intense human disturbance that often negatively affects biodiversity. The aim of this study was to determine how tree species phylogenetic diversity is affected by traditional forest management types and to understand the change in community phylogenetic structure during succession. Four types of forests with different management histories were selected for this purpose: old growth forests, understorey planted old growth forests, old secondary forests (∼200-years after slash and burn), and young secondary forests (15–50-years after slash and burn). We found that tree phylogenetic community structure changed from clustering to over-dispersion from early to late successional forests and finally became random in old-growth forest. We also found that the phylogenetic structure of the tree overstorey and understorey responded differentially to change in environmental conditions during succession. In addition, we show that slash and burn agriculture (swidden cultivation) can increase landscape level plant community evolutionary information content. PMID:23936268

Phylogenetic structure of soil bacterial communities predicts ecosystem functioning.

PubMed

Pérez-Valera, Eduardo; Goberna, Marta; Verdú, Miguel

2015-05-01

Quantifying diversity with phylogeny-informed metrics helps understand the effects of diversity on ecosystem functioning (EF). The sign of these effects remains controversial because phylogenetic diversity and taxonomic identity may interactively influence EF. Positive relationships, traditionally attributed to complementarity effects, seem unimportant in natural soil bacterial communities. Negative relationships could be attributed to fitness differences leading to the overrepresentation of few productive clades, a mechanism recently invoked to assemble soil bacteria communities. We tested in two ecosystems contrasting in terms of environmental heterogeneity whether two metrics of phylogenetic community structure, a simpler measure of phylogenetic diversity (NRI) and a more complex metric incorporating taxonomic identity (PCPS), correctly predict microbially mediated EF. We show that the relationship between phylogenetic diversity and EF depends on the taxonomic identity of the main coexisting lineages. Phylogenetic diversity was negatively related to EF in soils where a marked fertility gradient exists and a single and productive clade (Proteobacteria) outcompete other clades in the most fertile plots. However, phylogenetic diversity was unrelated to EF in soils where the fertility gradient is less marked and Proteobacteria coexist with other abundant lineages. Including the taxonomic identity of bacterial lineages in metrics of phylogenetic community structure allows the prediction of EF in both ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

PubMed Central

Salvi, Daniele; Macali, Armando; Mariottini, Paolo

2014-01-01

The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassotreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics. PMID:25250663

Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree.

PubMed

Salvi, Daniele; Macali, Armando; Mariottini, Paolo

2014-01-01

The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassostreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized [corrected]. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics.

Plant performance was greater in the soils of more distantly related plants for an herbaceous understory species.

PubMed

Sweet, Drake D; Burns, Jean H

2017-01-01

Growing evidence suggests that plant-soil interactions have important implications for plant community composition. However, the role of phylogenetic relatedness in governing interactions between plants and soil biota is unclear, and more case studies are needed to help build a general picture of whether and how phylogeny might influence plant-soil interactions. We performed a glasshouse experiment to test whether degree of phylogenetic relatedness between Aquilegia canadensis and six co-occurring heterospecifics affects A. canadensis biomass through soil legacy effects. We also compared performance of A. canadensis in soils conditioned by invasive Alliaria petiolata versus native heterospecifics, hypothesizing that conditioning by A. petiolata would suppress the performance of the focal native plant. A. canadensis performed significantly better in distant relatives' soils than in close relatives' soils, and this effect disappeared with soil sterilization, consistent with close relatives sharing similar pathogens. Contrary to our expectations, soils conditioned by the invasive species A. petiolata versus by native species had similar effects on A. canadensis . The greater performance of A. canadensis in soils of more versus less distant relatives is consistent with a hypothesis of phylogenetically constrained pathogen escape, a phenomenon expected to promote coexistence of phylogenetically distant species. However, pairwise plant-soil feedback experiments are needed to create a stronger coexistence prediction.

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure.

PubMed

Escobedo, Víctor M; Rios, Rodrigo S; Salgado-Luarte, Cristian; Stotz, Gisela C; Gianoli, Ernesto

2017-03-01

Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles. Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus , measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel's lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters. The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct. Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Plant Biodiversity Drivers in Brazilian Campos Rupestres: Insights from Phylogenetic Structure

PubMed Central

Zappi, Daniela C.; Moro, Marcelo F.; Meagher, Thomas R.; Nic Lughadha, Eimear

2017-01-01

Old, climate-buffered infertile landscapes (Ocbils) have attracted increasing levels of interest in recent years because of their exceptionally diverse plant communities. Brazil’s campos rupestres (rupestrian grasslands) are home to almost 15% of Brazil’s native flora in less than 0.8% of Brazil’s territory: an ideal study system for exploring variation in floristic diversity and phylogenetic structure in sites differing in geology and phytophysiognomy. We found significant differences in floristic diversity and phylogenetic structure across a range of study sites encompassing open vegetation and forest on quartzite (FQ) and on ironstone substrates, commonly termed canga. Substrate and physiognomy were key in structuring floristic diversity in the Espinhaço and physiognomy was more important than substrate in structuring phylogenetic diversity, with neither substrate nor its interaction with physiognomy accounting for significant variation in phylogenetic structure. Phylogenetic clustering was significant in open vegetation on both canga and quartzite, reflecting the potential role of environmental filtering in these exposed montane communities adapted to multiple environmental stressors. In forest communities, phylogenetic clustering was significant only at relatively deep nodes of the phylogeny in FQ while no significant phylogenetic clustering was detected across forest on canga (FC), which may be attributable to proximity to the megadiverse Atlantic forest biome and/or comparatively benign environmental conditions in FC with relatively deep, nutrient-rich soils and access to edaphic water reliable in comparison to those for open vegetation on canga and open or forest communities on quartzite. Clades representing relatively old lineages are significantly over-represented in campos rupestres on quartzite, consistent with the Gondwanan Heritage Hypothesis of Ocbil theory. In contrast, forested sites on canga are recognized as Yodfels. To be effective, conservation measures must take account of the distinct communities which are encompassed within the broad term campos rupestres, and the differing vulnerabilities of Ocbils and Yodfels. PMID:29312396

Plant Biodiversity Drivers in Brazilian Campos Rupestres: Insights from Phylogenetic Structure.

PubMed

Zappi, Daniela C; Moro, Marcelo F; Meagher, Thomas R; Nic Lughadha, Eimear

2017-01-01

Old, climate-buffered infertile landscapes (Ocbils) have attracted increasing levels of interest in recent years because of their exceptionally diverse plant communities. Brazil's campos rupestres (rupestrian grasslands) are home to almost 15% of Brazil's native flora in less than 0.8% of Brazil's territory: an ideal study system for exploring variation in floristic diversity and phylogenetic structure in sites differing in geology and phytophysiognomy. We found significant differences in floristic diversity and phylogenetic structure across a range of study sites encompassing open vegetation and forest on quartzite (FQ) and on ironstone substrates, commonly termed canga . Substrate and physiognomy were key in structuring floristic diversity in the Espinhaço and physiognomy was more important than substrate in structuring phylogenetic diversity, with neither substrate nor its interaction with physiognomy accounting for significant variation in phylogenetic structure. Phylogenetic clustering was significant in open vegetation on both canga and quartzite, reflecting the potential role of environmental filtering in these exposed montane communities adapted to multiple environmental stressors. In forest communities, phylogenetic clustering was significant only at relatively deep nodes of the phylogeny in FQ while no significant phylogenetic clustering was detected across forest on canga (FC), which may be attributable to proximity to the megadiverse Atlantic forest biome and/or comparatively benign environmental conditions in FC with relatively deep, nutrient-rich soils and access to edaphic water reliable in comparison to those for open vegetation on canga and open or forest communities on quartzite. Clades representing relatively old lineages are significantly over-represented in campos rupestres on quartzite, consistent with the Gondwanan Heritage Hypothesis of Ocbil theory. In contrast, forested sites on canga are recognized as Yodfels. To be effective, conservation measures must take account of the distinct communities which are encompassed within the broad term campos rupestres , and the differing vulnerabilities of Ocbils and Yodfels.

Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity

PubMed Central

Wei, Ran; Yan, Yue-Hong; Harris, AJ; Kang, Jong-Soo; Shen, Hui; Zhang, Xian-Chun

2017-01-01

Abstract The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae–Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates. PMID:28854625

Small-scale spatial variability in phylogenetic community structure during early plant succession depends on soil properties.

PubMed

Ulrich, Werner; Piwczyński, Marcin; Zaplata, Markus Klemens; Winter, Susanne; Schaaf, Wolfgang; Fischer, Anton

2014-07-01

During early plant succession, the phylogenetic structure of a community changes in response to important environmental filters and emerging species interactions. We traced the development of temperate-zone plant communities during the first 7 years of primary succession on catchment soils to explore patterns of initial species assembly. We found pronounced small-scale differences in the phylogenetic composition of neighbouring plant assemblages and a large-scale trend towards phylogenetic evenness. This small-scale variability appears to be mediated by soil properties, particularly carbonate content. Therefore, abiotic environmental conditions might counteract or even supersede the effects of interspecific competition among closely related species, which are usually predicted to exhibit patterns of phylogenetic evenness. We conclude that theories on phylogenetic community composition need to incorporate effects of small-scale variability of environmental factors.

Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily.

PubMed

Lakshmi, Balasubramanian; Mishra, Madhulika; Srinivasan, Narayanaswamy; Archunan, Govindaraju

2015-01-01

Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees.

PubMed

Bennett, Dominic J; Sutton, Mark D; Turvey, Samuel T

2017-01-07

Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks. We present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes. We present three use cases-pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover-that demonstrate the new package's speed and simplicity.

Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors.

PubMed

Cau, Andrea

2017-01-01

Bayesian phylogenetic methods integrating simultaneously morphological and stratigraphic information have been applied increasingly among paleontologists. Most of these studies have used Bayesian methods as an alternative to the widely-used parsimony analysis, to infer macroevolutionary patterns and relationships among species-level or higher taxa. Among recently introduced Bayesian methodologies, the Fossilized Birth-Death (FBD) model allows incorporation of hypotheses on ancestor-descendant relationships in phylogenetic analyses including fossil taxa. Here, the FBD model is used to infer the relationships among an ingroup formed exclusively by fossil individuals, i.e., dipnoan tooth plates from four localities in the Ain el Guettar Formation of Tunisia. Previous analyses of this sample compared the results of phylogenetic analysis using parsimony with stratigraphic methods, inferred a high diversity (five or more genera) in the Ain el Guettar Formation, and interpreted it as an artifact inflated by depositional factors. In the analysis performed here, the uncertainty on the chronostratigraphic relationships among the specimens was included among the prior settings. The results of the analysis confirm the referral of most of the specimens to the taxa Asiatoceratodus , Equinoxiodus, Lavocatodus and Neoceratodus , but reject those to Ceratodus and Ferganoceratodus . The resulting phylogeny constrained the evolution of the Tunisian sample exclusively in the Early Cretaceous, contrasting with the previous scenario inferred by the stratigraphically-calibrated topology resulting from parsimony analysis. The phylogenetic framework also suggests that (1) the sampled localities are laterally equivalent, (2) but three localities are restricted to the youngest part of the section; both results are in agreement with previous stratigraphic analyses of these localities. The FBD model of specimen-level units provides a novel tool for phylogenetic inference among fossils but also for independent tests of stratigraphic scenarios.

Characterizing the phylogenetic tree community structure of a protected tropical rain forest area in Cameroon.

PubMed

Manel, Stéphanie; Couvreur, Thomas L P; Munoz, François; Couteron, Pierre; Hardy, Olivier J; Sonké, Bonaventure

2014-01-01

Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world.

A novel transient structure with phylogenetic implications found in ratite spermatids

PubMed Central

2013-01-01

Background A novel transient structure was observed in the spermatids of three ratite species using transmission electron microscopy. Results The structure first appeared at the circular manchette stage of sperm development, was most prominent during the longitudinal manchette phase and disappeared abruptly prior to spermiation. It was composed of regularly-spaced finger-like projections which were closely associated with the outer nuclear membrane, giving the nucleus a cogwheel-like appearance. The projections were approximately 30 nm long and 14 nm wide. Although a similar structure has been described in certain lizard and crocodile species, this is the first report of a similar structure in the developing spermatids of birds. Conclusions The potential value of non-traditional characters, such as spermiogenesis and sperm ultrastructure, as phylogenetic markers has recently been advocated. The morphologically unique structure found in ratite spermatids provides additional evidence of a possible phylogenetic link between the reptiles and birds. It also endorses the basal positioning of the ratites as a monophyletic group within the avian phylogenetic tree. PMID:23705947

Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities.

PubMed

López-García, Álvaro; Varela-Cervero, Sara; Vasar, Martti; Öpik, Maarja; Barea, José M; Azcón-Aguilar, Concepción

2017-12-01

Functional diversity in ecosystems has traditionally been studied using aboveground plant traits. Despite the known effect of plant traits on the microbial community composition, their effects on the microbial functional diversity are only starting to be assessed. In this study, the phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities associated with plant species differing in life cycle and growth form, that is, plant life forms, was determined to unravel the effect of plant traits on the functional diversity of this fungal group. The results of the 454 pyrosequencing showed that the AM fungal community composition differed across plant life forms and this effect was dependent on the soil collection date. Plants with ruderal characteristics tended to associate with phylogenetically clustered AM fungal communities. By contrast, plants with resource-conservative traits associated with phylogenetically overdispersed AM fungal communities. Additionally, the soil collected in different seasons yielded AM fungal communities with different phylogenetic dispersion. In summary, we found that the phylogenetic structure, and hence the functional diversity, of AM fungal communities is dependent on plant traits. This finding adds value to the use of plant traits for the evaluation of belowground ecosystem diversity, functions and processes. © 2017 John Wiley & Sons Ltd.

The importance of accounting for imperfect detection when estimating functional and phylogenetic community structure.

PubMed

Si, Xingfeng; Cadotte, Marc W; Zhao, Yuhao; Zhou, Haonan; Zeng, Di; Li, Jiaqi; Jin, Tinghao; Ren, Peng; Wang, Yanping; Ding, Ping; Tingley, Morgan W

2018-06-26

Incorporating imperfect detection when estimating species richness has become commonplace in the past decade. However, the question of how imperfect detection of species affects estimates of functional and phylogenetic community structure remains untested. We used long-term counts of breeding bird species that were detected at least once on islands in a land-bridge island system, and employed multi-species occupancy models to assess the effects of imperfect detection of species on estimates of bird diversity and community structure by incorporating species traits and phylogenies. Our results showed that taxonomic, functional, and phylogenetic diversity were all underestimated significantly as a result of species' imperfect detection, with taxonomic diversity showing the greatest bias. The functional and phylogenetic structure calculated from observed communities were both more clustered than those from the detection-corrected communities due to missed distinct species. The discrepancy between observed and estimated diversity differed according to the measure of biodiversity employed. Our study demonstrates the importance of accounting for species' imperfect detection in biodiversity studies, especially for functional and phylogenetic community ecology, and when attempting to infer community assembly processes. With datasets that allow for detection-corrected community structure, we can better estimate diversity and infer the underlying mechanisms that structure community assembly, and thus make reliable management decisions for the conservation of biodiversity. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Phylogenetic community structure: temporal variation in fish assemblage

PubMed Central

Santorelli, Sergio; Magnusson, William; Ferreira, Efrem; Caramaschi, Erica; Zuanon, Jansen; Amadio, Sidnéia

2014-01-01

Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales (grouped at three temporal scales). Phylogenetic distance was measured as the mean pairwise distances (MPD) and as mean nearest-neighbor distance (MNTD). Both distances were based on counts of nodes. We compared the observed values of MPD and MNTD with values that were generated randomly using null model independent swap. A serial runs test was used to assess the temporal independence of indices over time. The phylogenetic pattern in the whole assemblage and the functional groups varied widely over time. Conclusions about phylogenetic clustering or dispersion depended on the temporal scales. Conclusions about the frequency with which biotic processes and environmental filters affect the local assembly do not depend only on taxonomic grouping and spatial scales. While these analyzes allow the assertion that all proposed patterns apply to the fish assemblages in the floodplain, the assessment of the relative importance of these processes, and how they vary depending on the temporal scale and functional group studied, cannot be determined with the effort commonly used. It appears that, at least in the system that we studied, the assemblages are forming and breaking continuously, resulting in various phylogeny-related structures that makes summarizing difficult. PMID:25360256

CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.

PubMed

Abaka, Gamze; Bıyıkoğlu, Türker; Erten, Cesim

2013-07-01

Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism. We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/. Supplementary data are available at Bioinformatics online.

The Evolutionary Ecology of Plant Disease: A Phylogenetic Perspective.

PubMed

Gilbert, Gregory S; Parker, Ingrid M

2016-08-04

An explicit phylogenetic perspective provides useful tools for phytopathology and plant disease ecology because the traits of both plants and microbes are shaped by their evolutionary histories. We present brief primers on phylogenetic signal and the analytical tools of phylogenetic ecology. We review the literature and find abundant evidence of phylogenetic signal in pathogens and plants for most traits involved in disease interactions. Plant nonhost resistance mechanisms and pathogen housekeeping functions are conserved at deeper phylogenetic levels, whereas molecular traits associated with rapid coevolutionary dynamics are more labile at branch tips. Horizontal gene transfer disrupts the phylogenetic signal for some microbial traits. Emergent traits, such as host range and disease severity, show clear phylogenetic signals. Therefore pathogen spread and disease impact are influenced by the phylogenetic structure of host assemblages. Phylogenetically rare species escape disease pressure. Phylogenetic tools could be used to develop predictive tools for phytosanitary risk analysis and reduce disease pressure in multispecies cropping systems.

Altitudinal Patterns of Species Diversity and Phylogenetic Diversity across Temperate Mountain Forests of Northern China.

PubMed

Zhang, Wenxin; Huang, Dizhou; Wang, Renqing; Liu, Jian; Du, Ning

2016-01-01

The spatial patterns of biodiversity and their underlying mechanisms have been an active area of research for a long time. In this study, a total of 63 samples (20m × 30m) were systematically established along elevation gradients on Mount Tai and Mount Lao, China. We explored altitudinal patterns of plant diversity in the two mountain systems. In order to understand the mechanisms driving current diversity patterns, we used phylogenetic approaches to detect the spatial patterns of phylogenetic diversity and phylogenetic structure along two elevation gradients. We found that total species richness had a monotonically decreasing pattern and tree richness had a unimodal pattern along the elevation gradients in the two study areas. However, altitudinal patterns in shrub richness and herbs richness were not consistent on the two mountains. At low elevation, anthropogenic disturbances contributed to the increase of plant diversity, especially for shrubs and herbs in understory layers, which are more sensitive to changes in microenvironment. The phylogenetic structure of plant communities exhibited an inverted hump-shaped pattern along the elevation gradient on Mount Tai, which demonstrates that environmental filtering is the main driver of plant community assembly at high and low elevations and inter-specific competition may be the main driver of plant community assembly in the middle elevations. However, the phylogenetic structure of plant communities did not display a clear pattern on Mount Lao where the climate is milder. Phylogenetic beta diversity and species beta diversity consistently increased with increasing altitudinal divergence in the two study areas. However, the altitudinal patterns of species richness did not completely mirror phylogenetic diversity patterns. Conservation areas should be selected taking into consideration the preservation of high species richness, while maximizing phylogenetic diversity to improve the potential for diversification in the future.

Minimal complexity control law synthesis

NASA Technical Reports Server (NTRS)

Bernstein, Dennis S.; Haddad, Wassim M.; Nett, Carl N.

1989-01-01

A paradigm for control law design for modern engineering systems is proposed: Minimize control law complexity subject to the achievement of a specified accuracy in the face of a specified level of uncertainty. Correspondingly, the overall goal is to make progress towards the development of a control law design methodology which supports this paradigm. Researchers achieve this goal by developing a general theory of optimal constrained-structure dynamic output feedback compensation, where here constrained-structure means that the dynamic-structure (e.g., dynamic order, pole locations, zero locations, etc.) of the output feedback compensation is constrained in some way. By applying this theory in an innovative fashion, where here the indicated iteration occurs over the choice of the compensator dynamic-structure, the paradigm stated above can, in principle, be realized. The optimal constrained-structure dynamic output feedback problem is formulated in general terms. An elegant method for reducing optimal constrained-structure dynamic output feedback problems to optimal static output feedback problems is then developed. This reduction procedure makes use of star products, linear fractional transformations, and linear fractional decompositions, and yields as a byproduct a complete characterization of the class of optimal constrained-structure dynamic output feedback problems which can be reduced to optimal static output feedback problems. Issues such as operational/physical constraints, operating-point variations, and processor throughput/memory limitations are considered, and it is shown how anti-windup/bumpless transfer, gain-scheduling, and digital processor implementation can be facilitated by constraining the controller dynamic-structure in an appropriate fashion.

Resource-aware taxon selection for maximizing phylogenetic diversity.

PubMed

Pardi, Fabio; Goldman, Nick

2007-06-01

Phylogenetic diversity (PD) is a useful metric for selecting taxa in a range of biological applications, for example, bioconservation and genomics, where the selection is usually constrained by the limited availability of resources. We formalize taxon selection as a conceptually simple optimization problem, aiming to maximize PD subject to resource constraints. This allows us to take into account the different amounts of resources required by the different taxa. Although this is a computationally difficult problem, we present a dynamic programming algorithm that solves it in pseudo-polynomial time. Our algorithm can also solve many instances of the Noah's Ark Problem, a more realistic formulation of taxon selection for biodiversity conservation that allows for taxon-specific extinction risks. These instances extend the set of problems for which solutions are available beyond previously known greedy-tractable cases. Finally, we discuss the relevance of our results to real-life scenarios.

The oldest known primate skeleton and early haplorhine evolution.

PubMed

Ni, Xijun; Gebo, Daniel L; Dagosto, Marian; Meng, Jin; Tafforeau, Paul; Flynn, John J; Beard, K Christopher

2013-06-06

Reconstructing the earliest phases of primate evolution has been impeded by gaps in the fossil record, so that disagreements persist regarding the palaeobiology and phylogenetic relationships of the earliest primates. Here we report the discovery of a nearly complete and partly articulated skeleton of a primitive haplorhine primate from the early Eocene of China, about 55 million years ago, the oldest fossil primate of this quality ever recovered. Coupled with detailed morphological examination using propagation phase contrast X-ray synchrotron microtomography, our phylogenetic analysis based on total available evidence indicates that this fossil is the most basal known member of the tarsiiform clade. In addition to providing further support for an early dichotomy between the strepsirrhine and haplorhine clades, this new primate further constrains the age of divergence between tarsiiforms and anthropoids. It also strengthens the hypothesis that the earliest primates were probably diurnal, arboreal and primarily insectivorous mammals the size of modern pygmy mouse lemurs.

Visualizing Phylogenetic Treespace Using Cartographic Projections

NASA Astrophysics Data System (ADS)

Sundberg, Kenneth; Clement, Mark; Snell, Quinn

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger datasets.

Automation and Evaluation of the SOWH Test with SOWHAT.

PubMed

Church, Samuel H; Ryan, Joseph F; Dunn, Casey W

2015-11-01

The Swofford-Olsen-Waddell-Hillis (SOWH) test evaluates statistical support for incongruent phylogenetic topologies. It is commonly applied to determine if the maximum likelihood tree in a phylogenetic analysis is significantly different than an alternative hypothesis. The SOWH test compares the observed difference in log-likelihood between two topologies to a null distribution of differences in log-likelihood generated by parametric resampling. The test is a well-established phylogenetic method for topology testing, but it is sensitive to model misspecification, it is computationally burdensome to perform, and its implementation requires the investigator to make several decisions that each have the potential to affect the outcome of the test. We analyzed the effects of multiple factors using seven data sets to which the SOWH test was previously applied. These factors include a number of sample replicates, likelihood software, the introduction of gaps to simulated data, the use of distinct models of evolution for data simulation and likelihood inference, and a suggested test correction wherein an unresolved "zero-constrained" tree is used to simulate sequence data. To facilitate these analyses and future applications of the SOWH test, we wrote SOWHAT, a program that automates the SOWH test. We find that inadequate bootstrap sampling can change the outcome of the SOWH test. The results also show that using a zero-constrained tree for data simulation can result in a wider null distribution and higher p-values, but does not change the outcome of the SOWH test for most of the data sets tested here. These results will help others implement and evaluate the SOWH test and allow us to provide recommendations for future applications of the SOWH test. SOWHAT is available for download from https://github.com/josephryan/SOWHAT. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Cell differentiation and germ-soma separation in Ediacaran animal embryo-like fossils

NASA Astrophysics Data System (ADS)

Chen, Lei; Xiao, Shuhai; Pang, Ke; Zhou, Chuanming; Yuan, Xunlai

2014-12-01

Phosphorites of the Ediacaran Doushantuo Formation (~600 million years old) yield spheroidal microfossils with a palintomic cell cleavage pattern. These fossils have been variously interpreted as sulphur-oxidizing bacteria, unicellular protists, mesomycetozoean-like holozoans, green algae akin to Volvox, and blastula embryos of early metazoans or bilaterian animals. However, their complete life cycle is unknown and it is uncertain whether they had a cellularly differentiated ontogenetic stage, making it difficult to test their various phylogenetic interpretations. Here we describe new spheroidal fossils from black phosphorites of the Doushantuo Formation that have been overlooked in previous studies. These fossils represent later developmental stages of previously published blastula-like fossils, and they show evidence for cell differentiation, germ-soma separation, and programmed cell death. Their complex multicellularity is inconsistent with a phylogenetic affinity with bacteria, unicellular protists, or mesomycetozoean-like holozoans. Available evidence also indicates that the Doushantuo fossils are unlikely crown-group animals or volvocine green algae. We conclude that an affinity with cellularly differentiated multicellular eukaryotes, including stem-group animals or algae, is likely but more data are needed to constrain further the exact phylogenetic affinity of the Doushantuo fossils.

Cell differentiation and germ-soma separation in Ediacaran animal embryo-like fossils.

PubMed

Chen, Lei; Xiao, Shuhai; Pang, Ke; Zhou, Chuanming; Yuan, Xunlai

2014-12-11

Phosphorites of the Ediacaran Doushantuo Formation (∼600 million years old) yield spheroidal microfossils with a palintomic cell cleavage pattern. These fossils have been variously interpreted as sulphur-oxidizing bacteria, unicellular protists, mesomycetozoean-like holozoans, green algae akin to Volvox, and blastula embryos of early metazoans or bilaterian animals. However, their complete life cycle is unknown and it is uncertain whether they had a cellularly differentiated ontogenetic stage, making it difficult to test their various phylogenetic interpretations. Here we describe new spheroidal fossils from black phosphorites of the Doushantuo Formation that have been overlooked in previous studies. These fossils represent later developmental stages of previously published blastula-like fossils, and they show evidence for cell differentiation, germ-soma separation, and programmed cell death. Their complex multicellularity is inconsistent with a phylogenetic affinity with bacteria, unicellular protists, or mesomycetozoean-like holozoans. Available evidence also indicates that the Doushantuo fossils are unlikely crown-group animals or volvocine green algae. We conclude that an affinity with cellularly differentiated multicellular eukaryotes, including stem-group animals or algae, is likely but more data are needed to constrain further the exact phylogenetic affinity of the Doushantuo fossils.

Phylogenetic turnover along local environmental gradients in tropical forest communities.

PubMed

Baldeck, C A; Kembel, S W; Harms, K E; Yavitt, J B; John, R; Turner, B L; Madawala, S; Gunatilleke, N; Gunatilleke, S; Bunyavejchewin, S; Kiratiprayoon, S; Yaacob, A; Supardi, M N N; Valencia, R; Navarrete, H; Davies, S J; Chuyong, G B; Kenfack, D; Thomas, D W; Dalling, J W

2016-10-01

While the importance of local-scale habitat niches in shaping tree species turnover along environmental gradients in tropical forests is well appreciated, relatively little is known about the influence of phylogenetic signal in species' habitat niches in shaping local community structure. We used detailed maps of the soil resource and topographic variation within eight 24-50 ha tropical forest plots combined with species phylogenies created from the APG III phylogeny to examine how phylogenetic beta diversity (indicating the degree of phylogenetic similarity of two communities) was related to environmental gradients within tropical tree communities. Using distance-based redundancy analysis we found that phylogenetic beta diversity, expressed as either nearest neighbor distance or mean pairwise distance, was significantly related to both soil and topographic variation in all study sites. In general, more phylogenetic beta diversity within a forest plot was explained by environmental variables this was expressed as nearest neighbor distance versus mean pairwise distance (3.0-10.3 % and 0.4-8.8 % of variation explained among plots, respectively), and more variation was explained by soil resource variables than topographic variables using either phylogenetic beta diversity metric. We also found that patterns of phylogenetic beta diversity expressed as nearest neighbor distance were consistent with previously observed patterns of niche similarity among congeneric species pairs in these plots. These results indicate the importance of phylogenetic signal in local habitat niches in shaping the phylogenetic structure of tropical tree communities, especially at the level of close phylogenetic neighbors, where similarity in habitat niches is most strongly preserved.

Landscape patterns in rainforest phylogenetic signal: isolated islands of refugia or structured continental distributions?

PubMed

Kooyman, Robert M; Rossetto, Maurizio; Sauquet, Hervé; Laffan, Shawn W

2013-01-01

Identify patterns of change in species distributions, diversity, concentrations of evolutionary history, and assembly of Australian rainforests. We used the distribution records of all known rainforest woody species in Australia across their full continental extent. These were analysed using measures of species richness, phylogenetic diversity (PD), phylogenetic endemism (PE) and phylogenetic structure (net relatedness index; NRI). Phylogenetic structure was assessed using both continental and regional species pools. To test the influence of growth-form, freestanding and climbing plants were analysed independently, and in combination. Species richness decreased along two generally orthogonal continental axes, corresponding with wet to seasonally dry and tropical to temperate habitats. The PE analyses identified four main areas of substantially restricted phylogenetic diversity, including parts of Cape York, Wet Tropics, Border Ranges, and Tasmania. The continental pool NRI results showed evenness (species less related than expected by chance) in groups of grid cells in coastally aligned areas of species rich tropical and sub-tropical rainforest, and in low diversity moist forest areas in the south-east of the Great Dividing Range and in Tasmania. Monsoon and drier vine forests, and moist forests inland from upland refugia showed phylogenetic clustering, reflecting lower diversity and more relatedness. Signals for evenness in Tasmania and clustering in northern monsoon forests weakened in analyses using regional species pools. For climbing plants, values for NRI by grid cell showed strong spatial structuring, with high diversity and PE concentrated in moist tropical and subtropical regions. Concentrations of rainforest evolutionary history (phylo-diversity) were patchily distributed within a continuum of species distributions. Contrasting with previous concepts of rainforest community distribution, our findings of continuous distributions and continental connectivity have significant implications for interpreting rainforest evolutionary history and current day ecological processes, and for managing rainforest diversity in changing circumstances.

Advances in the floral structural characterization of the major subclades of Malpighiales, one of the largest orders of flowering plants

PubMed Central

Endress, Peter K.; Davis, Charles C.; Matthews, Merran L.

2013-01-01

Background and Aims Malpighiales are one of the largest angiosperm orders and have undergone radical systematic restructuring based on molecular phylogenetic studies. The clade has been recalcitrant to molecular phylogenetic reconstruction, but has become much more resolved at the suprafamilial level. It now contains so many newly identified clades that there is an urgent need for comparative studies to understand their structure, biology and evolution. This is especially true because the order contains a disproportionally large diversity of rain forest species and includes numerous agriculturally important plants. This study is a first broad systematic step in this endeavour. It focuses on a comparative structural overview of the flowers across all recently identified suprafamilial clades of Malpighiales, and points towards areas that desperately need attention. Methods The phylogenetic comparative analysis of floral structure for the order is based on our previously published studies on four suprafamilial clades of Malpighiales, including also four related rosid orders (Celastrales, Crossosomatales, Cucurbitales, Oxalidales). In addition, the results are compiled from a survey of over 3000 publications on macrosystematics, floral structure and embryology across all orders of the core eudicots. Key Results Most new suprafamilial clades within Malpighiales are well supported by floral structural features. Inner morphological structures of the gynoecium (i.e. stigmatic lobes, inner shape of the locules, placentation, presence of obturators) and ovules (i.e. structure of the nucellus, thickness of the integuments, presence of vascular bundles in the integuments, presence of an endothelium in the inner integument) appear to be especially suitable for characterizing suprafamilial clades within Malpighiales. Conclusions Although the current phylogenetic reconstruction of Malpighiales is much improved compared with earlier versions, it is incomplete, and further focused phylogenetic and morphological studies are needed. Once all major subclades of Malpighiales are elucidated, more in-depth studies on promising structural features can be conducted. In addition, once the phylogenetic tree of Malpighiales, including closely related orders, is more fully resolved, character optimization studies will be possible to reconstruct evolution of structural and biological features within the order. PMID:23486341

Characterizing the Phylogenetic Tree Community Structure of a Protected Tropical Rain Forest Area in Cameroon

PubMed Central

Munoz, François; Couteron, Pierre; Hardy, Olivier J.; Sonké, Bonaventure

2014-01-01

Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world. PMID:24936786

An International Symposium and Exhibition on Active Materials and Adaptive Structures.

DTIC Science & Technology

1991-11-08

into Tubular Composite Structures Using Embedded Constraining Layers 232 S. Sattinger, Z. Sanjana, Westinghouse Science and Technology Center...struts, constrained layers , and tuned mass dampers. The most effective damping treatment was selected for each mode depending on its modal...paper) the passive damping component* in the structure will be deserth^ These »dude constrained layer viscoelastic struts« viscous DStrlJi . .^ of

Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants.

PubMed

Arnan, Xavier; Cerdá, Xim; Retana, Javier

2015-01-01

We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a better indicator of community assembly processes than phylogenetic diversity.

Effects of logging and recruitment on community phylogenetic structure in 32 permanent forest plots of Kampong Thom, Cambodia

PubMed Central

Toyama, Hironori; Kajisa, Tsuyoshi; Tagane, Shuichiro; Mase, Keiko; Chhang, Phourin; Samreth, Vanna; Ma, Vuthy; Sokh, Heng; Ichihashi, Ryuji; Onoda, Yusuke; Mizoue, Nobuya; Yahara, Tetsukazu

2015-01-01

Ecological communities including tropical rainforest are rapidly changing under various disturbances caused by increasing human activities. Recently in Cambodia, illegal logging and clear-felling for agriculture have been increasing. Here, we study the effects of logging, mortality and recruitment of plot trees on phylogenetic community structure in 32 plots in Kampong Thom, Cambodia. Each plot was 0.25 ha; 28 plots were established in primary evergreen forests and four were established in secondary dry deciduous forests. Measurements were made in 1998, 2000, 2004 and 2010, and logging, recruitment and mortality of each tree were recorded. We estimated phylogeny using rbcL and matK gene sequences and quantified phylogenetic α and β diversity. Within communities, logging decreased phylogenetic diversity, and increased overall phylogenetic clustering and terminal phylogenetic evenness. Between communities, logging increased phylogenetic similarity between evergreen and deciduous plots. On the other hand, recruitment had opposite effects both within and between communities. The observed patterns can be explained by environmental homogenization under logging. Logging is biased to particular species and larger diameter at breast height, and forest patrol has been effective in decreasing logging. PMID:25561669

A Phylogenetic Perspective on Biogeographical Divergence of the Flora in Yunnan, Southwestern China.

PubMed

Liu, Shuiyin; Zhu, Hua; Yang, Jie

2017-02-21

In recent years, an increasing number of studies incorporated biogeography with phylogenetic analyses to reveal the origin and evolutionary history of specific floras. In this study, we constructed the mega-phylogeny of the floras of three representative regions across Yunnan, southwestern China. We analyzed the phylogenetic structure and beta diversity based on the presence/absence of species (genus or family) data to investigate the phylogenetic patterns of regional floras. We found conspicuous divergence at the genus and species level in the pattern of phylogenetic structures, which most likely related to historical biogeography. The flora of southern Yunnan was shaped by the strike-slip extrusion of Indochina and the regional climatic stability, while the flora of northwestern Yunnan was shaped by the uplift of the Himalaya-Tibetan Plateau and the oscillations of the glacial-interglacial periods. The flora of central Yunnan had nearly equal proportions of the northern and southern floras that may be derived from a common Tertiary tropical or subtropical flora. Geological events fit well with the floristic and phylogenetic patterns across Yunnan. This study highlighted the importance of linking phylogenetic analyses to biogeographic interpretations to improve our understanding of the origin, evolution and divergence of regional floras.

Effects of logging and recruitment on community phylogenetic structure in 32 permanent forest plots of Kampong Thom, Cambodia.

PubMed

Toyama, Hironori; Kajisa, Tsuyoshi; Tagane, Shuichiro; Mase, Keiko; Chhang, Phourin; Samreth, Vanna; Ma, Vuthy; Sokh, Heng; Ichihashi, Ryuji; Onoda, Yusuke; Mizoue, Nobuya; Yahara, Tetsukazu

2015-02-19

Ecological communities including tropical rainforest are rapidly changing under various disturbances caused by increasing human activities. Recently in Cambodia, illegal logging and clear-felling for agriculture have been increasing. Here, we study the effects of logging, mortality and recruitment of plot trees on phylogenetic community structure in 32 plots in Kampong Thom, Cambodia. Each plot was 0.25 ha; 28 plots were established in primary evergreen forests and four were established in secondary dry deciduous forests. Measurements were made in 1998, 2000, 2004 and 2010, and logging, recruitment and mortality of each tree were recorded. We estimated phylogeny using rbcL and matK gene sequences and quantified phylogenetic α and β diversity. Within communities, logging decreased phylogenetic diversity, and increased overall phylogenetic clustering and terminal phylogenetic evenness. Between communities, logging increased phylogenetic similarity between evergreen and deciduous plots. On the other hand, recruitment had opposite effects both within and between communities. The observed patterns can be explained by environmental homogenization under logging. Logging is biased to particular species and larger diameter at breast height, and forest patrol has been effective in decreasing logging. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Periodic Forced Response of Structures Having Three-Dimensional Frictional Constraints

NASA Astrophysics Data System (ADS)

CHEN, J. J.; YANG, B. D.; MENQ, C. H.

2000-01-01

Many mechanical systems have moving components that are mutually constrained through frictional contacts. When subjected to cyclic excitations, a contact interface may undergo constant changes among sticks, slips and separations, which leads to very complex contact kinematics. In this paper, a 3-D friction contact model is employed to predict the periodic forced response of structures having 3-D frictional constraints. Analytical criteria based on this friction contact model are used to determine the transitions among sticks, slips and separations of the friction contact, and subsequently the constrained force which consists of the induced stick-slip friction force on the contact plane and the contact normal load. The resulting constrained force is often a periodic function and can be considered as a feedback force that influences the response of the constrained structures. By using the Multi-Harmonic Balance Method along with Fast Fourier Transform, the constrained force can be integrated with the receptance of the structures so as to calculate the forced response of the constrained structures. It results in a set of non-linear algebraic equations that can be solved iteratively to yield the relative motion as well as the constrained force at the friction contact. This method is used to predict the periodic response of a frictionally constrained 3-d.o.f. oscillator. The predicted results are compared with those of the direct time integration method so as to validate the proposed method. In addition, the effect of super-harmonic components on the resonant response and jump phenomenon is examined.

On the use of cartographic projections in visualizing phylo-genetic tree space

PubMed Central

2010-01-01

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger data sets. PMID:20529355

Phylogenetic diversity of macromycetes and woody plants along an elevational gradient in Eastern Mexico

Treesearch

Marko Gomez-Hernandez; Guadalupe Williams-Linera; D. Jean Lodge; Roger Guevara; Eduardo Ruiz-Sanchez; Etelvina Gandara

2016-01-01

Phylogenetic information provides insight into the ecological and evolutionary processes that organize species assemblages. We compared patterns of phylogenetic diversity among macromycete and woody plant communities along a steep elevational gradient in eastern Mexico to better understand the evolutionary processes that structure their communities. Macrofungi and...

Variation in Seed Germination of 134 Common Species on the Eastern Tibetan Plateau: Phylogenetic, Life History and Environmental Correlates

PubMed Central

Xu, Jing; Li, Wenlong; Zhang, Chunhui; Liu, Wei; Du, Guozhen

2014-01-01

Seed germination is a crucial stage in the life history of a species because it represents the pathway from adult to offspring, and it can affect the distribution and abundance of species in communities. In this study, we examined the effects of phylogenetic, life history and environmental factors on seed germination of 134 common species from an alpine/subalpine meadow on the eastern Tibetan Plateau. In one-way ANOVAs, phylogenetic groups (at or above order) explained 13.0% and 25.9% of the variance in germination percentage and mean germination time, respectively; life history attributes, such as seed size, dispersal mode, explained 3.7%, 2.1% of the variance in germination percentage and 6.3%, 8.7% of the variance in mean germination time, respectively; the environmental factors temperature and habitat explained 4.7%, 1.0% of the variance in germination percentage and 13.5%, 1.7% of the variance in mean germination time, respectively. Our results demonstrated that elevated temperature would lead to a significant increase in germination percentage and an accelerated germination. Multi-factorial ANOVAs showed that the three major factors contributing to differences in germination percentage and mean germination time in this alpine/subalpine meadow were phylogenetic attributes, temperature and seed size (explained 10.5%, 4.7% and 1.4% of the variance in germination percentage independently, respectively; and explained 14.9%, 13.5% and 2.7% of the variance in mean germination time independently, respectively). In addition, there were strong associations between phylogenetic group and life history attributes, and between life history attributes and environmental factors. Therefore, germination variation are constrained mainly by phylogenetic inertia in a community, and seed germination variation correlated with phylogeny is also associated with life history attributes, suggesting a role of niche adaptation in the conservation of germination variation within lineages. Meanwhile, selection can maintain the association between germination behavior and the environmental conditions within a lineage. PMID:24893308

Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges

PubMed Central

Carotenuto, Francesco; Diniz-Filho, José Alexandre F.

2016-01-01

Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes—speciation, extinction and dispersal—in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity. PMID:26977061

Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges.

PubMed

Villalobos, Fabricio; Carotenuto, Francesco; Raia, Pasquale; Diniz-Filho, José Alexandre F

2016-04-05

Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes--speciation, extinction and dispersal--in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity. © 2016 The Author(s).

Phylogenetic and Functional Structure of Wintering Waterbird Communities Associated with Ecological Differences.

PubMed

Che, Xianli; Zhang, Min; Zhao, Yanyan; Zhang, Qiang; Quan, Qing; Møller, Anders; Zou, Fasheng

2018-01-19

Ecological differences may be related to community component divisions between Oriental (west) and Sino-Japanese (east) realms, and such differences may result in weak geographical breaks in migratory species that are highly mobile. Here, we conducted comparative phylogenetic and functional structure analyses of wintering waterbird communities in southern China across two realms and subsequently examined possible climate drivers of the observed patterns. An analysis based on such highly migratory species is particularly telling because migration is bound to reduce or completely eliminate any divergence between communities. Phylogenetic and functional structure of eastern communities showed over-dispersion while western communities were clustered. Basal phylogenetic and functional turnover of western communities was significant lower than that of eastern communities. The break between eastern and western communities was masked by these two realms. Geographic patterns were related to mean temperature changes and temperature fluctuations, suggesting that temperature may filter waterbird lineages and traits, thus underlying geographical community divisions. These results suggest phylogenetic and functional divisions in southern China, coinciding with biogeography. This study shows that temperature fluctuations constitute an essential mechanism shaping geographical divisions that have largely gone undetected previously, even under climate change.

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution

PubMed Central

Kendall, Michelle; Colijn, Caroline

2016-01-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. Key words: phylogenetics, evolution, tree metrics, genetics, sequencing. PMID:27343287

Patterns of forest phylogenetic community structure across the United States and their possible forest health implications

Treesearch

Kevin M. Potter; Frank H. Koch

2014-01-01

The analysis of phylogenetic relationships among co-occurring tree species offers insights into the ecological organization of forest communities from an evolutionary perspective and, when employed regionally across thousands of plots, can assist in forest health assessment. Phylogenetic clustering of species, when species are more closely related than expected by...

Insights into the phylogenetic positions of photosynthetic bacteria obtained from 5S rRNA and 16S rRNA sequence data

NASA Technical Reports Server (NTRS)

Fox, G. E.

1985-01-01

Comparisons of complete 16S ribosomal ribonucleic acid (rRNA) sequences established that the secondary structure of these molecules is highly conserved. Earlier work with 5S rRNA secondary structure revealed that when structural conservation exists the alignment of sequences is straightforward. The constancy of structure implies minimal functional change. Under these conditions a uniform evolutionary rate can be expected so that conditions are favorable for phylogenetic tree construction.

Phylogenetic structure of arbuscular mycorrhizal fungal communities along an elevation gradient.

PubMed

Egan, Cameron P; Callaway, Ragan M; Hart, Miranda M; Pither, Jason; Klironomos, John

2017-04-01

Despite the importance of arbuscular mycorrhizal (AM) fungi within terrestrial ecosystems, we know little about how natural AM fungal communities are structured. To date, the majority of studies examining AM fungal community diversity have focused on single habitats with similar environmental conditions, with relatively few studies having assessed the diversity of AM fungi over large-scale environmental gradients. In this study, we characterized AM fungal communities in the soil along a high-elevation gradient in the North American Rocky Mountains. We focused on phylogenetic patterns of AM fungal communities to gain insight into how AM fungal communities are naturally assembled. We found that alpine AM fungal communities had lower phylogenetic diversity relative to lower elevation communities, as well as being more heterogeneous in composition than either treeline or subalpine communities. AM fungal communities were phylogenetically clustered at all elevations sampled, suggesting that environmental filtering, either selection by host plants or fungal niches, is the primary ecological process structuring communities along the gradient.

Power law tails in phylogenetic systems.

PubMed

Qin, Chongli; Colwell, Lucy J

2018-01-23

Covariance analysis of protein sequence alignments uses coevolving pairs of sequence positions to predict features of protein structure and function. However, current methods ignore the phylogenetic relationships between sequences, potentially corrupting the identification of covarying positions. Here, we use random matrix theory to demonstrate the existence of a power law tail that distinguishes the spectrum of covariance caused by phylogeny from that caused by structural interactions. The power law is essentially independent of the phylogenetic tree topology, depending on just two parameters-the sequence length and the average branch length. We demonstrate that these power law tails are ubiquitous in the large protein sequence alignments used to predict contacts in 3D structure, as predicted by our theory. This suggests that to decouple phylogenetic effects from the interactions between sequence distal sites that control biological function, it is necessary to remove or down-weight the eigenvectors of the covariance matrix with largest eigenvalues. We confirm that truncating these eigenvectors improves contact prediction.

The Role of Edaphic Environment and Climate in Structuring Phylogenetic Pattern in Seasonally Dry Tropical Plant Communities

PubMed Central

Moro, Marcelo Freire; Silva, Igor Aurélio; de Araújo, Francisca Soares; Nic Lughadha, Eimear; Meagher, Thomas R.; Martins, Fernando Roberto

2015-01-01

Seasonally dry tropical plant formations (SDTF) are likely to exhibit phylogenetic clustering owing to niche conservatism driven by a strong environmental filter (water stress), but heterogeneous edaphic environments and life histories may result in heterogeneity in degree of phylogenetic clustering. We investigated phylogenetic patterns across ecological gradients related to water availability (edaphic environment and climate) in the Caatinga, a SDTF in Brazil. Caatinga is characterized by semiarid climate and three distinct edaphic environments – sedimentary, crystalline, and inselberg –representing a decreasing gradient in soil water availability. We used two measures of phylogenetic diversity: Net Relatedness Index based on the entire phylogeny among species present in a site, reflecting long-term diversification; and Nearest Taxon Index based on the tips of the phylogeny, reflecting more recent diversification. We also evaluated woody species in contrast to herbaceous species. The main climatic variable influencing phylogenetic pattern was precipitation in the driest quarter, particularly for herbaceous species, suggesting that environmental filtering related to minimal periods of precipitation is an important driver of Caatinga biodiversity, as one might expect for a SDTF. Woody species tended to show phylogenetic clustering whereas herbaceous species tended towards phylogenetic overdispersion. We also found phylogenetic clustering in two edaphic environments (sedimentary and crystalline) in contrast to phylogenetic overdispersion in the third (inselberg). We conclude that while niche conservatism is evident in phylogenetic clustering in the Caatinga, this is not a universal pattern likely due to heterogeneity in the degree of realized environmental filtering across edaphic environments. Thus, SDTF, in spite of a strong shared environmental filter, are potentially heterogeneous in phylogenetic structuring. Our results support the need for scientifically informed conservation strategies in the Caatinga and other SDTF regions that have not previously been prioritized for conservation in order to take into account this heterogeneity. PMID:25798584

Constrained spectral clustering under a local proximity structure assumption

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri; Xu, Qianjun; des Jardins, Marie

2005-01-01

This work focuses on incorporating pairwise constraints into a spectral clustering algorithm. A new constrained spectral clustering method is proposed, as well as an active constraint acquisition technique and a heuristic for parameter selection. We demonstrate that our constrained spectral clustering method, CSC, works well when the data exhibits what we term local proximity structure.

Competitive interactions between forest trees are driven by species' trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly.

PubMed

Kunstler, Georges; Lavergne, Sébastien; Courbaud, Benoît; Thuiller, Wilfried; Vieilledent, Ghislain; Zimmermann, Niklaus E; Kattge, Jens; Coomes, David A

2012-08-01

The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that interaction strengths are mainly driven by trait hierarchy and not by functional or phylogenetic similarity. On the basis of this result, we thus propose that functional and phylogenetic convergence in local tree community might be due to competition-sorting species with different competitive abilities and not only environmental filtering as commonly assumed. We then show a functional and phylogenetic convergence of forest structure with increasing plot age, which supports this view. © 2012 Blackwell Publishing Ltd/CNRS.

Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti.

PubMed

Godreuil, S; Renaud, F; Choisy, M; Depina, J J; Garnotel, E; Morillon, M; Van de Perre, P; Bañuls, A L

2010-07-01

Djibouti is an East African country with a high tuberculosis incidence. This study was conducted over a 2-month period in Djibouti, during which 62 consecutive patients with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using mycobacterial interspersed repetitive-unit variable-number tandem-repeat typing and spoligotyping, was performed. The genetic and phylogenetic analysis revealed only three major families (Central Asian, East African Indian and T). The high diversity and linkage disequilibrium within each family suggest a long period of clonal evolution. A Bayesian approach shows that the phylogenetic structure observed in our sample of 62 isolates is very likely to be representative of the phylogenetic structure of the M. tuberculosis population in the total number of TB cases.

Effects of different substrates on the sprint performance of lizards.

PubMed

Tulli, Maria Jose; Abdala, Virginia; Cruz, Felix B

2012-03-01

The variation in substrate structure is one of the most important determinants of the locomotor abilities of lizards. Lizards are found across a range of habitats, from large rocks to loose sand, each of them with conflicting mechanical demands on locomotion. We examined the relationships among sprint speed, morphology and different types of substrate surfaces in species of lizards that exploit different structural habitats (arboreal, saxicolous, terrestrial and arenicolous) in a phylogenetic context. Our main goals were to assess which processes drive variability in morphology (i.e. phylogeny or adaptation to habitat) in order to understand how substrate structure affects sprint speed in species occupying different habitats and to determine the relationship between morphology and performance. Liolaemini lizards show that most morphological traits are constrained by phylogeny, particularly toe 3, the femur and foot. All ecological groups showed significant differences on rocky surfaces. Surprisingly, no ecological group performed better on the surface resembling its own habitat. Moreover, all groups exhibited significant differences in sprint speed among the three different types of experimental substrates and showed the best performance on sand, with the exception of the arboreal group. Despite the fact that species use different types of habitats, the highly conservative morphology of Liolaemini species and the similar levels of performance on different types of substrates suggest that they confer to the 'jack of all trades and master of none' principle.

Landscape Patterns in Rainforest Phylogenetic Signal: Isolated Islands of Refugia or Structured Continental Distributions?

PubMed Central

Kooyman, Robert M.; Rossetto, Maurizio; Sauquet, Hervé; Laffan, Shawn W.

2013-01-01

Objectives Identify patterns of change in species distributions, diversity, concentrations of evolutionary history, and assembly of Australian rainforests. Methods We used the distribution records of all known rainforest woody species in Australia across their full continental extent. These were analysed using measures of species richness, phylogenetic diversity (PD), phylogenetic endemism (PE) and phylogenetic structure (net relatedness index; NRI). Phylogenetic structure was assessed using both continental and regional species pools. To test the influence of growth-form, freestanding and climbing plants were analysed independently, and in combination. Results Species richness decreased along two generally orthogonal continental axes, corresponding with wet to seasonally dry and tropical to temperate habitats. The PE analyses identified four main areas of substantially restricted phylogenetic diversity, including parts of Cape York, Wet Tropics, Border Ranges, and Tasmania. The continental pool NRI results showed evenness (species less related than expected by chance) in groups of grid cells in coastally aligned areas of species rich tropical and sub-tropical rainforest, and in low diversity moist forest areas in the south-east of the Great Dividing Range and in Tasmania. Monsoon and drier vine forests, and moist forests inland from upland refugia showed phylogenetic clustering, reflecting lower diversity and more relatedness. Signals for evenness in Tasmania and clustering in northern monsoon forests weakened in analyses using regional species pools. For climbing plants, values for NRI by grid cell showed strong spatial structuring, with high diversity and PE concentrated in moist tropical and subtropical regions. Conclusions/Significance Concentrations of rainforest evolutionary history (phylo-diversity) were patchily distributed within a continuum of species distributions. Contrasting with previous concepts of rainforest community distribution, our findings of continuous distributions and continental connectivity have significant implications for interpreting rainforest evolutionary history and current day ecological processes, and for managing rainforest diversity in changing circumstances. PMID:24312493

Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae).

PubMed

Litsios, Glenn; Pellissier, Loïc; Forest, Félix; Lexer, Christian; Pearman, Peter B; Zimmermann, Niklaus E; Salamin, Nicolas

2012-09-22

The rate of environmental niche evolution describes the capability of species to explore the available environmental space and is known to vary among species owing to lineage-specific factors. Trophic specialization is a main force driving species evolution and is responsible for classical examples of adaptive radiations in fishes. We investigate the effect of trophic specialization on the rate of environmental niche evolution in the damselfish, Pomacentridae, which is an important family of tropical reef fishes. First, phylogenetic niche conservatism is not detected in the family using a standard test of phylogenetic signal, and we demonstrate that the environmental niches of damselfishes that differ in trophic specialization are not equivalent while they still overlap at their mean values. Second, we estimate the relative rates of niche evolution on the phylogenetic tree and show the heterogeneity among rates of environmental niche evolution of the three trophic groups. We suggest that behavioural characteristics related to trophic specialization can constrain the evolution of the environmental niche and lead to conserved niches in specialist lineages. Our results show the extent of influence of several traits on the evolution of the environmental niche and shed new light on the evolution of damselfishes, which is a key lineage in current efforts to conserve biodiversity in coral reefs.

Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae)

PubMed Central

Litsios, Glenn; Pellissier, Loïc; Forest, Félix; Lexer, Christian; Pearman, Peter B.; Zimmermann, Niklaus E.; Salamin, Nicolas

2012-01-01

The rate of environmental niche evolution describes the capability of species to explore the available environmental space and is known to vary among species owing to lineage-specific factors. Trophic specialization is a main force driving species evolution and is responsible for classical examples of adaptive radiations in fishes. We investigate the effect of trophic specialization on the rate of environmental niche evolution in the damselfish, Pomacentridae, which is an important family of tropical reef fishes. First, phylogenetic niche conservatism is not detected in the family using a standard test of phylogenetic signal, and we demonstrate that the environmental niches of damselfishes that differ in trophic specialization are not equivalent while they still overlap at their mean values. Second, we estimate the relative rates of niche evolution on the phylogenetic tree and show the heterogeneity among rates of environmental niche evolution of the three trophic groups. We suggest that behavioural characteristics related to trophic specialization can constrain the evolution of the environmental niche and lead to conserved niches in specialist lineages. Our results show the extent of influence of several traits on the evolution of the environmental niche and shed new light on the evolution of damselfishes, which is a key lineage in current efforts to conserve biodiversity in coral reefs. PMID:22719034

Damping Analysis of Cylindrical Composite Structures with Enhanced Viscoelastic Properties

NASA Astrophysics Data System (ADS)

Kliem, Mathias; Høgsberg, Jan; Vanwalleghem, Joachim; Filippatos, Angelos; Hoschützky, Stefan; Fotsing, Edith-Roland; Berggreen, Christian

2018-04-01

Constrained layer damping treatments are widely used in mechanical structures to damp acoustic noise and mechanical vibrations. A viscoelastic layer is thereby applied to a structure and covered by a stiff constraining layer. When the structure vibrates in a bending mode, the viscoelastic layer is forced to deform in shear mode. Thus, the vibration energy is dissipated as low grade frictional heat. This paper documents the efficiency of passive constrained layer damping treatments for low frequency vibrations of cylindrical composite specimens made of glass fibre-reinforced plastics. Different cross section geometries with shear webs have been investigated in order to study a beneficial effect on the damping characteristics of the cylinder. The viscoelastic damping layers are placed at different locations within the composite cylinder e.g. circumferential and along the neutral plane to evaluate the location-dependent efficiency of constrained layer damping treatments. The results of the study provide a thorough understanding of constrained layer damping treatments and an improved damping design of the cylindrical composite structure. The highest damping is achieved when placing the damping layer in the neutral plane perpendicular to the bending load. The results are based on free decay tests of the composite structure.

Herbicide and fertilizers promote analogous phylogenetic responses but opposite functional responses in plant communities

NASA Astrophysics Data System (ADS)

Pellissier, Loïc; Wisz, Mary S.; Strandberg, Beate; Damgaard, Christian

2014-01-01

Throughout the world, herbicides and fertilizers change species composition in agricultural communities, but how do the cumulative effects of these chemicals impact the functional and phylogenetic structure of non-targeted communities when they drift into adjacent semi-natural habitats? Based on long-term experiment we show that fertilizer and herbicides (glyphosate) have contrasting effects on functional structure, but can increase phylogenetic diversity in semi-natural plant communities. We found that an increase in nitrogen promoted an increase in the average specific leaf area and canopy height at the community level, but an increase in glyphosate promoted a decrease in those traits. Phylogenetic diversity of plant communities increased when herbicide and fertilizer were applied together, likely because functional traits facilitating plant success in those conditions were not phylogenetically conserved. Species richness also decreased with increasing levels of nitrogen and glyphosate. Our results suggest that predicting the cumulative effects of agrochemicals is more complex than anticipated due to their distinct selection of traits that may or may not be conserved phylogenetically. Precautionary efforts to mitigate drift of agricultural chemicals into semi-natural habitats are warranted to prevent unforeseeable biodiversity shifts.

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree.

PubMed

Kacar, B; Hanson-Smith, V; Adam, Z R; Boekelheide, N

2017-09-01

Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen-sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem-bearing, oxygen-evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen-sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event. © 2017 The Authors. Geobiology Published by John Wiley & Sons Ltd.

Helicobacter pylori from gastric cancer and duodenal ulcer show same phylogeographic origin in the Andean region in Colombia.

PubMed

Shiota, Seiji; Suzuki, Rumiko; Matsuo, Yuichi; Miftahussurur, Muhammad; Tran, Trang Thu Huyen; Binh, Tran Thanh; Yamaoka, Yoshio

2014-01-01

A recent report has shown that the phylogenetic origin of Helicobacter pylori based on multi-locus sequence typing (MLST) was significantly associated with the severity of gastritis in Colombia. However, the potential relationship between phylogenetic origin and clinical outcomes was not examined in that study. If the phylogenetic origin rather than virulence factors were truly associated with clinical outcomes, identifying a population at high risk for gastric cancer in Colombia would be relatively straightforward. In this study, we examined the phylogenetic origins of strains from gastric cancer and duodenal ulcer patients living in Bogota, Colombia. We included 35 gastric cancer patients and 31 duodenal ulcer patients, which are considered the variant outcomes. The genotypes of cagA and vacA were determined by polymerase chain reaction. The genealogy of these Colombian strains was analyzed by MLST. Bacterial population structure was analyzed using STRUCTURE software. H. pylori strains from gastric cancer and duodenal ulcer patients were scattered in the phylogenetic tree; thus, we did not detect any difference in phylogenetic distribution between gastric cancer and duodenal ulcer strains in the hpEurope group in Colombia. Sixty-six strains, with one exception, were classified as hpEurope irrespective of the cagA and vacA genotypes, and type of disease. STRUCTURE analysis revealed that Colombian hpEurope strains have a phylogenetic connection to Spanish strains. Our study showed that a phylogeographic origin determined by MLST was insufficient for distinguishing between gastric cancer and duodenal ulcer risk among hpEurope strains in the Andean region in Colombia. Our analysis also suggests that hpEurope strains in Colombia were primarily introduced by Spanish immigrants.

Stickleback fishes: Bridging the gap between population biology and paleobiology.

PubMed

Bell, M A

1988-12-01

Integration of evolutionary mechanisms and phylogeny requires study of phenotypes that change in the fossil record and continue to evolve in extant populations. Pelvic reduction in the three-spined stickle-back has evolved rapidly in a Miocene fossil assemblage and in numerous extant isolated lake populations throughout its distribution. Although pelvic reduction is caused by selection, expression of reduced pelvic phenotypes is constrained by development and other factors. However, lineages with pelvis reduction rapidly go extinct while lineages that retain the fully formed pelvic girdle tend to persist. Existence of pelvic reduction since the Miocene has depended on an equilibrium between divergence and extinction. The phylogenetic topology resulting from this process differs greatly from the conventional view of evolutionary history, and could only be recognized by analysis of both extant populations and fossil material. If this phylogenetic topology is common, it may help to account for the different perceptions that population biologists and paleobiologists have of evolutionary tempo. Copyright © 1988. Published by Elsevier Ltd.

Evolution of kin recognition mechanisms in a fish.

PubMed

Hain, Timothy J A; Garner, Shawn R; Ramnarine, Indar W; Neff, Bryan D

2017-03-01

Both selection and phylogenetic history can influence the evolution of phenotypic traits. Here we used recently characterized variation in kin recognition mechanisms among six guppy populations to explore the phylogenetic history of this trait. Guppies can use two different kin recognition mechanisms: either phenotype matching, in which individuals are identified based on comparison with a recognition template, or familiarity, in which individuals are remembered based on previous interactions. Across the six populations, we identified four transitions in recognition mechanism: phenotype matching evolved once and was subsequently lost in a single population, whereas familiarity evolved twice. Based on a molecular clock, these transitions occurred among populations that had diverged on a timescale of hundreds of thousands of years, which is two orders of magnitude faster than previously documented transitions in recognition mechanisms. A randomization test provided no evidence that recognition mechanisms were constrained by phylogeny, suggesting that recognition mechanisms have the capacity to evolve rapidly, although the specific selection pressures that may be contributing to variation in recognition mechanisms across populations remain unknown.

Phylogenetic diversity and biodiversity indices on phylogenetic networks.

PubMed

Wicke, Kristina; Fischer, Mareike

2018-04-01

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their contribution to overall phylogenetic diversity. However, in many cases evolution is not treelike and thus, phylogenetic networks have been developed as a generalization of phylogenetic trees, allowing for the representation of non-treelike evolutionary events, such as hybridization. Here, we extend the concepts of phylogenetic diversity and phylogenetic diversity indices from phylogenetic trees to phylogenetic networks. On the one hand, we consider the treelike content of a phylogenetic network, e.g. the (multi)set of phylogenetic trees displayed by a network and the so-called lowest stable ancestor tree associated with it. On the other hand, we derive the phylogenetic diversity of subsets of taxa and biodiversity indices directly from the internal structure of the network. We consider both approaches that are independent of so-called inheritance probabilities as well as approaches that explicitly incorporate these probabilities. Furthermore, we introduce our software package NetDiversity, which is implemented in Perl and allows for the calculation of all generalized measures of phylogenetic diversity and generalized phylogenetic diversity indices established in this note that are independent of inheritance probabilities. We apply our methods to a phylogenetic network representing the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by widespread hybridization. Copyright © 2018 Elsevier Inc. All rights reserved.

Cold tolerance of Littorinidae from southern Africa: intertidal snails are not constrained to freeze tolerance.

PubMed

Sinclair, Brent J; Marshall, David J; Singh, Sarika; Chown, Steven L

2004-11-01

All intertidal gastropods for which cold tolerance strategies have been assessed have been shown to be freeze tolerant. Thus, freeze tolerance is considered an adaptation to the intertidal environment. We investigated the cold tolerance strategies of three species of subtropical and temperate snails (Gastropoda: Littorinidae) to determine whether this group is phylogenetically constrained to freeze tolerance. We exposed 'dry' acclimated and 'wet' rehydrated snails to low temperatures to determine temperature of crystallisation (Tc), lower lethal temperature and LT(50) and to examine the relationship between ice formation and mortality. Tc was lowest in dry Afrolittorina knysnaensis (-13.6+/-0.4 degrees C), followed by dry Echinolittorina natalensis (-10.9+/-0.2 degrees C) and wet A. knysnaensis (-10.2+/-0.2 degrees C) . The Tc of both A. knysnaensis and E. natalensis increased with rehydration, whereas Tc of dry and wet Afrolittorina africana did not differ (-9.6+/-0.2 and -9.0+/-0.2 degrees C respectively). Wet snails of all species exhibited no or low survival of inoculative freezing, whereas dry individuals of A. knysnaensis could survive subzero temperatures above -8 degrees C when freezing was inoculated with ice . In the absence of external ice, Afrolittorina knysnaensis employs a freeze-avoidance strategy of cold tolerance, the first time this has been reported for an intertidal snail, indicating that there is no family-level phylogenetic constraint to freeze tolerance. Echinolittorina natalensis and A. africana both showed pre-freeze mortality and survival of some internal ice formation, but were not cold hardy in any strict sense.

Head shape evolution in Gymnophthalmidae: does habitat use constrain the evolution of cranial design in fossorial lizards?

PubMed

Barros, F C; Herrel, A; Kohlsdorf, T

2011-11-01

Habitat usage comprises interactions between ecological parameters and organismal capacities, and the selective pressures that ultimately determine the outcome of such processes in an evolutionary scale may be conflicting when the same morphological structure is recruited for different activities. Here, we investigate the roles of diet and locomotion in the evolution of cranial design in gymnophthalmid lizards and test the hypothesis that microhabitat use drives head shape evolution, particularly in head-first burrowers. Morphological factors were analysed in relation to continuous ecological indexes (prey hardness and substrate compactness) using conventional and phylogenetic approaches. Results suggest that the evolution of head morphology in Gymnophthalmidae was shaped under the influence of microhabitat use rather than diet: burrowers have shorter heads with lower rostral angulation, independently of the prey consumed. Food preferences appear to be relatively conserved throughout the phylogeny of the group, which may have permitted the extensive radiation of gymnophthalmids into fossorial microhabitats. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Phylogeny determines flower size-dependent sex allocation at flowering in a hermaphroditic family.

PubMed

Teixido, A L; Guzmán, B; Staggemeier, V G; Valladares, F

2017-11-01

In animal-pollinated hermaphroditic plants, optimal floral allocation determines relative investment into sexes, which is ultimately dependent on flower size. Larger flowers disproportionally increase maleness whereas smaller and less rewarding flowers favour female function. Although floral traits are considered strongly conserved, phylogenetic relationships in the interspecific patterns of resource allocation to floral sex remain overlooked. We investigated these patterns in Cistaceae, a hermaphroditic family. We reconstructed phylogenetic relationships among Cistaceae species and quantified phylogenetic signal for flower size, dry mass and nutrient allocation to floral structures in 23 Mediterranean species using Blomberg's K-statistic. Lastly, phylogenetically-controlled correlational and regression analyses were applied to examine flower size-based allometry in resource allocation to floral structures. Sepals received the highest dry mass allocation, followed by petals, whereas sexual structures increased nutrient allocation. Flower size and resource allocation to floral structures, except for carpels, showed a strong phylogenetic signal. Larger-flowered species allometrically allocated more resources to maleness, by increasing allocation to corollas and stamens. Our results suggest a major role of phylogeny in determining interspecific changes in flower size and subsequent floral sex allocation. This implies that flower size balances the male-female function over the evolutionary history of Cistaceae. While allometric resource investment in maleness is inherited across species diversification, allocation to the female function seems a labile trait that varies among closely related species that have diversified into different ecological niches. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

Influence of matrix type on tree community assemblages along tropical dry forest edges.

PubMed

Benítez-Malvido, Julieta; Gallardo-Vásquez, Julio César; Alvarez-Añorve, Mariana Y; Avila-Cabadilla, Luis Daniel

2014-05-01

• Anthropogenic habitat edges have strong negative consequences for the functioning of tropical ecosystems. However, edge effects on tropical dry forest tree communities have been barely documented.• In Chamela, Mexico, we investigated the phylogenetic composition and structure of tree assemblages (≥5 cm dbh) along edges abutting different matrices: (1) disturbed vegetation with cattle, (2) pastures with cattle and, (3) pastures without cattle. Additionally, we sampled preserved forest interiors.• All edge types exhibited similar tree density, basal area and diversity to interior forests, but differed in species composition. A nonmetric multidimensional scaling ordination showed that the presence of cattle influenced species composition more strongly than the vegetation structure of the matrix; tree assemblages abutting matrices with cattle had lower scores in the ordination. The phylogenetic composition of tree assemblages followed the same pattern. The principal plant families and genera were associated according to disturbance regimes as follows: pastures and disturbed vegetation (1) with cattle and (2) without cattle, and (3) pastures without cattle and interior forests. All habitats showed random phylogenetic structures, suggesting that tree communities are assembled mainly by stochastic processes. Long-lived species persisting after edge creation could have important implications in the phylogenetic structure of tree assemblages.• Edge creation exerts a stronger influence on TDF vegetation pathways than previously documented, leading to new ecological communities. Phylogenetic analysis may, however, be needed to detect such changes. © 2014 Botanical Society of America, Inc.

Do Muscles Constrain Skull Shape Evolution in Strepsirrhines?

PubMed

Fabre, Anne-Claire; Perry, Jonathan M G; Hartstone-Rose, Adam; Lowie, AuróLien; Boens, Andy; Dumont, MaÏtena

2018-02-01

Despite great interest and decades of research, the musculoskeletal relationships of the masticatory system in primates are still not fully understood. However, without a clear understanding of the interplay between muscles and bones it remains difficult to understand the functional significance of morphological traits of the skeleton. Here, we aim to study the impacts of the masticatory muscles on the shape of the cranium and the mandible as well as their co-variation in strepsirrhine primates. To do so, we use 3D geometric morphometric approaches to assess the shape of each bone of the skull of 20 species for which muscle data are available in the literature. Impacts of the masticatory muscles on the skull shape were assessed using non-phylogenetic regressions and phylogenetic regressions whereas co-variations were assessed using two-blocks partial least square (2B-PLS) and phylogenetic 2B-PLS. Our results show that there is a phylogenetic signal for skull shape and masticatory muscles. They also show that there is a significant impact of the masticatory muscles on cranial shape but not as much as on the mandible. The co-variations are also stronger between the masticatory muscles and cranial shape even when taking into account phylogeny. Interestingly, the results of co-variation between the masticatory muscles and mandibular shape show a more complex pattern in two different directions to get strong muscles associated with mandibular shape: a folivore way (with the bamboo lemurs and sifakas) and a hard-object eater one (with the aye-aye). Anat Rec, 301:291-310, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

PubMed Central

2010-01-01

Background The Maximal Pairing Problem (MPP) is the prototype of a class of combinatorial optimization problems that are of considerable interest in bioinformatics: Given an arbitrary phylogenetic tree T and weights ωxy for the paths between any two pairs of leaves (x, y), what is the collection of edge-disjoint paths between pairs of leaves that maximizes the total weight? Special cases of the MPP for binary trees and equal weights have been described previously; algorithms to solve the general MPP are still missing, however. Results We describe a relatively simple dynamic programming algorithm for the special case of binary trees. We then show that the general case of multifurcating trees can be treated by interleaving solutions to certain auxiliary Maximum Weighted Matching problems with an extension of this dynamic programming approach, resulting in an overall polynomial-time solution of complexity (n4 log n) w.r.t. the number n of leaves. The source code of a C implementation can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/Targeting. For binary trees, we furthermore discuss several constrained variants of the MPP as well as a partition function approach to the probabilistic version of the MPP. Conclusions The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations. PMID:20525185

Using phylogeny and functional traits for assessing community assembly along environmental gradients: A deterministic process driven by elevation.

PubMed

Xu, Jinshi; Chen, Yu; Zhang, Lixia; Chai, Yongfu; Wang, Mao; Guo, Yaoxin; Li, Ting; Yue, Ming

2017-07-01

Community assembly processes is the primary focus of community ecology. Using phylogenetic-based and functional trait-based methods jointly to explore these processes along environmental gradients are useful ways to explain the change of assembly mechanisms under changing world. Our study combined these methods to test assembly processes in wide range gradients of elevation and other habitat environmental factors. We collected our data at 40 plots in Taibai Mountain, China, with more than 2,300 m altitude difference in study area and then measured traits and environmental factors. Variance partitioning was used to distinguish the main environment factors leading to phylogeny and traits change among 40 plots. Principal component analysis (PCA) was applied to colligate other environment factors. Community assembly patterns along environmental gradients based on phylogenetic and functional methods were studied for exploring assembly mechanisms. Phylogenetic signal was calculated for each community along environmental gradients in order to detect the variation of trait performance on phylogeny. Elevation showed a better explanatory power than other environment factors for phylogenetic and most traits' variance. Phylogenetic and several functional structure clustered at high elevation while some conserved traits overdispersed. Convergent tendency which might be caused by filtering or competition along elevation was detected based on functional traits. Leaf dry matter content (LDMC) and leaf nitrogen content along PCA 1 axis showed conflicting patterns comparing to patterns showed on elevation. LDMC exhibited the strongest phylogenetic signal. Only the phylogenetic signal of maximum plant height showed explicable change along environmental gradients. Synthesis . Elevation is the best environment factors for predicting phylogeny and traits change. Plant's phylogenetic and some functional structures show environmental filtering in alpine region while it shows different assembly processes in middle- and low-altitude region by different trait/phylogeny. The results highlight deterministic processes dominate community assembly in large-scale environmental gradients. Performance of phylogeny and traits along gradients may be independent with each other. The novel method for calculating functional structure which we used in this study and the focus of phylogenetic signal change along gradients may provide more useful ways to detect community assembly mechanisms.

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

PubMed

Kendall, Michelle; Colijn, Caroline

2016-10-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. phylogenetics, evolution, tree metrics, genetics, sequencing. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Climate-driven extinctions shape the phylogenetic structure of temperate tree floras.

PubMed

Eiserhardt, Wolf L; Borchsenius, Finn; Plum, Christoffer M; Ordonez, Alejandro; Svenning, Jens-Christian

2015-03-01

When taxa go extinct, unique evolutionary history is lost. If extinction is selective, and the intrinsic vulnerabilities of taxa show phylogenetic signal, more evolutionary history may be lost than expected under random extinction. Under what conditions this occurs is insufficiently known. We show that late Cenozoic climate change induced phylogenetically selective regional extinction of northern temperate trees because of phylogenetic signal in cold tolerance, leading to significantly and substantially larger than random losses of phylogenetic diversity (PD). The surviving floras in regions that experienced stronger extinction are phylogenetically more clustered, indicating that non-random losses of PD are of increasing concern with increasing extinction severity. Using simulations, we show that a simple threshold model of survival given a physiological trait with phylogenetic signal reproduces our findings. Our results send a strong warning that we may expect future assemblages to be phylogenetically and possibly functionally depauperate if anthropogenic climate change affects taxa similarly. © 2015 John Wiley & Sons Ltd/CNRS.

Determinants of plant community assembly in a mosaic of landscape units in central Amazonia: ecological and phylogenetic perspectives.

PubMed

Umaña, María Natalia; Norden, Natalia; Cano, Angela; Stevenson, Pablo R

2012-01-01

The Amazon harbours one of the richest ecosystems on Earth. Such diversity is likely to be promoted by plant specialization, associated with the occurrence of a mosaic of landscape units. Here, we integrate ecological and phylogenetic data at different spatial scales to assess the importance of habitat specialization in driving compositional and phylogenetic variation across the Amazonian forest. To do so, we evaluated patterns of floristic dissimilarity and phylogenetic turnover, habitat association and phylogenetic structure in three different landscape units occurring in terra firme (Hilly and Terrace) and flooded forests (Igapó). We established two 1-ha tree plots in each of these landscape units at the Caparú Biological Station, SW Colombia, and measured edaphic, topographic and light variables. At large spatial scales, terra firme forests exhibited higher levels of species diversity and phylodiversity than flooded forests. These two types of forests showed conspicuous differences in species and phylogenetic composition, suggesting that environmental sorting due to flood is important, and can go beyond the species level. At a local level, landscape units showed floristic divergence, driven both by geographical distance and by edaphic specialization. In terms of phylogenetic structure, Igapó forests showed phylogenetic clustering, whereas Hilly and Terrace forests showed phylogenetic evenness. Within plots, however, local communities did not show any particular trend. Overall, our findings suggest that flooded forests, characterized by stressful environments, impose limits to species occurrence, whereas terra firme forests, more environmentally heterogeneous, are likely to provide a wider range of ecological conditions and therefore to bear higher diversity. Thus, Amazonia should be considered as a mosaic of landscape units, where the strength of habitat association depends upon their environmental properties.

Determinants of Plant Community Assembly in a Mosaic of Landscape Units in Central Amazonia: Ecological and Phylogenetic Perspectives

PubMed Central

Umaña, María Natalia; Norden, Natalia; Cano, Ángela; Stevenson, Pablo R.

2012-01-01

The Amazon harbours one of the richest ecosystems on Earth. Such diversity is likely to be promoted by plant specialization, associated with the occurrence of a mosaic of landscape units. Here, we integrate ecological and phylogenetic data at different spatial scales to assess the importance of habitat specialization in driving compositional and phylogenetic variation across the Amazonian forest. To do so, we evaluated patterns of floristic dissimilarity and phylogenetic turnover, habitat association and phylogenetic structure in three different landscape units occurring in terra firme (Hilly and Terrace) and flooded forests (Igapó). We established two 1-ha tree plots in each of these landscape units at the Caparú Biological Station, SW Colombia, and measured edaphic, topographic and light variables. At large spatial scales, terra firme forests exhibited higher levels of species diversity and phylodiversity than flooded forests. These two types of forests showed conspicuous differences in species and phylogenetic composition, suggesting that environmental sorting due to flood is important, and can go beyond the species level. At a local level, landscape units showed floristic divergence, driven both by geographical distance and by edaphic specialization. In terms of phylogenetic structure, Igapó forests showed phylogenetic clustering, whereas Hilly and Terrace forests showed phylogenetic evenness. Within plots, however, local communities did not show any particular trend. Overall, our findings suggest that flooded forests, characterized by stressful environments, impose limits to species occurrence, whereas terra firme forests, more environmentally heterogeneous, are likely to provide a wider range of ecological conditions and therefore to bear higher diversity. Thus, Amazonia should be considered as a mosaic of landscape units, where the strength of habitat association depends upon their environmental properties. PMID:23028844

A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea

PubMed Central

2011-01-01

Background Cetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters. Results We combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses. Conclusions The parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our study fell outside crown Mysticeti and crown Odontoceti, suggesting that these two clades radiated in the late Oligocene or later, contra some recent molecular clock studies. Our trees also imply that many character states shared by river dolphins evolved in their oceanic ancestors, contradicting the hypothesis that these characters are convergent adaptations to fluvial habitats. PMID:21518443

A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea.

PubMed

Geisler, Jonathan H; McGowen, Michael R; Yang, Guang; Gatesy, John

2011-04-25

Cetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters. We combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses. The parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our study fell outside crown Mysticeti and crown Odontoceti, suggesting that these two clades radiated in the late Oligocene or later, contra some recent molecular clock studies. Our trees also imply that many character states shared by river dolphins evolved in their oceanic ancestors, contradicting the hypothesis that these characters are convergent adaptations to fluvial habitats.

Phylogenetic analysis and protein structure modelling identifies distinct Ca(2+)/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species.

PubMed

Pittman, Jon K; Hirschi, Kendal D

2016-12-01

The Ca(2+)/Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K(+)-dependent and K(+)-indendent Na(+)/Ca(2+) exchangers (NCKX and NCX) are important CaCA members. Recently it was proposed that all rice and Arabidopsis CaCA proteins should be classified as NCX proteins. Here we performed phylogenetic analysis of CaCA genes and protein structure homology modelling to further characterise members of this transporter superfamily. Phylogenetic analysis of rice and Arabidopsis CaCAs in comparison with selected CaCA members from non-plant species demonstrated that these genes form clearly distinct families, with the H(+)/Cation exchanger (CAX) and cation/Ca(2+) exchanger (CCX) families dominant in higher plants but the NCKX and NCX families absent. NCX-related Mg(2+)/H(+) exchanger (MHX) and CAX-related Na(+)/Ca(2+) exchanger-like (NCL) proteins are instead present. Analysis of genomes of ten closely-related rice species and four Arabidopsis-related species found that CaCA gene family structures are highly conserved within related plants, apart from minor variation. Protein structures were modelled for OsCAX1a and OsMHX1. Despite exhibiting broad structural conservation, there are clear structural differences observed between the different CaCA types. Members of the CaCA superfamily form clearly distinct families with different phylogenetic, structural and functional characteristics, and therefore should not be simply classified as NCX proteins, which should remain as a separate gene family.

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes

PubMed Central

Gallus, Susanne; Janke, Axel

2017-01-01

Abstract Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. PMID:28985298

Analysis of elastically tailored viscoelastic damping member

NASA Technical Reports Server (NTRS)

Chen, G.-S.; Dolgin, B. P.

1990-01-01

For more than two decades, viscoelastic materials have been commonly used as a passive damping source in a variety of structures because of their high material loss factors. In most of the applications, viscoelastic materials are used either in series with or parallel to the structural load path. The latter is also known as the constrained-layer damping treatment. The advantage of the constrained-layer damping treatment is that it can be incorporated without loss in structural integrity, namely, stiffness and strength. However, the disadvantages are that: (1) it is not the most effective use of the viscoelastic material when compared with the series-type application, and (2) weight penalty from the stiff constraining layer requirement can be excessive. To overcome the disadvantages of the constrained-layer damping treatment, a new approach for using viscoelastic material in axial-type structural components, e.g., truss members, was studied in this investigation.

Lineage diversification and morphological evolution in a large-scale continental radiation: The neotropical ovenbirds and woodcreepers (Aves: Furnariidae)

USGS Publications Warehouse

Derryberry, Elizabeth P.; Claramunt, Santiago; Derryberry, Graham; Chesser, R. Terry; Cracraft, Joel; Aleixo, Alexandre; Pérez-Emán, Jorge; Remsen, J.V.; Brumfield, Robb T.

2011-01-01

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents.

The origin and evolution of tRNA inferred from phylogenetic analysis of structure.

PubMed

Sun, Feng-Jie; Caetano-Anollés, Gustavo

2008-01-01

The evolutionary history of the two structural and functional domains of tRNA is controversial but harbors the secrets of early translation and the genetic code. To explore the origin and evolution of tRNA, we reconstructed phylogenetic trees directly from molecular structure. Forty-two structural characters describing the geometry of 571 tRNAs and three statistical parameters describing thermodynamic and mechanical features of molecules quantitatively were used to derive phylogenetic trees of molecules and molecular substructures. Trees of molecules failed to group tRNA according to amino acid specificity and did not reveal the tripartite nature of life, probably due to loss of phylogenetic signal or because tRNA diversification predated organismal diversification. Trees of substructures derived from both structural and statistical characters support the origin of tRNA in the acceptor arm and the hypothesis that the top half domain composed of acceptor and pseudouridine (TPsiC) arms is more ancient than the bottom half domain composed of dihydrouridine (DHU) and anticodon arms. This constitutes the cornerstone of the genomic tag hypothesis that postulates tRNAs were ancient telomeres in the RNA world. The trees of substructures suggest a model for the evolution of the major functional and structural components of tRNA. In this model, short RNA hairpins with stems homologous to the acceptor arm of present day tRNAs were extended with regions homologous to TPsiC and anticodon arms. The DHU arm was then incorporated into the resulting three-stemmed structure to form a proto-cloverleaf structure. The variable region was the last structural addition to the molecular repertoire of evolving tRNA substructures.

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny

PubMed Central

Jones, Aaron A.; Bennett, Philip C.

2017-01-01

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities. PMID:28400754

Community phylogenetics at the biogeographical scale: cold tolerance, niche conservatism and the structure of North American forests.

PubMed

Hawkins, Bradford A; Rueda, Marta; Rangel, Thiago F; Field, Richard; Diniz-Filho, José Alexandre F; Linder, Peter

2014-01-01

Aim The fossil record has led to a historical explanation for forest diversity gradients within the cool parts of the Northern Hemisphere, founded on a limited ability of woody angiosperm clades to adapt to mid-Tertiary cooling. We tested four predictions of how this should be manifested in the phylogenetic structure of 91,340 communities: (1) forests to the north should comprise species from younger clades (families) than forests to the south; (2) average cold tolerance at a local site should be associated with the mean family age (MFA) of species; (3) minimum temperature should account for MFA better than alternative environmental variables; and (4) traits associated with survival in cold climates should evolve under a niche conservatism constraint. Location The contiguous United States. Methods We extracted angiosperms from the US Forest Service's Forest Inventory and Analysis database. MFA was calculated by assigning age of the family to which each species belongs and averaging across the species in each community. We developed a phylogeny to identify phylogenetic signal in five traits: realized cold tolerance, seed size, seed dispersal mode, leaf phenology and height. Phylogenetic signal representation curves and phylogenetic generalized least squares were used to compare patterns of trait evolution against Brownian motion. Eleven predictors structured at broad or local scales were generated to explore relationships between environment and MFA using random forest and general linear models. Results Consistent with predictions, (1) southern communities comprise angiosperm species from older families than northern communities, (2) cold tolerance is the trait most strongly associated with local MFA, (3) minimum temperature in the coldest month is the environmental variable that best describes MFA, broad-scale variables being much stronger correlates than local-scale variables, and (4) the phylogenetic structures of cold tolerance and at least one other trait associated with survivorship in cold climates indicate niche conservatism. Main conclusions Tropical niche conservatism in the face of long-term climate change, probably initiated in the Late Cretaceous associated with the rise of the Rocky Mountains, is a strong driver of the phylogenetic structure of the angiosperm component of forest communities across the USA. However, local deterministic and/or stochastic processes account for perhaps a quarter of the variation in the MFA of local communities.

Picante: R tools for integrating phylogenies and ecology.

PubMed

Kembel, Steven W; Cowan, Peter D; Helmus, Matthew R; Cornwell, William K; Morlon, Helene; Ackerly, David D; Blomberg, Simon P; Webb, Campbell O

2010-06-01

Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).

Estimating the Effects of Damping Treatments on the Vibration of Complex Structures

DTIC Science & Technology

2012-09-26

26 4.3 Literature review 26 4.3.1 CLD Theory 26 4.3.2 Temperature Profiling 28 4.4 Constrained Layer Damping Analysis 29 4.5 Results 35...Coordinate systems and length scales are noted. Constraining layer, viscoelastic layer and base layer pertain to the nomenclature used through CLD ...for vibrational damping 4.1 Introduction Constrained layer damping ( CLD ) treatment systems are widely used in complex structures to dissipate

The affinities of Homo floresiensis based on phylogenetic analyses of cranial, dental, and postcranial characters.

PubMed

Argue, Debbie; Groves, Colin P; Lee, Michael S Y; Jungers, William L

2017-06-01

Although the diminutive Homo floresiensis has been known for a decade, its phylogenetic status remains highly contentious. A broad range of potential explanations for the evolution of this species has been explored. One view is that H. floresiensis is derived from Asian Homo erectus that arrived on Flores and subsequently evolved a smaller body size, perhaps to survive the constrained resources they faced in a new island environment. Fossil remains of H. erectus, well known from Java, have not yet been discovered on Flores. The second hypothesis is that H. floresiensis is directly descended from an early Homo lineage with roots in Africa, such as Homo habilis; the third is that it is Homo sapiens with pathology. We use parsimony and Bayesian phylogenetic methods to test these hypotheses. Our phylogenetic data build upon those characters previously presented in support of these hypotheses by broadening the range of traits to include the crania, mandibles, dentition, and postcrania of Homo and Australopithecus. The new data and analyses support the hypothesis that H. floresiensis is an early Homo lineage: H. floresiensis is sister either to H. habilis alone or to a clade consisting of at least H. habilis, H. erectus, Homo ergaster, and H. sapiens. A close phylogenetic relationship between H. floresiensis and H. erectus or H. sapiens can be rejected; furthermore, most of the traits separating H. floresiensis from H. sapiens are not readily attributable to pathology (e.g., Down syndrome). The results suggest H. floresiensis is a long-surviving relict of an early (>1.75 Ma) hominin lineage and a hitherto unknown migration out of Africa, and not a recent derivative of either H. erectus or H. sapiens. Copyright © 2017 Elsevier Ltd. All rights reserved.

Patterns of species diversity and phylogenetic structure of vascular plants on the Qinghai-Tibetan Plateau.

PubMed

Yan, Yujing; Yang, Xian; Tang, Zhiyao

2013-11-01

Large-scale patterns of species richness and the underlying mechanisms regulating these patterns have long been the central issues in biogeography and macroecology. Phylogenetic community structure is a result of combined effects of contemporary ecological interactions, environmental filtering, and evolutionary history, and it links community ecology with biogeography and trait evolution. The Qinghai-Tibetan Plateau provides a good opportunity to test the influence of contemporary climate on shaping species richness because of its unique geological history, cold climate, and high biodiversity. In this study, based on high-resolution distributions of ˜9000 vascular plant species, we explored how species richness and phylogenetic structure of vascular plants correlate with climates on the highest (and species rich) plateau on the Earth. The results showed that most of the vascular plants were distributed on the eastern part of the plateau; there was a strong association between species richness and climate, even after the effects of habitat heterogeneity were controlled. However, the responses of richness to climate remarkably depended on life-forms. Richness of woody plants showed stronger climatic associations than that of herbaceous plants; energy and water availability together regulated richness pattern of woody plants; whereas water availability predominantly regulated richness pattern of herbaceous plants. The phylogenetic structure of vascular species clustered in most areas of the plateau, suggesting that rapid speciation and environment filtering dominated the assembly of communities on the plateau. We further propose that biodiversity conservation in this area should better take into account ecological features for different life-forms and phylogenetic lineages.

Patterns of species diversity and phylogenetic structure of vascular plants on the Qinghai-Tibetan Plateau

PubMed Central

Yan, Yujing; Yang, Xian; Tang, Zhiyao

2013-01-01

Large-scale patterns of species richness and the underlying mechanisms regulating these patterns have long been the central issues in biogeography and macroecology. Phylogenetic community structure is a result of combined effects of contemporary ecological interactions, environmental filtering, and evolutionary history, and it links community ecology with biogeography and trait evolution. The Qinghai-Tibetan Plateau provides a good opportunity to test the influence of contemporary climate on shaping species richness because of its unique geological history, cold climate, and high biodiversity. In this study, based on high-resolution distributions of ˜9000 vascular plant species, we explored how species richness and phylogenetic structure of vascular plants correlate with climates on the highest (and species rich) plateau on the Earth. The results showed that most of the vascular plants were distributed on the eastern part of the plateau; there was a strong association between species richness and climate, even after the effects of habitat heterogeneity were controlled. However, the responses of richness to climate remarkably depended on life-forms. Richness of woody plants showed stronger climatic associations than that of herbaceous plants; energy and water availability together regulated richness pattern of woody plants; whereas water availability predominantly regulated richness pattern of herbaceous plants. The phylogenetic structure of vascular species clustered in most areas of the plateau, suggesting that rapid speciation and environment filtering dominated the assembly of communities on the plateau. We further propose that biodiversity conservation in this area should better take into account ecological features for different life-forms and phylogenetic lineages. PMID:24340197

Macroevolution of plant defenses against herbivores in the evening primroses.

PubMed

Johnson, Marc T J; Ives, Anthony R; Ahern, Jeffrey; Salminen, Juha-Pekka

2014-07-01

Plant species vary greatly in defenses against herbivores, but existing theory has struggled to explain this variation. Here, we test how phylogenetic relatedness, tradeoffs, trait syndromes, and sexual reproduction affect the macroevolution of defense. To examine the macroevolution of defenses, we studied 26 Oenothera (Onagraceae) species, combining chemistry, comparative phylogenetics and experimental assays of resistance against generalist and specialist herbivores. We detected dozens of phenolic metabolites within leaves, including ellagitannins (ETs), flavonoids, and caffeic acid derivatives (CAs). The concentration and composition of phenolics exhibited low to moderate phylogenetic signal. There were clear negative correlations between multiple traits, supporting the prediction of allocation tradeoffs. There were also positively covarying suites of traits, but these suites did not strongly predict resistance to herbivores and thus did not act as defensive syndromes. By contrast, specific metabolites did correlate with the performance of generalist and specialist herbivores. Finally, that repeated losses of sex in Oenothera was associated with the evolution of increased flavonoid diversity and altered phenolic composition. These results show that secondary chemistry has evolved rapidly during the diversification of Oenothera. This evolution has been marked by allocation tradeoffs between traits, some of which are related to herbivore performance. The repeated loss of sex appears also to have constrained the evolution of plant secondary chemistry, which may help to explain variation in defense among plants. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

The confounding effects of hybridization on phylogenetic estimation in the New Zealand cicada genus Kikihia.

PubMed

Banker, Sarah E; Wade, Elizabeth J; Simon, Chris

2017-11-01

Phylogenetic studies of multiple independently inherited nuclear genes considered in combination with patterns of inheritance of organelle DNA have provided considerable insight into the history of species evolution. In particular, investigations of cicadas in the New Zealand genus Kikihia have identified interesting cases where mitochondrial DNA (mtDNA) crosses species boundaries in some species pairs but not others. Previous phylogenetic studies focusing on mtDNA largely corroborated Kikihia species groups identified by song, morphology and ecology with the exception of a unique South Island mitochondrial haplotype clade-the Westlandica group. This newly identified group consists of diverse taxa previously classified as belonging to three different sub-generic clades. We sequenced five nuclear loci from multiple individuals from every species of Kikihia to assess the nuclear gene concordance for this newly-identified mtDNA lineage. Bayes Factor analysis of the constrained phylogeny suggests some support for the mtDNA-based hypotheses, despite the fact that neither concatenation nor multiple species tree methods resolve the Westlandica group as monophyletic. The nuclear analyses suggest a geographic distinction between clearly defined monophyletic North Island clades and unresolved South Island clades. We suggest that more extreme habitat modification on South Island during the Pliocene and Pleistocene resulted in secondary contact and hybridization between species pairs and a series of mitochondrial capture events followed by subsequent lineage evolution. Copyright © 2017 Elsevier Inc. All rights reserved.

‘ Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family

DOE PAGES

Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina; ...

2016-12-21

Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. Here, we describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader doesmore » not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160 ± 3 μmol L -1 d -1. The DCM degrader attained 5.25 × 10 7 ± 1.0 × 10 7 cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4 ± 0.8 μm long and 0.4 ± 0.1 μm wide. Furthermore, based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, ‘Candidatus Dichloromethanomonas elyunquensis’.« less

‘ Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina

Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. Here, we describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader doesmore » not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160 ± 3 μmol L -1 d -1. The DCM degrader attained 5.25 × 10 7 ± 1.0 × 10 7 cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4 ± 0.8 μm long and 0.4 ± 0.1 μm wide. Furthermore, based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, ‘Candidatus Dichloromethanomonas elyunquensis’.« less

Body Size Diversity and Frequency Distributions of Neotropical Cichlid Fishes (Cichliformes: Cichlidae: Cichlinae)

PubMed Central

Steele, Sarah E.; López-Fernández, Hernán

2014-01-01

Body size is an important correlate of life history, ecology and distribution of species. Despite this, very little is known about body size evolution in fishes, particularly freshwater fishes of the Neotropics where species and body size diversity are relatively high. Phylogenetic history and body size data were used to explore body size frequency distributions in Neotropical cichlids, a broadly distributed and ecologically diverse group of fishes that is highly representative of body size diversity in Neotropical freshwater fishes. We test for divergence, phylogenetic autocorrelation and among-clade partitioning of body size space. Neotropical cichlids show low phylogenetic autocorrelation and divergence within and among taxonomic levels. Three distinct regions of body size space were identified from body size frequency distributions at various taxonomic levels corresponding to subclades of the most diverse tribe, Geophagini. These regions suggest that lineages may be evolving towards particular size optima that may be tied to specific ecological roles. The diversification of Geophagini appears to constrain the evolution of body size among other Neotropical cichlid lineages; non-Geophagini clades show lower species-richness in body size regions shared with Geophagini. Neotropical cichlid genera show less divergence and extreme body size than expected within and among tribes. Body size divergence among species may instead be present or linked to ecology at the community assembly scale. PMID:25180970

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes.

PubMed

Lammers, Fritjof; Gallus, Susanne; Janke, Axel; Nilsson, Maria A

2017-10-01

Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama

PubMed Central

Matterson, Kenan O.; Freeman, Christopher J.; Archer, Stephanie K.; Thacker, Robert W.

2015-01-01

Recent studies have renewed interest in sponge ecology by emphasizing the functional importance of sponges in a broad array of ecosystem services. Many critically important habitats occupied by sponges face chronic stressors that might lead to alterations in their diversity, relatedness, and functional attributes. We addressed whether proximity to human activity might be a significant factor in structuring sponge community composition, as well as potential functional roles, by monitoring sponge diversity and abundance at two structurally similar sites that vary in distance to areas of high coastal development in Bocas Del Toro, Panama. We surveyed sponge communities at each site using belt transects and differences between two sites were compared using the following variables: (1) sponge species richness, Shannon diversity, and inverse Simpson’s diversity; (2) phylogenetic diversity; (3) taxonomic and phylogenetic beta diversity; (4) trait diversity and dissimilarity; and (5) phylogenetic and trait patterns in community structure. We observed significantly higher sponge diversity at Punta Caracol, the site most distant from human development (∼5 km). Although phylogenetic diversity was lower at Saigon Bay, the site adjacent to a large village including many houses, businesses, and an airport, the sites did not exhibit significantly different patterns of phylogenetic relatedness in species composition. However, each site had a distinct taxonomic and phylogenetic composition (beta diversity). In addition, the sponge community at Saigon included a higher relative abundance of sponges with high microbial abundance and high chlorophyll a concentration, whereas the community at Punta Caracol had a more even distribution of these traits, yielding a significant difference in functional trait diversity between sites. These results suggest that lower diversity and potentially altered community function might be associated with proximity to human populations. This study highlights the importance of evaluating functional traits and phylogenetic diversity in addition to common diversity metrics when assessing potential environmental impacts on benthic communities. PMID:26587347

Bioinformatics analysis of the predicted polyprenol reductase genes in higher plants

NASA Astrophysics Data System (ADS)

Basyuni, M.; Wati, R.

2018-03-01

The present study evaluates the bioinformatics methods to analyze twenty-four predicted polyprenol reductase genes from higher plants on GenBank as well as predicted the structure, composition, similarity, subcellular localization, and phylogenetic. The physicochemical properties of plant polyprenol showed diversity among the observed genes. The percentage of the secondary structure of plant polyprenol genes followed the ratio order of α helix > random coil > extended chain structure. The values of chloroplast but not signal peptide were too low, indicated that few chloroplast transit peptide in plant polyprenol reductase genes. The possibility of the potential transit peptide showed variation among the plant polyprenol reductase, suggested the importance of understanding the variety of peptide components of plant polyprenol genes. To clarify this finding, a phylogenetic tree was drawn. The phylogenetic tree shows several branches in the tree, suggested that plant polyprenol reductase genes grouped into divergent clusters in the tree.

Small steps or giant leaps for male-killers? Phylogenetic constraints to male-killer host shifts

PubMed Central

Tinsley, Matthew C; Majerus, Michael EN

2007-01-01

Background Arthropods are infected by a wide diversity of maternally transmitted microbes. Some of these manipulate host reproduction to facilitate population invasion and persistence. Such parasites transmit vertically on an ecological timescale, but rare horizontal transmission events have permitted colonisation of new species. Here we report the first systematic investigation into the influence of the phylogenetic distance between arthropod species on the potential for reproductive parasite interspecific transfer. Results We employed a well characterised reproductive parasite, a coccinellid beetle male-killer, and artificially injected the bacterium into a series of novel species. Genetic distances between native and novel hosts were ascertained by sequencing sections of the 16S and 12S mitochondrial rDNA genes. The bacterium colonised host tissues and transmitted vertically in all cases tested. However, whilst transmission efficiency was perfect within the native genus, this was reduced following some transfers of greater phylogenetic distance. The bacterium's ability to distort offspring sex ratios in novel hosts was negatively correlated with the genetic distance of transfers. Male-killing occurred with full penetrance following within-genus transfers; but whilst sex ratio distortion generally occurred, it was incomplete in more distantly related species. Conclusion This study indicates that the natural interspecific transmission of reproductive parasites might be constrained by their ability to tolerate the physiology or genetics of novel hosts. Our data suggest that horizontal transfers are more likely between closely related species. Successful bacterial transfer across large phylogenetic distances may require rapid adaptive evolution in the new species. This finding has applied relevance regarding selection of suitable bacteria to manipulate insect pest and vector populations by symbiont gene-drive systems. PMID:18047670

False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing.

PubMed

Xiao, Jian; Cao, Hongyuan; Chen, Jun

2017-09-15

Next generation sequencing technologies have enabled the study of the human microbiome through direct sequencing of microbial DNA, resulting in an enormous amount of microbiome sequencing data. One unique characteristic of microbiome data is the phylogenetic tree that relates all the bacterial species. Closely related bacterial species have a tendency to exhibit a similar relationship with the environment or disease. Thus, incorporating the phylogenetic tree information can potentially improve the detection power for microbiome-wide association studies, where hundreds or thousands of tests are conducted simultaneously to identify bacterial species associated with a phenotype of interest. Despite much progress in multiple testing procedures such as false discovery rate (FDR) control, methods that take into account the phylogenetic tree are largely limited. We propose a new FDR control procedure that incorporates the prior structure information and apply it to microbiome data. The proposed procedure is based on a hierarchical model, where a structure-based prior distribution is designed to utilize the phylogenetic tree. By borrowing information from neighboring bacterial species, we are able to improve the statistical power of detecting associated bacterial species while controlling the FDR at desired levels. When the phylogenetic tree is mis-specified or non-informative, our procedure achieves a similar power as traditional procedures that do not take into account the tree structure. We demonstrate the performance of our method through extensive simulations and real microbiome datasets. We identified far more alcohol-drinking associated bacterial species than traditional methods. R package StructFDR is available from CRAN. chen.jun2@mayo.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Does skull morphology constrain bone ornamentation? A morphometric analysis in the Crocodylia.

PubMed

Clarac, F; Souter, T; Cubo, J; de Buffrénil, V; Brochu, C; Cornette, R

2016-08-01

Previous quantitative assessments of the crocodylians' dermal bone ornamentation (this ornamentation consists of pits and ridges) has shown that bone sculpture results in a gain in area that differs between anatomical regions: it tends to be higher on the skull table than on the snout. Therefore, a comparative phylogenetic analysis within 17 adult crocodylian specimens representative of the morphological diversity of the 24 extant species has been performed, in order to test if the gain in area due to ornamentation depends on the skull morphology, i.e. shape and size. Quantitative assessment of skull size and shape through geometric morphometrics, and of skull ornamentation through surface analyses, produced a dataset that was analyzed using phylogenetic least-squares regression. The analyses reveal that none of the variables that quantify ornamentation, be they on the snout or the skull table, is correlated with the size of the specimens. Conversely, there is more disparity in the relationships between skull conformations (longirostrine vs. brevirostrine) and ornamentation. Indeed, both parameters GApit (i.e. pit depth and shape) and OArelat (i.e. relative area of the pit set) are negatively correlated with snout elongation, whereas none of the values quantifying ornamentation on the skull table is correlated with skull conformation. It can be concluded that bone sculpture on the snout is influenced by different developmental constrains than on the skull table and is sensible to differences in the local growth 'context' (allometric processes) prevailing in distinct skull parts. Whatever the functional role of bone ornamentation on the skull, if any, it seems to be restricted to some anatomical regions at least for the longirostrine forms that tend to lose ornamentation on the snout. © 2016 Anatomical Society.

Virasoro symmetry of the constrained multicomponent Kadomtsev-Petviashvili hierarchy and its integrable discretization

NASA Astrophysics Data System (ADS)

Li, Chuanzhong; He, Jingsong

2016-06-01

We construct Virasoro-type additional symmetries of a kind of constrained multicomponent Kadomtsev-Petviashvili (KP) hierarchy and obtain the Virasoro flow equation for the eigenfunctions and adjoint eigenfunctions. We show that the algebraic structure of the Virasoro symmetry is retained under discretization from the constrained multicomponent KP hierarchy to the discrete constrained multicomponent KP hierarchy.

A worldview of root traits: the influence of ancestry, growth form, climate and mycorrhizal association on the functional trait variation of fine-root tissues in seed plants.

PubMed

Valverde-Barrantes, Oscar J; Freschet, Grégoire T; Roumet, Catherine; Blackwood, Christopher B

2017-09-01

Fine-root traits play key roles in ecosystem processes, but the drivers of fine-root trait diversity remain poorly understood. The plant economic spectrum (PES) hypothesis predicts that leaf and root traits evolved in coordination. Mycorrhizal association type, plant growth form and climate may also affect root traits. However, the extent to which these controls are confounded with phylogenetic structuring remains unclear. Here we compiled information about root and leaf traits for > 600 species. Using phylogenetic relatedness, climatic ranges, growth form and mycorrhizal associations, we quantified the importance of these factors in the global distribution of fine-root traits. Phylogenetic structuring accounts for most of the variation for all traits excepting root tissue density, with root diameter and nitrogen concentration showing the strongest phylogenetic signal and specific root length showing intermediate values. Climate was the second most important factor, whereas mycorrhizal type had little effect. Substantial trait coordination occurred between leaves and roots, but the strength varied between growth forms and clades. Our analyses provide evidence that the integration of roots and leaves in the PES requires better accounting of the variation in traits across phylogenetic clades. Inclusion of phylogenetic information provides a powerful framework for predictions of belowground functional traits at global scales. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Phylogenetic analysis of several Thermus strains from Rehai of Tengchong, Yunnan, China.

PubMed

Lin, Lianbing; Zhang, Jie; Wei, Yunlin; Chen, Chaoyin; Peng, Qian

2005-10-01

Several Thermus strains were isolated from 10 hot springs of the Rehai geothermal area in Tengchong, Yunnan province. The diversity of Thermus strains was examined by sequencing the 16S rRNA genes and comparing their sequences. Phylogenetic analysis showed that the 16S rDNA sequences from the Rehai geothermal isolates form four branches in the phylogenetic tree and had greater than 95.9% similarity in the phylogroup. Secondary structure comparison also indicated that the 16S rRNA from the Rehai geothermal isolates have unique secondary structure characteristics in helix 6, helix 9, and helix 10 (reference to Escherichia coli). This research is the first attempt to reveal the diversity of Thermus strains that are distributed in the Rehai geothermal area.

A critical survey of vestigial structures in the postcranial skeletons of extant mammals

PubMed Central

Moch, John G.

2015-01-01

In the Mammalia, vestigial skeletal structures abound but have not previously been the focus of study, with a few exceptions (e.g., whale pelves). Here we use a phylogenetic bracketing approach to identify vestigial structures in mammalian postcranial skeletons and present a descriptive survey of such structures in the Mammalia. We also correct previous misidentifications, including the previous misidentification of vestigial caviid metatarsals as sesamoids. We also examine the phylogenetic distribution of vestigiality and loss. This distribution indicates multiple vestigialization and loss events in mammalian skeletal structures, especially in the hand and foot, and reveals no correlation in such events between mammalian fore and hind limbs. PMID:26623192

Comparison of natural and nonnative two-species communities of Anolis lizards.

PubMed

Poe, Steven

2014-07-01

Human-mediated colonizations present an informative model system for understanding assembly of organismal communities. However, it is unclear whether communities including naturalized species are accurate analogs of natural communities or unique combinations not present in nature. I compared morphology and phylogenetic structure of natural and naturalized two-species communities of Anolis lizards. Natural communities are phylogenetically clustered, whereas naturalized communities show no significant phylogenetic structure. This result likely reflects differences in colonization pools for these communities-that is, invasion from anywhere for naturalized communities but from proximal and thus phylogenetically close lineages in natural communities. Both natural and naturalized communities each include pairs of species that are significantly similar to each other in morphology, and both sets of communities are composed of species that possess traits of good colonizers. These similarities suggest that the formation of natural and naturalized communities may be at least partially governed by similar processes. Human-mediated invasions may be credibly viewed as modern incarnations of natural colonizations in this case.

Strong influence of regional species pools on continent-wide structuring of local communities.

PubMed

Lessard, Jean-Philippe; Borregaard, Michael K; Fordyce, James A; Rahbek, Carsten; Weiser, Michael D; Dunn, Robert R; Sanders, Nathan J

2012-01-22

There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use a continent-wide dataset of local ant communities and implement ecologically explicit source pool definitions to examine the relative importance of regional species pools and local interactions for shaping community structure. Then we assess which factors underlie systematic variation in the structure of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong.

Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest.

PubMed

Xu, Wumei; Ci, Xiuqin; Song, Caiyun; He, Tianhua; Zhang, Wenfu; Li, Qiaoming; Li, Jie

2016-12-01

The niche theory predicts that environmental heterogeneity and species diversity are positively correlated in tropical forests, whereas the neutral theory suggests that stochastic processes are more important in determining species diversity. This study sought to investigate the effects of soil nutrient (nitrogen and phosphorus) heterogeneity on tree species diversity in the Xishuangbanna tropical seasonal rainforest in southwestern China. Thirty-nine plots of 400 m 2 (20 × 20 m) were randomly located in the Xishuangbanna tropical seasonal rainforest. Within each plot, soil nutrient (nitrogen and phosphorus) availability and heterogeneity, tree species diversity, and community phylogenetic structure were measured. Soil phosphorus heterogeneity and tree species diversity in each plot were positively correlated, while phosphorus availability and tree species diversity were not. The trees in plots with low soil phosphorus heterogeneity were phylogenetically overdispersed, while the phylogenetic structure of trees within the plots became clustered as heterogeneity increased. Neither nitrogen availability nor its heterogeneity was correlated to tree species diversity or the phylogenetic structure of trees within the plots. The interspecific competition in the forest plots with low soil phosphorus heterogeneity could lead to an overdispersed community. However, as heterogeneity increase, more closely related species may be able to coexist together and lead to a clustered community. Our results indicate that soil phosphorus heterogeneity significantly affects tree diversity in the Xishuangbanna tropical seasonal rainforest, suggesting that deterministic processes are dominant in this tropical forest assembly.

Resource predictability and specialization in avian malaria parasites.

PubMed

Svensson-Coelho, Maria; Loiselle, Bette A; Blake, John G; Ricklefs, Robert E

2016-09-01

We tested the hypothesis that avian haemosporidian (malaria) parasites specialize on hosts that can be characterized as predictable resources at a site in Amazonian Ecuador. We incorporated host phylogenetic relationship and relative abundance in assessing parasite specialization, and we examined associations between parasite specialization and three host characteristics - abundance, mass and longevity - using quantile regression, phylogenetic logistic regression and t-tests. Hosts of specialist malaria parasite lineages were on average more abundant than hosts of generalist parasite lineages, but the relationship between host abundance and parasite specialization was not consistent across analyses. We also found support for a positive association between parasite specialization and host longevity, but this also was not consistent across analyses. Nonetheless, our findings suggest that the predictability of a host resource may play a role in the evolution of specialization. However, we also discuss two alternative explanations to the resource predictability hypothesis for specialization: (i) that interspecific interactions among the parasites themselves might constrain some parasites to a specialist strategy, and (ii) that frequent encounters with multiple host species, mediated by blood-sucking insects, might promote generalization within this system. © 2016 John Wiley & Sons Ltd.

A palaeoequatorial ornithischian and new constraints on early dinosaur diversification.

PubMed

Barrett, Paul M; Butler, Richard J; Mundil, Roland; Scheyer, Torsten M; Irmis, Randall B; Sánchez-Villagra, Marcelo R

2014-09-22

Current characterizations of early dinosaur evolution are incomplete: existing palaeobiological and phylogenetic scenarios are based on a fossil record dominated by saurischians and the implications of the early ornithischian record are often overlooked. Moreover, the timings of deep phylogenetic divergences within Dinosauria are poorly constrained owing to the absence of a rigorous chronostratigraphical framework for key Late Triassic-Early Jurassic localities. A new dinosaur from the earliest Jurassic of the Venezuelan Andes is the first basal ornithischian recovered from terrestrial deposits directly associated with a precise radioisotopic date and the first-named dinosaur from northern South America. It expands the early palaeogeographical range of Ornithischia to palaeoequatorial regions, an area sometimes thought to be devoid of early dinosaur taxa, and offers insights into early dinosaur growth rates, the evolution of sociality and the rapid tempo of the global dinosaur radiation following the end-Triassic mass extinction, helping to underscore the importance of the ornithischian record in broad-scale discussions of early dinosaur history. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Soil bacterial communities are shaped by temporal and environmental filtering: evidence from a long-term chronosequence.

PubMed

Freedman, Zachary; Zak, Donald R

2015-09-01

Soil microbial communities are abundant, hyper-diverse and mediate global biogeochemical cycles, but we do not yet understand the processes mediating their assembly. Current hypothetical frameworks suggest temporal (e.g. dispersal limitation) and environmental (e.g. soil pH) filters shape microbial community composition; however, there is limited empirical evidence supporting this framework in the hyper-diverse soil environment, particularly at large spatial (i.e. regional to continental) and temporal (i.e. 100 to 1000 years) scales. Here, we present evidence from a long-term chronosequence (4000 years) that temporal and environmental filters do indeed shape soil bacterial community composition. Furthermore, nearly 20 years of environmental monitoring allowed us to control for potentially confounding environmental variation. Soil bacterial communities were phylogenetically distinct across the chronosequence. We determined that temporal and environmental factors accounted for significant portions of bacterial phylogenetic structure using distance-based linear models. Environmental factors together accounted for the majority of phylogenetic structure, namely, soil temperature (19%), pH (17%) and litter carbon:nitrogen (C:N; 17%). However, of all individual factors, time since deglaciation accounted for the greatest proportion of bacterial phylogenetic structure (20%). Taken together, our results provide empirical evidence that temporal and environmental filters act together to structure soil bacterial communities across large spatial and long-term temporal scales. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparing Ontogenetic and Phylogenetic Stages of Human Development

ERIC Educational Resources Information Center

Clarken, Rodney H.

2005-01-01

This paper will present evidence to support ontogenetic and phylogenetic parallels and draw from these comparisons to further illuminate our understanding of micro and macro human development. Individual and collective stages of physical, psychological and spiritual development will be compared and their homologous structures examined.…

Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods

PubMed Central

2013-01-01

Background Birnaviruses form a distinct family of double-stranded RNA viruses infecting animals as different as vertebrates, mollusks, insects and rotifers. With such a wide host range, they constitute a good model for studying the adaptation to the host. Additionally, several lines of evidence link birnaviruses to positive strand RNA viruses and suggest that phylogenetic analyses may provide clues about transition. Results We characterized the genome of a birnavirus from the rotifer Branchionus plicalitis. We used X-ray structures of RNA-dependent RNA polymerases and capsid proteins to obtain multiple structure alignments that allowed us to obtain reliable multiple sequence alignments and we employed “advanced” phylogenetic methods to study the evolutionary relationships between some positive strand and double-stranded RNA viruses. We showed that the rotifer birnavirus genome exhibited an organization remarkably similar to other birnaviruses. As this host was phylogenetically very distant from the other known species targeted by birnaviruses, we revisited the evolutionary pathways within the Birnaviridae family using phylogenetic reconstruction methods. We also applied a number of phylogenetic approaches based on structurally conserved domains/regions of the capsid and RNA-dependent RNA polymerase proteins to study the evolutionary relationships between birnaviruses, other double-stranded RNA viruses and positive strand RNA viruses. Conclusions We show that there is a good correlation between the phylogeny of the birnaviruses and that of their hosts at the phylum level using the RNA-dependent RNA polymerase (genomic segment B) on the one hand and a concatenation of the capsid protein, protease and ribonucleoprotein (genomic segment A) on the other hand. This correlation tends to vanish within phyla. The use of advanced phylogenetic methods and robust structure-based multiple sequence alignments allowed us to obtain a more accurate picture (in terms of probability of the tree topologies) of the evolutionary affinities between double-stranded RNA and positive strand RNA viruses. In particular, we were able to show that there exists a good statistical support for the claims that dsRNA viruses are not monophyletic and that viruses with permuted RdRps belong to a common evolution lineage as previously proposed by other groups. We also propose a tree topology with a good statistical support describing the evolutionary relationships between the Picornaviridae, Caliciviridae, Flaviviridae families and a group including the Alphatetraviridae, Nodaviridae, Permutotretraviridae, Birnaviridae, and Cystoviridae families. PMID:23865988

Towards an eco-phylogenetic framework for infectious disease ecology.

PubMed

Fountain-Jones, Nicholas M; Pearse, William D; Escobar, Luis E; Alba-Casals, Ana; Carver, Scott; Davies, T Jonathan; Kraberger, Simona; Papeş, Monica; Vandegrift, Kurt; Worsley-Tonks, Katherine; Craft, Meggan E

2018-05-01

Identifying patterns and drivers of infectious disease dynamics across multiple scales is a fundamental challenge for modern science. There is growing awareness that it is necessary to incorporate multi-host and/or multi-parasite interactions to understand and predict current and future disease threats better, and new tools are needed to help address this task. Eco-phylogenetics (phylogenetic community ecology) provides one avenue for exploring multi-host multi-parasite systems, yet the incorporation of eco-phylogenetic concepts and methods into studies of host pathogen dynamics has lagged behind. Eco-phylogenetics is a transformative approach that uses evolutionary history to infer present-day dynamics. Here, we present an eco-phylogenetic framework to reveal insights into parasite communities and infectious disease dynamics across spatial and temporal scales. We illustrate how eco-phylogenetic methods can help untangle the mechanisms of host-parasite dynamics from individual (e.g. co-infection) to landscape scales (e.g. parasite/host community structure). An improved ecological understanding of multi-host and multi-pathogen dynamics across scales will increase our ability to predict disease threats. © 2017 Cambridge Philosophical Society.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

PubMed

Fan, Chunyu; Tan, Lingzhao; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

2017-10-30

One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach. As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which considered the spatial dispersion of species generated a taxonomic structure which proved to be more consistent with that in the observed community. As sampling sizes increased from 20 m × 20 m to 50 m × 50 m, the magnitudes of SESs of taxonomic ratios increased. Based on the phylogenetic analysis, we found that the Jiaohe plot was phylogenetically clustered at almost all scales. We detected significant phylogenetically overdispersion at the 20 m × 20 m and 30 m × 30 m scales in the Liangshui plot. The results suggest that the effect of abiotic filtering is greater than the effects of interspecific competition in shaping the local community at almost all scales. Local processes influence the taxonomic structures, but their combined effects vary with the spatial scale. The taxonomic approach provides similar insights as the phylogenetic approach, especially when we applied a more conservative null model. Analysing taxonomic structure may be a useful tool for communities where well-resolved phylogenetic data are not available.

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

PubMed Central

Kumar, Yadhu; Westram, Ralf; Kipfer, Peter; Meier, Harald; Ludwig, Wolfgang

2006-01-01

Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via . PMID:16672074

Tree-Based Unrooted Phylogenetic Networks.

PubMed

Francis, A; Huber, K T; Moulton, V

2018-02-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.

Predicting rates of interspecific interaction from phylogenetic trees.

PubMed

Nuismer, Scott L; Harmon, Luke J

2015-01-01

Integrating phylogenetic information can potentially improve our ability to explain species' traits, patterns of community assembly, the network structure of communities, and ecosystem function. In this study, we use mathematical models to explore the ecological and evolutionary factors that modulate the explanatory power of phylogenetic information for communities of species that interact within a single trophic level. We find that phylogenetic relationships among species can influence trait evolution and rates of interaction among species, but only under particular models of species interaction. For example, when interactions within communities are mediated by a mechanism of phenotype matching, phylogenetic trees make specific predictions about trait evolution and rates of interaction. In contrast, if interactions within a community depend on a mechanism of phenotype differences, phylogenetic information has little, if any, predictive power for trait evolution and interaction rate. Together, these results make clear and testable predictions for when and how evolutionary history is expected to influence contemporary rates of species interaction. © 2014 John Wiley & Sons Ltd/CNRS.

Phylogenetic assemblage structure of North American trees is more strongly shaped by glacial-interglacial climate variability in gymnosperms than in angiosperms.

PubMed

Ma, Ziyu; Sandel, Brody; Svenning, Jens-Christian

2016-05-01

How fast does biodiversity respond to climate change? The relationship of past and current climate with phylogenetic assemblage structure helps us to understand this question. Studies of angiosperm tree diversity in North America have already suggested effects of current water-energy balance and tropical niche conservatism. However, the role of glacial-interglacial climate variability remains to be determined, and little is known about any of these relationships for gymnosperms. Moreover, phylogenetic endemism, the concentration of unique lineages in restricted ranges, may also be related to glacial-interglacial climate variability and needs more attention. We used a refined phylogeny of both angiosperms and gymnosperms to map phylogenetic diversity, clustering and endemism of North American trees in 100-km grid cells, and climate change velocity since Last Glacial Maximum together with postglacial accessibility to recolonization to quantify glacial-interglacial climate variability. We found: (1) Current climate is the dominant factor explaining the overall patterns, with more clustered angiosperm assemblages toward lower temperature, consistent with tropical niche conservatism. (2) Long-term climate stability is associated with higher angiosperm endemism, while higher postglacial accessibility is linked to to more phylogenetic clustering and endemism in gymnosperms. (3) Factors linked to glacial-interglacial climate change have stronger effects on gymnosperms than on angiosperms. These results suggest that paleoclimate legacies supplement current climate in shaping phylogenetic patterns in North American trees, and especially so for gymnosperms.

Cyclic Peptides Arising by Evolutionary Parallelism via Asparaginyl-Endopeptidase–Mediated Biosynthesis[C][W

PubMed Central

Mylne, Joshua S.; Chan, Lai Yue; Chanson, Aurelie H.; Daly, Norelle L.; Schaefer, Hanno; Bailey, Timothy L.; Nguyencong, Philip; Cascales, Laura; Craik, David J.

2012-01-01

The cyclic miniprotein Momordica cochinchinensis Trypsin Inhibitor II (MCoTI-II) (34 amino acids) is a potent trypsin inhibitor (TI) and a favored scaffold for drug design. We have cloned the corresponding genes and determined that each precursor protein contains a tandem series of cyclic TIs terminating with the more commonly known, and potentially ancestral, acyclic TI. Expression of the precursor protein in Arabidopsis thaliana showed that production of the cyclic TIs, but not the terminal acyclic TI, depends on asparaginyl endopeptidase (AEP) for maturation. The nature of their repetitive sequences and the almost identical structures of emerging TIs suggest these cyclic peptides evolved by internal gene amplification associated with recruitment of AEP for processing between domain repeats. This is the third example of similar AEP-mediated processing of a class of cyclic peptides from unrelated precursor proteins in phylogenetically distant plant families. This suggests that production of cyclic peptides in angiosperms has evolved in parallel using AEP as a constraining evolutionary channel. We believe this is evolutionary evidence that, in addition to its known roles in proteolysis, AEP is especially suited to performing protein cyclization. PMID:22822203

Reconstruction of structural evolution in the trnL intron P6b loop of symbiotic Nostoc (Cyanobacteria).

PubMed

Olsson, Sanna; Kaasalainen, Ulla; Rikkinen, Jouko

2012-02-01

In this study we reconstruct the structural evolution of the hyper-variable P6b region of the group I trnLeu intron in a monophyletic group of lichen-symbiotic Nostoc strains and establish it as a useful marker in the phylogenetic analysis of these organisms. The studied cyanobacteria occur as photosynthetic and/or nitrogen-fixing symbionts in lichen species of the diverse Nephroma guild. Phylogenetic analyses and secondary structure reconstructions are used to improve the understanding of the replication mechanisms in the P6b stem-loop and to explain the observed distribution patterns of indels. The variants of the P6b region in the Nostoc clade studied consist of different combinations of five sequence modules. The distribution of indels together with the ancestral character reconstruction performed enables the interpretation of the evolution of each sequence module. Our results indicate that the indel events are usually associated with single nucleotide changes in the P6b region and have occurred several times independently. In spite of their homoplasy, they provide phylogenetic information for closely related taxa. Thus we recognize that features of the P6b region can be used as molecular markers for species identification and phylogenetic studies involving symbiotic Nostoc cyanobacteria.

Computational biomechanics changes our view on insect head evolution.

PubMed

Blanke, Alexander; Watson, Peter J; Holbrey, Richard; Fagan, Michael J

2017-02-08

Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to objectively identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution. © 2017 The Author(s).

Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM

NASA Astrophysics Data System (ADS)

Quax, Rick; van de Vijver, David A. M. C.; Frentz, Dineke; Sloot, Peter M. A.

2013-09-01

The HIV-1 epidemic in Europe is primarily sustained by a dynamic topology of sexual interactions among MSM who have individual immune systems and behavior. This epidemiological process shapes the phylogeny of the virus population. Both fields of epidemic modeling and phylogenetics have a long history, however it remains difficult to use phylogenetic data to infer epidemiological parameters such as the structure of the sexual network and the per-act infectiousness. This is because phylogenetic data is necessarily incomplete and ambiguous. Here we show that the cluster-size distribution indeed contains information about epidemiological parameters using detailed numberical experiments. We simulate the HIV epidemic among MSM many times using the Monte Carlo method with all parameter values and their ranges taken from literature. For each simulation and the corresponding set of parameter values we calculate the likelihood of reproducing an observed cluster-size distribution. The result is an estimated likelihood distribution of all parameters from the phylogenetic data, in particular the structure of the sexual network, the per-act infectiousness, and the risk behavior reduction upon diagnosis. These likelihood distributions encode the knowledge provided by the observed cluster-size distrbution, which we quantify using information theory. Our work suggests that the growing body of genetic data of patients can be exploited to understand the underlying epidemiological process.

Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

PubMed

Kay, Richard F

2015-01-01

Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa. Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium. I sample 16 extant taxa (one from each platyrrhine genus) and 20 extinct taxa of platyrrhines. The tree structure is constrained with a "molecular scaffold" of extant species as implemented in maximum parsimony using PAUP with the molecular-based 'backbone' approach. The data set encompasses most of the known extinct species of platyrrhines, ranging in age from latest Oligocene (∼26 Ma) to the Recent. The tree is rooted with extant catarrhines, and Late Eocene and Early Oligocene African anthropoids. Among the more interesting patterns to emerge are: (1) known early platyrrhines from the Late Oligocene through Early Miocene (26-16.5Ma) represent only stem platyrrhine taxa; (2) representatives of the three living platyrrhine families first occur between 15.7 Ma and 13.5 Ma; and (3) recently extinct primates from the Greater Antilles (Cuba, Jamaica, Hispaniola) are sister to the clade of extant platyrrhines and may have diverged in the Early Miocene. It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates. The following biogeographic scenario is consistent with the phylogenetic findings and climatic and geologic evidence: Tropical South America has been a center for platyrrhine diversification since platyrrhines arrived on the continent in the middle Cenozoic. Platyrrhines dispersed from tropical South America to Patagonia at ∼25-24 Ma via a "Paraná Portal" through eastern South America across a retreating Paranense Sea. Phylogenetic bracketing suggests Antillean primates arrived via a sweepstakes route or island chain from northern South America in the Early Miocene, not via a proposed land bridge or island chain (GAARlandia) in the Early Oligocene (∼34 Ma). Patagonian and Antillean platyrrhines went extinct without leaving living descendants, the former at the end of the Early Miocene and the latter within the past six thousand years. Molecular evidence suggests crown platyrrhines arrived in Central America by crossing an intermittent connection through the Isthmus of Panama at or after 3.5Ma. Any more ancient Central American primates, should they be discovered, are unlikely to have given rise to the extant Central American taxa in situ. Copyright © 2013 Elsevier Inc. All rights reserved.

Structural evolution of nrDNA ITS in Pinaceae and its phylogenetic implications.

PubMed

Kan, Xian-Zhao; Wang, Shan-Shan; Ding, Xin; Wang, Xiao-Quan

2007-08-01

Nuclear ribosomal DNA (nrDNA) has been considered as an important tool for inferring phylogenetic relationships at many taxonomic levels. In comparison with its fast concerted evolution in angiosperms, nrDNA is symbolized by slow concerted evolution and substantial ITS region length variation in gymnosperms, particularly in Pinaceae. Here we studied structure characteristics, including subrepeat composition, size, GC content and secondary structure, of nrDNA ITS regions of all Pinaceae genera. The results showed that the ITS regions of all taxa studied contained subrepeat units, ranging from 2 to 9 in number, and these units could be divided into two types, longer subrepeat (LSR) without the motif (5'-GGCCACCCTAGTC) and shorter subrepeat (SSR) with the motif. Phylogenetic analyses indicate that the homology of some SSRs still can be recognized, providing important informations for the evolutionary history of nrDNA ITS and phylogeny of Pinaceae. In particular, the adjacent tandem SSRs are not more closely related to one another than they are to remote SSRs in some genera, which may imply that multiple structure variations such as recombination have occurred in the ITS1 region of these groups. This study also found that GC content in the ITS1 region is relevant to its sequence length and subrepeat number, and could provide some phylogenetic information, especially supporting the close relationships among Picea, Pinus, and Cathaya. Moreover, several characteristics of the secondary structure of Pinaceae ITS1 were found as follows: (1) the structure is dominated by several extended hairpins; (2) the configuration complexity is positively correlated with subrepeat number; (3) paired subrepeats often partially overlap at the conserved motif (5'-GGCCACCCTAGTC), and form a long stem, while other subrepeats fold onto itself, leaving part of the conserved motif exposed in hairpin loops.

Recovery of Forest and Phylogenetic Structure in Abandoned Cocoa Agroforestry in the Atlantic Forest of Brazil

NASA Astrophysics Data System (ADS)

Rolim, Samir Gonçalves; Sambuichi, Regina Helena Rosa; Schroth, Götz; Nascimento, Marcelo Trindade; Gomes, José Manoel Lucio

2017-03-01

Cocoa agroforests like the cabrucas of Brazil's Atlantic forest are among the agro-ecosystems with greatest potential for biodiversity conservation. Despite a global trend for their intensification, cocoa agroforests are also being abandoned for socioeconomic reasons especially on marginal sites, because they are incorporated in public or private protected areas, or are part of mandatory set-asides under Brazilian environmental legislation. However, little is known about phylogenetic structure, the processes of forest regeneration after abandonment and the conservation value of former cabruca sites. Here we compare the vegetation structure and composition of a former cabruca 30-40 years after abandonment with a managed cabruca and mature forest in the Atlantic forest region of Espirito Santo, Brazil. The forest in the abandoned cabruca had recovered a substantial part of its original structure. Abandoned cabruca have a higher density (mean ± CI95 %: 525.0 ± 40.3 stems per ha), basal area (34.0 ± 6.5 m2 per ha) and species richness (148 ± 11.5 species) than managed cabruca (96.0 ± 17.7; 24.15 ± 3.9 and 114.5 ± 16.0, respectively) but no significant differences to mature forest in density (581.0 ± 42.2), basal area (29.9.0 ± 3.3) and species richness (162.6 ± 15.5 species). Thinning (understory removal) changes phylogenetic structure from evenness in mature forest to clustering in managed cabruca, but after 30-40 years abandoned cabruca had a random phylogenetic structure, probably due to a balance between biotic and abiotic filters at this age. We conclude that abandoned cocoa agroforests present highly favorable conditions for the regeneration of Atlantic forest and could contribute to the formation of an interconnected network of forest habitat in this biodiversity hotspot.

Seasonal cycles, phylogenetic assembly, and functional diversity of orchid bee communities.

PubMed

Ramírez, Santiago R; Hernández, Carlos; Link, Andres; López-Uribe, Margarita M

2015-05-01

Neotropical rainforests sustain some of the most diverse terrestrial communities on Earth. Euglossine (or orchid) bees are a diverse lineage of insect pollinators distributed throughout the American tropics, where they provide pollination services to a staggering diversity of flowering plant taxa. Elucidating the seasonal patterns of phylogenetic assembly and functional trait diversity of bee communities can shed new light into the mechanisms that govern the assembly of bee pollinator communities and the potential effects of declining bee populations. Male euglossine bees collect, store, and accumulate odoriferous compounds (perfumes) to subsequently use during courtship display. Thus, synthetic chemical baits can be used to attract and monitor euglossine bee populations. We conducted monthly censuses of orchid bees in three sites in the Magdalena valley of Colombia - a region where Central and South American biotas converge - to investigate the structure, diversity, and assembly of euglossine bee communities through time in relation to seasonal climatic cycles. In particular, we tested the hypothesis that phylogenetic community structure and functional trait diversity changed in response to seasonal rainfall fluctuations. All communities exhibited strong to moderate phylogenetic clustering throughout the year, with few pronounced bursts of phylogenetic overdispersion that coincided with the transition from wet-to-dry seasons. Despite the heterogeneous distribution of functional traits (e.g., body size, body mass, and proboscis length) and the observed seasonal fluctuations in phylogenetic diversity, we found that functional trait diversity, evenness, and divergence remained constant during all seasons in all communities. However, similar to the pattern observed with phylogenetic diversity, functional trait richness fluctuated markedly with rainfall in all sites. These results emphasize the importance of considering seasonal fluctuations in community assembly and provide a glimpse to the potential effects that climatic alterations may have on both pollinator communities and the ecosystem services they provide.

Structural and parameteric uncertainty quantification in cloud microphysics parameterization schemes

NASA Astrophysics Data System (ADS)

van Lier-Walqui, M.; Morrison, H.; Kumjian, M. R.; Prat, O. P.; Martinkus, C.

2017-12-01

Atmospheric model parameterization schemes employ approximations to represent the effects of unresolved processes. These approximations are a source of error in forecasts, caused in part by considerable uncertainty about the optimal value of parameters within each scheme -- parameteric uncertainty. Furthermore, there is uncertainty regarding the best choice of the overarching structure of the parameterization scheme -- structrual uncertainty. Parameter estimation can constrain the first, but may struggle with the second because structural choices are typically discrete. We address this problem in the context of cloud microphysics parameterization schemes by creating a flexible framework wherein structural and parametric uncertainties can be simultaneously constrained. Our scheme makes no assuptions about drop size distribution shape or the functional form of parametrized process rate terms. Instead, these uncertainties are constrained by observations using a Markov Chain Monte Carlo sampler within a Bayesian inference framework. Our scheme, the Bayesian Observationally-constrained Statistical-physical Scheme (BOSS), has flexibility to predict various sets of prognostic drop size distribution moments as well as varying complexity of process rate formulations. We compare idealized probabilistic forecasts from versions of BOSS with varying levels of structural complexity. This work has applications in ensemble forecasts with model physics uncertainty, data assimilation, and cloud microphysics process studies.

Floral colour versus phylogeny in structuring subalpine flowering communities.

PubMed

McEwen, Jamie R; Vamosi, Jana C

2010-10-07

The relative number of seeds produced by competing species can influence the community structure; yet, traits that influence seed production, such as pollinator attraction and floral colour, have received little attention in community ecology. Here, we analyse floral colour using reflectance spectra that include near-UV and examined the phylogenetic signal of floral colour. We found that coflowering species within communities tended to be more divergent in floral colour than expected by chance. However, coflowering species were not phylogenetically dispersed, in part due to our finding that floral colour is a labile trait with a weak phylogenetic signal. Furthermore, while we found that locally rare and common species exhibited equivalent floral colour distances from their coflowering neighbours, frequent species (those found in more communities) exhibited higher colour distances from their coflowering neighbours. Our findings support recent studies, which have found that (i) plant lineages exhibit frequent floral colour transitions; and (ii) traits that influence local population dynamics contribute to community structure.

Evolutionary characterization of the West Nile Virus complete genome.

PubMed

Gray, R R; Veras, N M C; Santos, L A; Salemi, M

2010-07-01

The spatial dynamics of the West Nile Virus epidemic in North America are largely unknown. Previous studies that investigated the evolutionary history of the virus used sequence data from the structural genes (prM and E); however, these regions may lack phylogenetic information and obscure true evolutionary relationships. This study systematically evaluated the evolutionary patterns in the eleven genes of the WNV genome in order to determine which region(s) were most phylogenetically informative. We found that while the E region lacks resolution and can potentially result in misleading conclusions, the full NS3 or NS5 regions have strong phylogenetic signal. Furthermore, we show that geographic structure of WNV infection within the US is more pronounced than previously reported in studies that used the structural genes. We conclude that future evolutionary studies should focus on NS3 and NS5 in order to maximize the available sequences while retaining maximal interpretative power to infer temporal and geographic trends among WNV strains. Copyright 2010 Elsevier Inc. All rights reserved.

Potomacapnos apeleutheron gen. et sp. nov., a new Early Cretaceous angiosperm from the Potomac Group and its implications for the evolution of eudicot leaf architecture.

PubMed

Jud, Nathan A; Hickey, Leo J

2013-12-01

Eudicots diverged early in the evolution of flowering plants and now comprise more than 70% of angiosperm species. In spite of the importance of eudicots, our understanding of the early evolution of this clade is limited by a poor fossil record and uncertainty about the order of early phylogenetic branching. The study of Lower Cretaceous fossils can reveal much about the evolution, morphology, and ecology of the eudicots. Fossils described here were collected from Aptian sediments of the Potomac Group exposed at the Dutch Gap locality in Virginia, USA. Specimens were prepared by degaging, then described and compared with leaves of relevant extant and fossil plants. We conducted a phylogenetic analysis of morphological characters using parsimony while constraining the tree search with the topology found through molecular phylogenetic analyses. The new species is closely related to ranunculalean eudicots and has leaf architecture remarkably similar to some living Fumarioideae (Papaveraceae). These are the oldest eudicot megafossils from North America, and they show complex leaf architecture reflecting developmental pathways unique to extant eudicots. The morphology and small size of the fossils suggest that they were herbaceous plants, as is seen in other putative early eudicots. The absence of co-occurring tricolpate pollen at Dutch Gap either (1) reflects low preservation probability for pollen of entomophilous herbs or (2) indicates that some leaf features of extant eudicots appeared before the origin of tricolpate pollen.

Phylogenetics of Australasian gall flies (Diptera: Fergusoninidae): Evolutionary patterns of host-shifting and gall morphology.

PubMed

Scheffer, S J; Davies, K A; Taylor, G S; Thornhill, A H; Lewis, M L; Winkler, I S; Yeates, D K; Purcell, M F; Makinson, J; Giblin-Davis, R M

2017-10-01

This study investigated host-specificity and phylogenetic relationships in Australian galling flies, Fergusonina Malloch (Diptera: Fergusoninidae), in order to assess diversity and explore the evolutionary history of host plant affiliation and gall morphology. A DNA barcoding approach using COI data from 203 Fergusonina specimens from 5gall types on 56 host plant species indicated 85 presumptive fly species. These exhibited a high degree of host specificity; of the 40 species with multiple representatives, each fed only on a single host genus, 29 (72.5%) were strictly monophagous, and 11 (27.5%) were reared from multiple closely related hosts. COI variation within species was not correlated with either sample size or geographic distance. However variation was greater within oligophagous species, consistent with expectations of the initial stages of host-associated divergence during speciation. Phylogenetic analysis using both nuclear and mitochondrial genes revealed host genus-restricted clades but also clear evidence of multiple colonizations of both host plant genus and host species. With the exception of unilocular peagalls, evolution of gall type was somewhat constrained, but to a lesser degree than host plant association. Unilocular peagalls arose more often than any other gall type, were primarily located at the tips of the phylogeny, and did not form clades comprising more than a few species. For ecological reasons, species of this gall type are predicted to harbor substantially less genetic variation than others, possibly reducing evolutionary flexibility resulting in reduced diversification in unilocular gallers. Published by Elsevier Inc.

Contextualising primate origins--an ecomorphological framework.

PubMed

Soligo, Christophe; Smaers, Jeroen B

2016-04-01

Ecomorphology - the characterisation of the adaptive relationship between an organism's morphology and its ecological role - has long been central to theories of the origin and early evolution of the primate order. This is exemplified by two of the most influential theories of primate origins: Matt Cartmill's Visual Predation Hypothesis, and Bob Sussman's Angiosperm Co-Evolution Hypothesis. However, the study of primate origins is constrained by the absence of data directly documenting the events under investigation, and has to rely instead on a fragmentary fossil record and the methodological assumptions inherent in phylogenetic comparative analyses of extant species. These constraints introduce particular challenges for inferring the ecomorphology of primate origins, as morphology and environmental context must first be inferred before the relationship between the two can be considered. Fossils can be integrated in comparative analyses and observations of extant model species and laboratory experiments of form-function relationships are critical for the functional interpretation of the morphology of extinct species. Recent developments have led to important advancements, including phylogenetic comparative methods based on more realistic models of evolution, and improved methods for the inference of clade divergence times, as well as an improved fossil record. This contribution will review current perspectives on the origin and early evolution of primates, paying particular attention to their phylogenetic (including cladistic relationships and character evolution) and environmental (including chronology, geography, and physical environments) contextualisation, before attempting an up-to-date ecomorphological synthesis of primate origins. © 2016 Anatomical Society.

Biomass Allocation of Stoloniferous and Rhizomatous Plant in Response to Resource Availability: A Phylogenetic Meta-Analysis

PubMed Central

Xie, Xiu-Fang; Hu, Yu-Kun; Pan, Xu; Liu, Feng-Hong; Song, Yao-Bin; Dong, Ming

2016-01-01

Resource allocation to different functions is central in life-history theory. Plasticity of functional traits allows clonal plants to regulate their resource allocation to meet changing environments. In this study, biomass allocation traits of clonal plants were categorized into absolute biomass for vegetative growth vs. for reproduction, and their relative ratios based on a data set including 115 species and derived from 139 published literatures. We examined general pattern of biomass allocation of clonal plants in response to availabilities of resource (e.g., light, nutrients, and water) using phylogenetic meta-analysis. We also tested whether the pattern differed among clonal organ types (stolon vs. rhizome). Overall, we found that stoloniferous plants were more sensitive to light intensity than rhizomatous plants, preferentially allocating biomass to vegetative growth, aboveground part and clonal reproduction under shaded conditions. Under nutrient- and water-poor condition, rhizomatous plants were constrained more by ontogeny than by resource availability, preferentially allocating biomass to belowground part. Biomass allocation between belowground and aboveground part of clonal plants generally supported the optimal allocation theory. No general pattern of trade-off was found between growth and reproduction, and neither between sexual and clonal reproduction. Using phylogenetic meta-analysis can avoid possible confounding effects of phylogeny on the results. Our results shown the optimal allocation theory explained a general trend, which the clonal plants are able to plastically regulate their biomass allocation, to cope with changing resource availability, at least in stoloniferous and rhizomatous plants. PMID:27200071

Effects of species' similarity and dominance on the functional and phylogenetic structure of a plant meta-community.

PubMed

Chalmandrier, L; Münkemüller, T; Lavergne, S; Thuiller, W

2015-01-01

Different assembly processes drive the spatial structure of meta-communities (beta-diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high beta-diversity along environmental gradients should be the result of environmental filtering while low beta-diversity should stem from competitive interactions. So far, studies trying to disentangle the relative importance of these assembly processes have provided mixed results. One reason for this may be that these studies often rely on a single measure of diversity and thus implicitly make a choice on how they account for species relative abundances and how species similarities are captured by functional traits or phylogeny. Here, we tested the effect of gradually scaling the importance of dominance (the weight given to dominant vs. rare species) and species similarity (the weight given to small vs. large similarities) on resulting beta-diversity patterns of an alpine plant meta-community. To this end, we combined recent extensions of the Hill numbers framework with Pagel's phylogenetic tree transformation approach. We included functional (based on the leaf-height-seed spectrum) and phylogenetic facets of beta-diversity in our analysis and explicitly accounted for effects of environmental and spatial covariates. We found that functional beta-diversity, was high when the same weight was given to dominant vs. rare species and to large vs. small species' similarities. In contrast, phylogenetic beta-diversity was low when greater weight was given to dominant species and small species' similarities. Those results suggested that different environments along the gradients filtered different species according to their functional traits, while, the same competitive lineages dominated communities across the gradients. Our results highlight that functional vs. phylogenetic facets, presence-absence vs. abundance structure and different weights of species' dissimilarity provide complementary and important information on the drivers of meta-community structure. By utilizing the full extent of information provided by the flexible frameworks of Hill numbers and Pagel's tree transformation, we propose a new approach to disentangle the patterns resulting from different assembly processes.

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages

PubMed Central

Fukasawa, Yoshinori; Oda, Toshiyuki; Tomii, Kentaro

2017-01-01

Abstract Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases’ evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex. PMID:28369657

Lineage diversification and morphological evolution in a large-scale continental radiation: the neotropical ovenbirds and woodcreepers (aves: Furnariidae).

PubMed

Derryberry, Elizabeth P; Claramunt, Santiago; Derryberry, Graham; Chesser, R Terry; Cracraft, Joel; Aleixo, Alexandre; Pérez-Emán, Jorge; Remsen, J V; Brumfield, Robb T

2011-10-01

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Structural Brain Connectivity Constrains within-a-Day Variability of Direct Functional Connectivity

PubMed Central

Park, Bumhee; Eo, Jinseok; Park, Hae-Jeong

2017-01-01

The idea that structural white matter connectivity constrains functional connectivity (interactions among brain regions) has widely been explored in studies of brain networks; studies have mostly focused on the “average” strength of functional connectivity. The question of how structural connectivity constrains the “variability” of functional connectivity remains unresolved. In this study, we investigated the variability of resting state functional connectivity that was acquired every 3 h within a single day from 12 participants (eight time sessions within a 24-h period, 165 scans per session). Three different types of functional connectivity (functional connectivity based on Pearson correlation, direct functional connectivity based on partial correlation, and the pseudo functional connectivity produced by their difference) were estimated from resting state functional magnetic resonance imaging data along with structural connectivity defined using fiber tractography of diffusion tensor imaging. Those types of functional connectivity were evaluated with regard to properties of structural connectivity (fiber streamline counts and lengths) and types of structural connectivity such as intra-/inter-hemispheric edges and topological edge types in the rich club organization. We observed that the structural connectivity constrained the variability of direct functional connectivity more than pseudo-functional connectivity and that the constraints depended strongly on structural connectivity types. The structural constraints were greater for intra-hemispheric and heterologous inter-hemispheric edges than homologous inter-hemispheric edges, and feeder and local edges than rich club edges in the rich club architecture. While each edge was highly variable, the multivariate patterns of edge involvement, especially the direct functional connectivity patterns among the rich club brain regions, showed low variability over time. This study suggests that structural connectivity not only constrains the strength of functional connectivity, but also the within-a-day variability of functional connectivity and connectivity patterns, particularly the direct functional connectivity among brain regions. PMID:28848416

Using seismically constrained magnetotelluric inversion to recover velocity structure in the shallow lithosphere

NASA Astrophysics Data System (ADS)

Moorkamp, M.; Fishwick, S.; Jones, A. G.

2015-12-01

Typical surface wave tomography can recover well the velocity structure of the upper mantle in the depth range between 70-200km. For a successful inversion, we have to constrain the crustal structure and assess the impact on the resulting models. In addition,we often observe potentially interesting features in the uppermost lithosphere which are poorly resolved and thus their interpretationhas to be approached with great care.We are currently developing a seismically constrained magnetotelluric (MT) inversion approach with the aim of better recovering the lithospheric properties (and thus seismic velocities) in these problematic areas. We perform a 3D MT inversion constrained by a fixed seismic velocity model from surface wave tomography. In order to avoid strong bias, we only utilize information on structural boundaries to combine these two methods. Within the region that is well resolved by both methods, we can then extract a velocity-conductivity relationship. By translating the conductivitiesretrieved from MT into velocities in areas where the velocity model is poorly resolved, we can generate an updated velocity model and test what impactthe updated velocities have on the predicted data.We test this new approach using a MT dataset acquired in central Botswana over the Okwa terrane and the adjacent Kaapvaal and Zimbabwe Cratons togetherwith a tomographic models for the region. Here, both datasets have previously been used to constrain lithospheric structure and show some similarities.We carefully asses the validity of our results by comparing with observations and petrophysical predictions for the conductivity-velocity relationship.

Greatly reduced phylogenetic structure in the cultivated potato clade of potatoes, Solanum section Petota

USDA-ARS?s Scientific Manuscript database

The species boundaries of wild and cultivated potatoes, Solanum section Petota, are controversial with most of the taxonomic problems in a clade containing cultivated potatoes. We here provide the first in-depth phylogenetic study of the cultivated potato clade to explore possible causes of these pr...

Low Temperature Decreases the Phylogenetic Diversity of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofiltration Systems▿ †

PubMed Central

Urakawa, Hidetoshi; Tajima, Yoshiyuki; Numata, Yoshiyuki; Tsuneda, Satoshi

2008-01-01

The phylogenetic diversity and species richness of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were examined with aquarium biofiltration systems. Species richness, deduced from rarefaction analysis, and diversity indices indicated that the phylogenetic diversity and species richness of AOA are greater than those of AOB; the diversity of AOA and of AOB is minimized in cold-water aquaria. This finding implies that temperature is a key factor influencing the population structure and diversity of AOA and AOB in aquarium biofiltration systems. PMID:18065610

The complex roles of space and environment in structuring functional, taxonomic and phylogenetic beta diversity of frogs in the Atlantic Forest

PubMed Central

Luiz, Amom Mendes; Sawaya, Ricardo J.

2018-01-01

Ecological communities are complex entities that can be maintained and structured by niche-based processes such as environmental conditions, and spatial processes such as dispersal. Thus, diversity patterns may be shaped simultaneously at different spatial scales by very distinct processes. Herein we assess whether and how functional, taxonomic, and phylogenetic beta diversities of frog tadpoles are explained by environmental and/or spatial predictors. We implemented a distance–based redundancy analysis to explore variation in components of beta diversity explained by pure environmental and pure spatial predictors, as well as their interactions, at both fine and broad spatial scales. Our results indicated important but complex roles of spatial and environmental predictors in structuring phylogenetic, taxonomic and functional beta diversities. The pure fine-scales spatial fraction was more important in structuring all beta diversity components, especially to functional and taxonomical spatial turnover. Environmental variables such as canopy cover and vegetation structure were important predictors of all components, but especially to functional and taxonomic beta diversity. We emphasize that distinct factors related to environment and space are affecting distinct components of beta diversity in different ways. Although weaker, phylogenetic beta diversity, which is structured more on biogeographical scales, and thus can be represented by spatially structured processes, was more related to broad spatial processes than other components. However, selected fine-scale spatial predictors denoted negative autocorrelation, which may be revealing the existence of differences in unmeasured habitat variables among samples. Although overall important, local environmental-based processes explained better functional and taxonomic beta diversity, as these diversity components carry an important ecological value. We highlight the importance of assessing different components of diversity patterns at different scales by spatially explicit models in order to improve our understanding of community structure and help to unravel the complex nature of biodiversity. PMID:29672575

Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process

PubMed Central

Chai, Yongfu; Yue, Ming; Liu, Xiao; Guo, Yaoxin; Wang, Mao; Xu, Jinshi; Zhang, Chenguang; Chen, Yu; Zhang, Lixia; Zhang, Ruichang

2016-01-01

Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient. PMID:27272407

Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process.

PubMed

Chai, Yongfu; Yue, Ming; Liu, Xiao; Guo, Yaoxin; Wang, Mao; Xu, Jinshi; Zhang, Chenguang; Chen, Yu; Zhang, Lixia; Zhang, Ruichang

2016-06-08

Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient.

Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks.

PubMed

Oh, S June; Joung, Je-Gun; Chang, Jeong-Ho; Zhang, Byoung-Tak

2006-06-06

To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees. To compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes. By combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway structures using meta-level information rather than sequence information. This method may yield further information about biological evolution, such as the history of horizontal transfer of each gene, by studying the detailed structure of the phylogenetic tree constructed by the kernel-based method.

On the distribution of interspecies correlation for Markov models of character evolution on Yule trees.

PubMed

Mulder, Willem H; Crawford, Forrest W

2015-01-07

Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule process, in which new species are "born" from existing lineages at a constant rate. Recent work has illuminated some of the structural properties of Yule trees, but it remains mostly unknown how these properties affect sequence and trait patterns observed at the tips of the phylogenetic tree. Understanding the interplay between speciation and mutation under simple models of evolution is essential for deriving valid phylogenetic inference methods and gives insight into the optimal design of phylogenetic studies. In this work, we derive the probability distribution of interspecies covariance under Brownian motion and Ornstein-Uhlenbeck models of phenotypic change on a Yule tree. We compute the probability distribution of the number of mutations shared between two randomly chosen taxa in a Yule tree under discrete Markov mutation models. Our results suggest summary measures of phylogenetic information content, illuminate the correlation between site patterns in sequences or traits of related organisms, and provide heuristics for experimental design and reconstruction of phylogenetic trees. Copyright © 2014 Elsevier Ltd. All rights reserved.

Local-scale Partitioning of Functional and Phylogenetic Beta Diversity in a Tropical Tree Assemblage.

PubMed

Yang, Jie; Swenson, Nathan G; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J W; Lin, Luxiang

2015-08-03

The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees.

Biophysical and structural considerations for protein sequence evolution

PubMed Central

2011-01-01

Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model. PMID:22171550

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data

PubMed Central

Panzer, Katrin; Yilmaz, Pelin; Weiß, Michael; Reich, Lothar; Richter, Michael; Wiese, Jutta; Schmaljohann, Rolf; Labes, Antje; Imhoff, Johannes F.; Glöckner, Frank Oliver; Reich, Marlis

2015-01-01

Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases. PMID:26226014

Relative Roles of Deterministic and Stochastic Processes in Driving the Vertical Distribution of Bacterial Communities in a Permafrost Core from the Qinghai-Tibet Plateau, China.

PubMed

Hu, Weigang; Zhang, Qi; Tian, Tian; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; Stegen, James C; An, Lizhe; Feng, Huyuan

2015-01-01

Understanding the processes that influence the structure of biotic communities is one of the major ecological topics, and both stochastic and deterministic processes are expected to be at work simultaneously in most communities. Here, we investigated the vertical distribution patterns of bacterial communities in a 10-m-long soil core taken within permafrost of the Qinghai-Tibet Plateau. To get a better understanding of the forces that govern these patterns, we examined the diversity and structure of bacterial communities, and the change in community composition along the vertical distance (spatial turnover) from both taxonomic and phylogenetic perspectives. Measures of taxonomic and phylogenetic beta diversity revealed that bacterial community composition changed continuously along the soil core, and showed a vertical distance-decay relationship. Multiple stepwise regression analysis suggested that bacterial alpha diversity and phylogenetic structure were strongly correlated with soil conductivity and pH but weakly correlated with depth. There was evidence that deterministic and stochastic processes collectively drived bacterial vertically-structured pattern. Bacterial communities in five soil horizons (two originated from the active layer and three from permafrost) of the permafrost core were phylogenetically random, indicator of stochastic processes. However, we found a stronger effect of deterministic processes related to soil pH, conductivity, and organic carbon content that were structuring the bacterial communities. We therefore conclude that the vertical distribution of bacterial communities was governed primarily by deterministic ecological selection, although stochastic processes were also at work. Furthermore, the strong impact of environmental conditions (for example, soil physicochemical parameters and seasonal freeze-thaw cycles) on these communities underlines the sensitivity of permafrost microorganisms to climate change and potentially subsequent permafrost thaw.

Relative Roles of Deterministic and Stochastic Processes in Driving the Vertical Distribution of Bacterial Communities in a Permafrost Core from the Qinghai-Tibet Plateau, China

PubMed Central

Tian, Tian; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; Stegen, James C.; An, Lizhe; Feng, Huyuan

2015-01-01

Understanding the processes that influence the structure of biotic communities is one of the major ecological topics, and both stochastic and deterministic processes are expected to be at work simultaneously in most communities. Here, we investigated the vertical distribution patterns of bacterial communities in a 10-m-long soil core taken within permafrost of the Qinghai-Tibet Plateau. To get a better understanding of the forces that govern these patterns, we examined the diversity and structure of bacterial communities, and the change in community composition along the vertical distance (spatial turnover) from both taxonomic and phylogenetic perspectives. Measures of taxonomic and phylogenetic beta diversity revealed that bacterial community composition changed continuously along the soil core, and showed a vertical distance-decay relationship. Multiple stepwise regression analysis suggested that bacterial alpha diversity and phylogenetic structure were strongly correlated with soil conductivity and pH but weakly correlated with depth. There was evidence that deterministic and stochastic processes collectively drived bacterial vertically-structured pattern. Bacterial communities in five soil horizons (two originated from the active layer and three from permafrost) of the permafrost core were phylogenetically random, indicator of stochastic processes. However, we found a stronger effect of deterministic processes related to soil pH, conductivity, and organic carbon content that were structuring the bacterial communities. We therefore conclude that the vertical distribution of bacterial communities was governed primarily by deterministic ecological selection, although stochastic processes were also at work. Furthermore, the strong impact of environmental conditions (for example, soil physicochemical parameters and seasonal freeze-thaw cycles) on these communities underlines the sensitivity of permafrost microorganisms to climate change and potentially subsequent permafrost thaw. PMID:26699734

Parallel-vector computation for structural analysis and nonlinear unconstrained optimization problems

NASA Technical Reports Server (NTRS)

Nguyen, Duc T.

1990-01-01

Practical engineering application can often be formulated in the form of a constrained optimization problem. There are several solution algorithms for solving a constrained optimization problem. One approach is to convert a constrained problem into a series of unconstrained problems. Furthermore, unconstrained solution algorithms can be used as part of the constrained solution algorithms. Structural optimization is an iterative process where one starts with an initial design, a finite element structure analysis is then performed to calculate the response of the system (such as displacements, stresses, eigenvalues, etc.). Based upon the sensitivity information on the objective and constraint functions, an optimizer such as ADS or IDESIGN, can be used to find the new, improved design. For the structural analysis phase, the equation solver for the system of simultaneous, linear equations plays a key role since it is needed for either static, or eigenvalue, or dynamic analysis. For practical, large-scale structural analysis-synthesis applications, computational time can be excessively large. Thus, it is necessary to have a new structural analysis-synthesis code which employs new solution algorithms to exploit both parallel and vector capabilities offered by modern, high performance computers such as the Convex, Cray-2 and Cray-YMP computers. The objective of this research project is, therefore, to incorporate the latest development in the parallel-vector equation solver, PVSOLVE into the widely popular finite-element production code, such as the SAP-4. Furthermore, several nonlinear unconstrained optimization subroutines have also been developed and tested under a parallel computer environment. The unconstrained optimization subroutines are not only useful in their own right, but they can also be incorporated into a more popular constrained optimization code, such as ADS.

Disentangling the phylogenetic and ecological components of spider phenotypic variation.

PubMed

Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

2014-01-01

An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure.

Disentangling the Phylogenetic and Ecological Components of Spider Phenotypic Variation

PubMed Central

Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

2014-01-01

An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure. PMID:24651264

Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective

PubMed Central

González-Rocha, Gerardo; Muñoz-Cartes, Gabriel; Canales-Aguirre, Cristian B.; Lima, Celia A.; Domínguez-Yévenes, Mariana; Bello-Toledo, Helia

2017-01-01

It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet ‘Everything is everywhere, but, the environment selects’ by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis—in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica. PMID:28632790

Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective.

PubMed

González-Rocha, Gerardo; Muñoz-Cartes, Gabriel; Canales-Aguirre, Cristian B; Lima, Celia A; Domínguez-Yévenes, Mariana; Bello-Toledo, Helia; Hernández, Cristián E

2017-01-01

It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica.

Oil-producing flowers within the Iridoideae (Iridaceae): evolutionary trends in the flowers of the New World genera.

PubMed

Chauveau, Olivier; Eggers, Lilian; Souza-Chies, Tatiana T; Nadot, Sophie

2012-08-01

Oil-producing flowers related to oil-bee pollination are a major innovation in Neotropical and Mexican Iridaceae. In this study, phylogenetic relationships were investigated among a wide array of New World genera of the tribes Sisyrinchieae, Trimezieae and Tigridieae (Iridaceae: Iridoideae) and the evolution of floral glandular structures, which are predominantly trichomal elaiophores, was examined in relation to the diversification of New World Iridaceae. Phylogenetic analyses based on seven molecular markers obtained from 97 species were conducted to produce the first extensive phylogeny of the New World tribes of subfamily Iridoideae. The resulting phylogenetic hypothesis was used to trace the evolutionary history of glandular structures present in the flowers of numerous species in each tribe. Hypotheses of differential diversification rates among lineages were also investigated using both topological and Binary-State Speciation and Extinction methods. Floral glandular structures and especially trichomal elaiophores evolved multiple times independently in the American tribes of Iridoideae. The distribution pattern of species displaying glandular trichomes across the phylogeny reveals lability in the pollination system and suggests that these structures may have played a significant role in the diversification of the Iridoideae on the American continent.

A Unique Box in 28S rRNA Is Shared by the Enigmatic Insect Order Zoraptera and Dictyoptera

PubMed Central

Dang, Kai; Wu, Haoyang; Wang, Ying; Xie, Qiang; Bu, Wenjun

2013-01-01

The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages. PMID:23301099

Exploring phylogenetic and functional signals in complex morphologies: the hamate of extant anthropoids as a test-case study.

PubMed

Almécija, Sergio; Orr, Caley M; Tocheri, Matthew W; Patel, Biren A; Jungers, William L

2015-01-01

Three-dimensional geometric morphometrics (3DGM) is a powerful tool for capturing and visualizing the "pure" shape of complex structures. However, these shape differences are sometimes difficult to interpret from a functional viewpoint, unless specific approaches (mostly based on biomechanical modeling) are employed. Here, we use 3DGM to explore the complex shape variation of the hamate, the disto-ulnar wrist bone, in anthropoid primates. Major trends of shape variation are explored using principal components analysis along with analyses of shape and size covariation. We also evaluate the phylogenetic patterning of hamate shape by plotting an anthropoid phylogenetic tree onto the shape space (i.e., phylomorphospace) and test against complete absence of phylogenetic signal using posterior permutation. Finally, the covariation of hamate shape and locomotor categories is explored by means of 2-block partial least squares (PLS) using shape coordinates and a matrix of data on arboreal locomotor behavior. Our results show that 3DGM is a valuable and versatile tool for characterizing the shape of complex structures such as wrist bones in anthropoids. For the hamate, a significant phylogenetic pattern is found in both hamate shape and size, indicating that closely related taxa are typically the most similar in hamate form. Our allometric analyses show that major differences in hamate shape among taxa are not a direct consequence of differences in hamate size. Finally, our PLS indicates a significant covariation of hamate shape and different types of arboreal locomotion, highlighting the relevance of this approach in future 3DGM studies seeking to capture a functional signal from complex biological structures. © 2014 Wiley Periodicals, Inc.

Critical Robotic Lunar Missions

NASA Astrophysics Data System (ADS)

Plescia, J. B.

2018-04-01

Perhaps the most critical missions to understanding lunar history are in situ dating and network missions. These would constrain the volcanic and thermal history and interior structure. These data would better constrain lunar evolution models.

A multi-frequency receiver function inversion approach for crustal velocity structure

NASA Astrophysics Data System (ADS)

Li, Xuelei; Li, Zhiwei; Hao, Tianyao; Wang, Sheng; Xing, Jian

2017-05-01

In order to constrain the crustal velocity structures better, we developed a new nonlinear inversion approach based on multi-frequency receiver function waveforms. With the global optimizing algorithm of Differential Evolution (DE), low-frequency receiver function waveforms can primarily constrain large-scale velocity structures, while high-frequency receiver function waveforms show the advantages in recovering small-scale velocity structures. Based on the synthetic tests with multi-frequency receiver function waveforms, the proposed approach can constrain both long- and short-wavelength characteristics of the crustal velocity structures simultaneously. Inversions with real data are also conducted for the seismic stations of KMNB in southeast China and HYB in Indian continent, where crustal structures have been well studied by former researchers. Comparisons of inverted velocity models from previous and our studies suggest good consistency, but better waveform fitness with fewer model parameters are achieved by our proposed approach. Comprehensive tests with synthetic and real data suggest that the proposed inversion approach with multi-frequency receiver function is effective and robust in inverting the crustal velocity structures.

Thunder-induced ground motions: 2. Site characterization

NASA Astrophysics Data System (ADS)

Lin, Ting-L.; Langston, Charles A.

2009-04-01

Thunder-induced ground motion, near-surface refraction, and Rayleigh wave dispersion measurements were used to constrain near-surface velocity structure at an unconsolidated sediment site. We employed near-surface seismic refraction measurements to first define ranges for site structure parameters. Air-coupled and hammer-generated Rayleigh wave dispersion curves were used to further constrain the site structure by a grid search technique. The acoustic-to-seismic coupling is modeled as an incident plane P wave in a fluid half-space impinging into a solid layered half-space. We found that the infrasound-induced ground motions constrained substrate velocities and the average thickness and velocities of the near-surface layer. The addition of higher-frequency near-surface Rayleigh waves produced tighter constraints on the near-surface velocities. This suggests that natural or controlled airborne pressure sources can be used to investigate the near-surface site structures for earthquake shaking hazard studies.

[Molecular phylogeny and systematics of flowering plants of the family Crassulaceae DC].

PubMed

Goncharova, S B; Goncharov, A A

2009-01-01

Crassulaceae is the most species rich (ca. 1400) family in the order Saxifragales. Most members of the family are succulent plants. Phenotypic diversity and a large number of species complicate systematics of the family and reconstruction of relationship within it. Phylogenetic analyses based on morphological and molecular markers placed Crassulaceae as one of the crown clades of Saxifragales. In this contribution a review of phylogenetic studies of the family Crassulaceae, based on DNA nucleotide sequence comparisons is presented; major clades established in the family are characterised; their structure and polyphylesis of some genera related to it are discussed. It was shown that the traditional taxonomic structure of Crassulaceae contradicts pattern of phylogenetic relationships between its members. We critically analysed recent taxonomic systems of the family and stress that homoplasy of morphological characters does not allow to use them to reconstruct relationships between crassulacean taxa even at the low taxonomic levels.

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene

PubMed Central

2017-01-01

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference. PMID:29136663

Temperate Snake Community in South America: Is Diet Determined by Phylogeny or Ecology?

PubMed Central

Etchepare, Eduardo G.

2015-01-01

Communities are complex and dynamic systems that change with time. The first attempts to explain how they were structured involve contemporary phenomena like ecological interactions between species (e.g., competition and predation) and led to the competition-predation hypothesis. Recently, the deep history hypothesis has emerged, which suggests that profound differences in the evolutionary history of organisms resulted in a number of ecological features that remain largely on species that are part of existing communities. Nevertheless, both phylogenetic structure and ecological interactions can act together to determine the structure of a community. Because diet is one of the main niche axes, in this study we evaluated, for the first time, the impact of ecological and phylogenetic factors on the diet of Neotropical snakes from the subtropical-temperate region of South America. Additionally, we studied their relationship with morphological and environmental aspects to understand the natural history and ecology of this community. A canonical phylogenetical ordination analysis showed that phylogeny explained most of the variation in diet, whereas ecological characters explained very little of this variation. Furthermore, some snakes that shared the habitat showed some degree of diet convergence, in accordance with the competition-predation hypothesis, although phylogeny remained the major determinant in structuring this community. The clade with the greatest variability was the subfamily Dipsadinae, whose members had a very different type of diet, based on soft-bodied invertebrates. Our results are consistent with the deep history hypothesis, and we suggest that the community under study has a deep phylogenetic effect that explains most of the variation in the diet. PMID:25945501

Tempo and mode of climatic niche evolution in Primates.

PubMed

Duran, Andressa; Pie, Marcio R

2015-09-01

Climatic niches have increasingly become a nexus in our understanding of a variety of ecological and evolutionary phenomena, from species distributions to latitudinal diversity gradients. Despite the increasing availability of comprehensive datasets on species ranges, phylogenetic histories, and georeferenced environmental conditions, studies on the evolution of climate niches have only begun to understand how niches evolve over evolutionary timescales. Here, using primates as a model system, we integrate recently developed phylogenetic comparative methods, species distribution patterns, and climatic data to explore primate climatic niche evolution, both among clades and over time. In general, we found that simple, constant-rate models provide a poor representation of how climatic niches evolve. For instance, there have been shifts in the rate of climatic niche evolution in several independent clades, particularly in response to the increasingly cooler climates of the past 10 My. Interestingly, rate accelerations greatly outnumbered rate decelerations. These results highlight the importance of considering more realistic evolutionary models that allow for the detection of heterogeneity in the tempo and mode of climatic niche evolution, as well as to infer possible constraining factors for species distributions in geographical space. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Biogeography of boreal passerine range dynamics in western North America: past, present, and future

USGS Publications Warehouse

Stralberg, Diana; Matsuoka, Steven M.; Handel, Colleen M.; Schmiegelow, Fiona K.A.; Hamann, Andreas; Bayne, Erin M.

2017-01-01

Many of the Neotropical migrant bird species that breed throughout the Canadian boreal region are not found in the Alaskan boreal region, separated by the northwestern cordilleran mountains, despite the presence of climatically suitable habitat. We asked whether biological or climatic factors constrain certain species from crossing this geographic barrier. Analyzing a comprehensive dataset for 80 boreal passerine species, we used phylogenetic logistic regression to evaluate the relative importance of physical, migratory and competition metrics versus current and paleoclimatic suitability factors. Controlling for current climatic suitability within boreal Alaska, we found that species with the greatest climatic suitability across the northwestern cordillera, presently and also during the mid-Holocene period, were most likely to be regular breeders in the Alaskan boreal region. Migratory strategy also played a role, but could not be disentangled from its strong phylogenetic basis. Our analysis suggests that the perceived barrier of the northwestern cordillera may be easily weakened as climate change improves conditions there for many forest species. The weakening of this barrier may lead to relatively rapid range expansions and the reshuffling of species communities. Species’ realized distributional shifts will be a function of the interplay between a changing climate and static topographic features.

Recursive algorithms for phylogenetic tree counting.

PubMed

Gavryushkina, Alexandra; Welch, David; Drummond, Alexei J

2013-10-28

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.

Analyzing endocrine system conservation and evolution.

PubMed

Bonett, Ronald M

2016-08-01

Analyzing variation in rates of evolution can provide important insights into the factors that constrain trait evolution, as well as those that promote diversification. Metazoan endocrine systems exhibit apparent variation in evolutionary rates of their constituent components at multiple levels, yet relatively few studies have quantified these patterns and analyzed them in a phylogenetic context. This may be in part due to historical and current data limitations for many endocrine components and taxonomic groups. However, recent technological advancements such as high-throughput sequencing provide the opportunity to collect large-scale comparative data sets for even non-model species. Such ventures will produce a fertile data landscape for evolutionary analyses of nucleic acid and amino acid based endocrine components. Here I summarize evolutionary rate analyses that can be applied to categorical and continuous endocrine traits, and also those for nucleic acid and protein-based components. I emphasize analyses that could be used to test whether other variables (e.g., ecology, ontogenetic timing of expression, etc.) are related to patterns of rate variation and endocrine component diversification. The application of phylogenetic-based rate analyses to comparative endocrine data will greatly enhance our understanding of the factors that have shaped endocrine system evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Dietary quality and encephalization in platyrrhine primates.

PubMed

Allen, Kari L; Kay, Richard F

2012-02-22

The high energetic costs of building and maintaining large brains are thought to constrain encephalization. The 'expensive-tissue hypothesis' (ETH) proposes that primates (especially humans) overcame this constraint through reduction of another metabolically expensive tissue, the gastrointestinal tract. Small guts characterize animals specializing on easily digestible diets. Thus, the hypothesis may be tested via the relationship between brain size and diet quality. Platyrrhine primates present an interesting test case, as they are more variably encephalized than other extant primate clades (excluding Hominoidea). We find a high degree of phylogenetic signal in the data for diet quality, endocranial volume and body size. Controlling for phylogenetic effects, we find no significant correlation between relative diet quality and relative endocranial volume. Thus, diet quality fails to account for differences in platyrrhine encephalization. One taxon, in particular, Brachyteles, violates predictions made by ETH in having a large brain and low-quality diet. Dietary reconstructions of stem platyrrhines further indicate that a relatively high-quality diet was probably in place prior to increases in encephalization. Therefore, it is unlikely that a shift in diet quality was a primary constraint release for encephalization in platyrrhines and, by extrapolation, humans.

Does aquatic foraging impact head shape evolution in snakes?

PubMed Central

Cornette, Raphaël; Fabre, Anne-Claire; Godoy-Diana, Ramiro; Herrel, Anthony

2016-01-01

Evolutionary trajectories are often biased by developmental and historical factors. However, environmental factors can also impose constraints on the evolutionary trajectories of organisms leading to convergence of morphology in similar ecological contexts. The physical properties of water impose strong constraints on aquatic feeding animals by generating pressure waves that can alert prey and potentially push them away from the mouth. These hydrodynamic constraints have resulted in the independent evolution of suction feeding in most groups of secondarily aquatic tetrapods. Despite the fact that snakes cannot use suction, they have invaded the aquatic milieu many times independently. Here, we test whether the aquatic environment has constrained head shape evolution in snakes and whether shape converges on that predicted by biomechanical models. To do so, we used three-dimensional geometric morphometrics and comparative, phylogenetically informed analyses on a large sample of aquatic snake species. Our results show that aquatic snakes partially conform to our predictions and have a narrower anterior part of the head and dorsally positioned eyes and nostrils. This morphology is observed, irrespective of the phylogenetic relationships among species, suggesting that the aquatic environment does indeed drive the evolution of head shape in snakes, thus biasing the evolutionary trajectory of this group of animals. PMID:27581887

The structural analysis of the mitochondrial SSUrRNA implies a close phylogenetic relationship between mitochondria from plants and from the heterotrophic alga Prototheca wickerhamii.

PubMed

Wolff, G; Kück, U

1990-04-01

The gene for the mitochondrial small subunit rRNA (SSUrRNA) from the heterotrophic alga Prototheca wickerhamii has been isolated from a gene library of extranuclear DNA. Sequence and structural analyses allow the determination of a secondary structure model for this rRNA. In addition, several sequence motifs are present which are typically found in SSUrRNAs of various mitochondrial origins. Unexpectedly, the Prototheca RNA sequence has more features in common with mitochondrial SSUrRNAs from plants than with that from the green alga Chlamydomonas reinhardtii. The phylogenetic relationship between mitochondria from plants and algae is discussed.

A rate-constrained fast full-search algorithm based on block sum pyramid.

PubMed

Song, Byung Cheol; Chun, Kang-Wook; Ra, Jong Beom

2005-03-01

This paper presents a fast full-search algorithm (FSA) for rate-constrained motion estimation. The proposed algorithm, which is based on the block sum pyramid frame structure, successively eliminates unnecessary search positions according to rate-constrained criterion. This algorithm provides the identical estimation performance to a conventional FSA having rate constraint, while achieving considerable reduction in computation.

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

Treesearch

Kasey K. Pham; Andrew L. Hipp; Paul S. Manos; Richard C. Cronn

2017-01-01

Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect...

Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins.

PubMed

Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor; Hermoso, Juan A

2013-01-09

Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as "short-chain" with the firmicutes flavodoxins and the "long-chain" with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

Phylogenetic support for the Tropical Niche Conservatism Hypothesis despite the absence of a clear latitudinal species richness gradient in Yunnan's woody flora

NASA Astrophysics Data System (ADS)

Tang, G.; Zhang, M. G.; Liu, C.; Zhou, Z.; Chen, W.; Slik, J. W. F.

2014-05-01

The Tropical Niche Conservatism Hypothesis (TCH) tries to explain the generally observed latitudinal gradient of increasing species diversity towards the tropics. To date, few studies have used phylogenetic approaches to assess its validity, even though such methods are especially suited to detect changes in niche structure. We test the TCH using modeled distributions of 1898 woody species in Yunnan Province (southwest China) in combination with a family level phylogeny. Unlike predicted, species richness and phylogenetic diversity did not show a latitudinal gradient, but identified two high diversity zones, one in Northwest and one in South Yunnan. Despite this, the underlying residual phylogenetic diversity showed a clear decline away from the tropics, while the species composition became progressingly more phylogenetically clustered towards the North. These latitudinal changes were strongly associated with more extreme temperature variability and declining precipitation and soil water availability, especially during the dry season. Our results suggests that the climatically more extreme conditions outside the tropics require adaptations for successful colonization, most likely related to the plant hydraulic system, that have been acquired by only a limited number of phylogenetically closely related plant lineages. We emphasize the importance of phylogenetic approaches for testing the TCH.

Enhanced use of phylogenetic data to inform public health approaches to HIV among MSM

PubMed Central

German, Danielle; Grabowski, Mary Kate; Beyrer, Chris

2017-01-01

The multi-dimensional nature and continued evolution of HIV epidemics among men who have sex with men (MSM) requires innovative intervention approaches. Strategies are needed that recognize the individual, social, and structural factors driving HIV transmission; that can pinpoint networks with heightened transmission risk; and that can help target intervention in real-time. HIV phylogenetics is a rapidly evolving field with strong promise for informing innovative responses to the HIV epidemic among MSM. Currently, HIV phylogenetic insights are providing new understandings of characteristics of HIV epidemics involving MSM, social networks influencing transmission, characteristics of HIV transmission clusters involving MSM, targets for antiretroviral and other prevention strategies, and dynamics of emergent epidemics. Maximizing the potential of HIV phylogenetics for HIV responses among MSM will require attention to key methodological challenges and ethical considerations, as well as resolving key implementation and scientific questions. Enhanced and integrated use of HIV surveillance, socio-behavioral, and phylogenetic data resources are becoming increasingly critical for informing public health approaches to HIV among MSM. PMID:27584826

Increased competition does not lead to increased phylogenetic overdispersion in a native grassland.

PubMed

Bennett, Jonathan A; Lamb, Eric G; Hall, Jocelyn C; Cardinal-McTeague, Warren M; Cahill, James F

2013-09-01

That competition is stronger among closely related species and leads to phylogenetic overdispersion is a common assumption in community ecology. However, tests of this assumption are rare and field-based experiments lacking. We tested the relationship between competition, the degree of relatedness, and overdispersion among plants experimentally and using a field survey in a native grassland. Relatedness did not affect competition, nor was competition associated with phylogenetic overdispersion. Further, there was only weak evidence for increased overdispersion at spatial scales where plants are likely to compete. These results challenge traditional theory, but are consistent with recent theories regarding the mechanisms of plant competition and its potential effect on phylogenetic structure. We suggest that specific conditions related to the form of competition and trait conservatism must be met for competition to cause phylogenetic overdispersion. Consequently, overdispersion as a result of competition is likely to be rare in natural communities. © 2013 John Wiley & Sons Ltd/CNRS.

Mammalian phylogenetic diversity-area relationships at a continental scale

PubMed Central

Mazel, Florent; Renaud, Julien; Guilhaumon, François; Mouillot, David; Gravel, Dominique; Thuiller, Wilfried

2015-01-01

In analogy to the species-area relationship (SAR), one of the few laws in Ecology, the phylogenetic diversity-area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increase with area. Although investigating PDAR has the potential to unravel the underlying processes shaping assemblages across spatial scales and to predict PD loss through habitat reduction, it has been little investigated so far. Focusing on PD has noticeable advantages compared to species richness (SR) since PD also gives insights on processes such as speciation/extinction, assembly rules and ecosystem functioning. Here we investigate the universality and pervasiveness of the PDAR at continental scale using terrestrial mammals as study case. We define the relative robustness of PD (compared to SR) to habitat loss as the area between the standardized PDAR and standardized SAR (i.e. standardized by the diversity of the largest spatial window) divided by the area under the standardized SAR only. This metric quantifies the relative increase of PD robustness compared to SR robustness. We show that PD robustness is higher than SR robustness but that it varies among continents. We further use a null model approach to disentangle the relative effect of phylogenetic tree shape and non random spatial distribution of evolutionary history on the PDAR. We find that for most spatial scales and for all continents except Eurasia, PDARs are not different from expected by a model using only the observed SAR and the shape of the phylogenetic tree at continental scale. Interestingly, we detect a strong phylogenetic structure of the Eurasian PDAR that can be predicted by a model that specifically account for a finer biogeographical delineation of this continent. In conclusion, the relative robustness of PD to habitat loss compared to species richness is determined by the phylogenetic tree shape but also depends on the spatial structure of PD. PMID:26649401

ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)

PubMed Central

2008-01-01

Background Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment. Results The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae. Conclusion In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics. PMID:18655698

[A phylogenetic analysis of plant communities of Teberda Biosphere Reserve].

PubMed

Shulakov, A A; Egorov, A V; Onipchenko, V G

2016-01-01

Phylogenetic analysis of communities is based on the comparison of distances on the phylogenetic tree between species of a community under study and those distances in random samples taken out of local flora. It makes it possible to determine to what extent a community composition is formed by more closely related species (i.e., "clustered") or, on the opposite, it is more even and includes species that are less related with each other. The first case is usually interpreted as a result of strong influence caused by abiotic factors, due to which species with similar ecology, a priori more closely related, would remain: In the second case, biotic factors, such as competition, may come to the fore and lead to forming a community out of distant clades due to divergence of their ecological niches: The aim of this' study Was Ad explore the phylogenetic structure in communities of the northwestern Caucasus at two spatial scales - the scale of area from 4 to 100 m2 and the smaller scale within a community. The list of local flora of the alpine belt has been composed using the database of geobotanic descriptions carried out in Teberda Biosphere Reserve at true altitudes exceeding.1800 m. It includes 585 species of flowering plants belonging to 57 families. Basal groups of flowering plants are.not represented in the list. At the scale of communities of three classes, namely Thlaspietea rotundifolii - commumties formed on screes and pebbles, Calluno-Ulicetea - alpine meadow, and Mulgedio-Aconitetea subalpine meadows, have not demonstrated significant distinction of phylogenetic structure. At intra level, for alpine meadows the larger share of closely related species. (clustered community) is detected. Significantly clustered happen to be those communities developing on rocks (class Asplenietea trichomanis) and alpine (class Juncetea trifidi). At the same time, alpine lichen proved to have even phylogenetic structure at the small scale. Alpine (class Salicetea herbaceae) that develop under conditions of winter snow accumulation were more,even at the both.scale, i.e., contained more diverse and distantly related plant species compared with random samples. (Scheuchzerio-Caricetea fuscae) aquatic communities in cold (Montio-Cardaminetea), sedge meadows (Carici rupestris-Kobresietea bellardii), and communities, in which shrubs and predominated (juniper and rhododendron elfin woods, class Loiseleurio-Vaccinietea), have been studied only at the larger scale and showed significant evenness of species composition, i.e., were phylogenetically more diverse compared with random samples.

Revision of “Balaena” belgica reveals a new right whale species, the possible ancestry of the northern right whale, Eubalaena glacialis, and the ages of divergence for the living right whale species

PubMed Central

Bosselaers, Mark

2017-01-01

In 1941, Abel established Balaena belgica based on a series of fused cervical vertebrae and citing other cranial fragments from the late Neogene of the Antwerp harbor (northern Belgium). Later, Plisnier-Ladame & Quinet (1969) added a neurocranium and other skeletal remains from the same area to this species. Recently, the neurocranium was re-assigned to the genus Eubalaena thanks to newer phylogenetic analyses. Here, a new description is provided of materials previously assigned to “Balaena” belgica together with taxonomic revisions. Our work suggests that the cervical complex originally designated as the type of “Balaena” belgica is too poorly preserved to be used as such and is assigned to Balaenidae gen. et sp. indet., thus making “Balaena” belgica a nomen dubium. In addition to the neurocranium, the other remains consist in a fragment of maxilla assigned to Balaenidae gen. et sp. indet. and in a humerus assigned to Eubalaena sp. Discovered in the Kruisschans Sands Member of the Lillo Formation (3.2–2.8 Ma, Piacenzian, Late Pliocene), the neurocranium is designated as the holotype of the new species Eubalaena ianitrix. Our phylogenetic analysis supports a sister-group relationship of Eubalaena ianitrix and Eubalaena glacialis, and helps constraining the ages of origin for balaenid clades. Ecological and phylogenetic data suggest that Eubalaena ianitrix may represent the direct ancestor of Eubalaena glacialis, the latter having evolved through phyletic transformation including body size increase during the temperature decline of the Late Pliocene. PMID:28663936

Lack of host specificity of copepod crustaceans associated with mushroom corals in the Red Sea.

PubMed

Ivanenko, Viatcheslav N; Hoeksema, Bert W; Mudrova, Sofya V; Nikitin, Mikhail A; Martínez, Alejandro; Rimskaya-Korsakova, Nadezda N; Berumen, Michael L; Fontaneto, Diego

2018-06-14

The radiation of symbiotic copepods (Crustacea: Copepoda) living in association with stony corals (Cnidaria: Scleractinia) is considered host-specific and linked to the phylogenetic diversification of their hosts. However, symbiotic copepods are poorly investigated, occurrence records are mostly anecdotal, and no explicit analysis exists regarding their relationship with the hosts. Here, we analysed the occurrence of symbiotic copepods on different co-occurring and phylogenetically closely related scleractinian corals. We used an innovative approach of DNA extraction from single microscopic specimens that preserves the shape of the organisms for integrative morphological studies. The rationale of the study involved: (i) sampling of mushroom corals (Fungiidae) belonging to 13 species and eight genera on different reefs along the Saudi coastline in the Red Sea, (ii) extraction of all the associated copepods, (iii) morphological screening and identification of copepod species, (iv) use of DNA taxonomy on mitochondrial and nuclear markers to determine species boundaries for morphologically unknown copepod species, (v) reconstruction of phylogenies to understand their evolutionary relationships, and (vi) analysis of the ecological drivers of the occurrence, diversity and host specificity of the copepods. The seven species of coral-associated copepods, all new to science, did not show any statistically significant evidence of host-specificity or other pattern of ecological association. We thus suggest that, contrary to most assumptions and previous anecdotal evidence on this coral-copepod host-symbiont system, the association between copepods and their host corals is rather labile, not strict, and not phylogenetically constrained, changing our perception on evolutionary patterns and processes in symbiotic copepods. Copyright © 2018. Published by Elsevier Inc.

Revision of "Balaena" belgica reveals a new right whale species, the possible ancestry of the northern right whale, Eubalaena glacialis, and the ages of divergence for the living right whale species.

PubMed

Bisconti, Michelangelo; Lambert, Olivier; Bosselaers, Mark

2017-01-01

In 1941, Abel established Balaena belgica based on a series of fused cervical vertebrae and citing other cranial fragments from the late Neogene of the Antwerp harbor (northern Belgium). Later, Plisnier-Ladame & Quinet (1969) added a neurocranium and other skeletal remains from the same area to this species. Recently, the neurocranium was re-assigned to the genus Eubalaena thanks to newer phylogenetic analyses. Here, a new description is provided of materials previously assigned to " Balaena " belgica together with taxonomic revisions. Our work suggests that the cervical complex originally designated as the type of " Balaena " belgica is too poorly preserved to be used as such and is assigned to Balaenidae gen. et sp. indet., thus making " Balaena " belgica a nomen dubium. In addition to the neurocranium, the other remains consist in a fragment of maxilla assigned to Balaenidae gen. et sp. indet. and in a humerus assigned to Eubalaena sp. Discovered in the Kruisschans Sands Member of the Lillo Formation (3.2-2.8 Ma, Piacenzian, Late Pliocene), the neurocranium is designated as the holotype of the new species Eubalaena ianitrix . Our phylogenetic analysis supports a sister-group relationship of Eubalaena ianitrix and Eubalaena glacialis , and helps constraining the ages of origin for balaenid clades. Ecological and phylogenetic data suggest that Eubalaena ianitrix may represent the direct ancestor of Eubalaena glacialis , the latter having evolved through phyletic transformation including body size increase during the temperature decline of the Late Pliocene.

Early Miocene hippopotamids (Cetartiodactyla) constrain the phylogenetic and spatiotemporal settings of hippopotamid origin

PubMed Central

Orliac, Maeva; Boisserie, Jean-Renaud; MacLatchy, Laura; Lihoreau, Fabrice

2010-01-01

The affinities of the Hippopotamidae are at the core of the phylogeny of Cetartiodactyla (even-toed mammals: cetaceans, ruminants, camels, suoids, and hippos). Molecular phylogenies support Cetacea as sister group of the Hippopotamidae, implying a long ghost lineage between the earliest cetaceans (∼53 Ma) and the earliest hippopotamids (∼16 Ma). Morphological studies have proposed two different sister taxa for hippopotamids: suoids (notably palaeochoerids) or anthracotheriids. Evaluating these phylogenetic hypotheses requires substantiating the poorly known early history of the Hippopotamidae. Here, we undertake an original morphological phylogenetic analysis including several “suiform” families and previously unexamined early Miocene taxa to test previous conflicting hypotheses. According to our results, Morotochoerus ugandensis and Kulutherium rusingensis, until now regarded as the sole African palaeochoerid and the sole African bunodont anthracotheriid, respectively, are unambiguously included within the Hippopotamidae. They are the earliest known hippopotamids and set the family fossil record back to the early Miocene (∼21 Ma). The analysis reveals that hippopotamids displayed an unsuspected taxonomic and body size diversity and remained restricted to Africa during most of their history, until the latest Miocene. Our results also confirm the deep nesting of Hippopotamidae within the paraphyletic Anthracotheriidae; this finding allows us to reconstruct the sequence of dental innovations that links advanced selenodont anthracotheriids to hippopotamids, previously a source of major disagreements on hippopotamid origins. The analysis demonstrates a close relationship between Eocene choeropotamids and anthracotheriids, a relationship that potentially fills the evolutionary gap between earliest hippopotamids and cetaceans implied by molecular analyses. PMID:20547829

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis.

PubMed

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence.

Recovery of Forest and Phylogenetic Structure in Abandoned Cocoa Agroforestry in the Atlantic Forest of Brazil.

PubMed

Rolim, Samir Gonçalves; Sambuichi, Regina Helena Rosa; Schroth, Götz; Nascimento, Marcelo Trindade; Gomes, José Manoel Lucio

2017-03-01

Cocoa agroforests like the cabrucas of Brazil's Atlantic forest are among the agro-ecosystems with greatest potential for biodiversity conservation. Despite a global trend for their intensification, cocoa agroforests are also being abandoned for socioeconomic reasons especially on marginal sites, because they are incorporated in public or private protected areas, or are part of mandatory set-asides under Brazilian environmental legislation. However, little is known about phylogenetic structure, the processes of forest regeneration after abandonment and the conservation value of former cabruca sites. Here we compare the vegetation structure and composition of a former cabruca 30-40 years after abandonment with a managed cabruca and mature forest in the Atlantic forest region of Espirito Santo, Brazil. The forest in the abandoned cabruca had recovered a substantial part of its original structure. Abandoned cabruca have a higher density (mean ± CI95 %: 525.0 ± 40.3 stems per ha), basal area (34.0 ± 6.5 m 2 per ha) and species richness (148 ± 11.5 species) than managed cabruca (96.0 ± 17.7; 24.15 ± 3.9 and 114.5 ± 16.0, respectively) but no significant differences to mature forest in density (581.0 ± 42.2), basal area (29.9.0 ± 3.3) and species richness (162.6 ± 15.5 species). Thinning (understory removal) changes phylogenetic structure from evenness in mature forest to clustering in managed cabruca, but after 30-40 years abandoned cabruca had a random phylogenetic structure, probably due to a balance between biotic and abiotic filters at this age. We conclude that abandoned cocoa agroforests present highly favorable conditions for the regeneration of Atlantic forest and could contribute to the formation of an interconnected network of forest habitat in this biodiversity hotspot.

A comparative study of the inner ear structures of artiodactyls and early cetaceans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klingshirn, M.A.; Luo, Z.

1994-12-31

It has been suggested that the order Cetacea (whales and porpoises) are closely related to artiodactyls, even-hoofed ungulate mammals such as the pig and cow. Paleontological and molecular data strongly supports this concept of phylogenetic relationships. In a study of DNA sequences of two mitochondrial ribosomal gene segments of cetaceans, the artiodactyls were found to be closest related to Cetaceans. These well accepted studies on the phylogenetic affinities of artiodactyls and cetaceans cause us to conduct a comparative study of the bony structure of the inner ear of these two taxa.

pez: phylogenetics for the environmental sciences.

PubMed

Pearse, William D; Cadotte, Marc W; Cavender-Bares, Jeannine; Ives, Anthony R; Tucker, Caroline M; Walker, Steve C; Helmus, Matthew R

2015-09-01

pez is an R package that permits measurement, modelling and simulation of phylogenetic structure in ecological data. pez contains the first implementation of many methods in R, and aggregates existing data structures and methods into a single, coherent package. pez is released under the GPL v3 open-source license, available on the Internet from CRAN (http://cran.r-project.org). The package is under active development, and the authors welcome contributions (see http://github.com/willpearse/pez). will.pearse@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Efficient Transition State Optimization of Periodic Structures through Automated Relaxed Potential Energy Surface Scans.

PubMed

Plessow, Philipp N

2018-02-13

This work explores how constrained linear combinations of bond lengths can be used to optimize transition states in periodic structures. Scanning of constrained coordinates is a standard approach for molecular codes with localized basis functions, where a full set of internal coordinates is used for optimization. Common plane wave-codes for periodic boundary conditions almost exlusively rely on Cartesian coordinates. An implementation of constrained linear combinations of bond lengths with Cartesian coordinates is described. Along with an optimization of the value of the constrained coordinate toward the transition states, this allows transition optimization within a single calculation. The approach is suitable for transition states that can be well described in terms of broken and formed bonds. In particular, the implementation is shown to be effective and efficient in the optimization of transition states in zeolite-catalyzed reactions, which have high relevance in industrial processes.

Applications of Ecophylogenetics to Benthic Communities in the Northern Gulf of Mexico: Do Functional Traits Follow Phylogeny?

NASA Astrophysics Data System (ADS)

Gadeken, K.; Dorgan, K. M.; Moore, J.; Berke, S. K.

2016-02-01

Evolutionary relationships may shed light on observed patterns of diversity and functional traits when viewed through the lens of phylogeny. The potential for phylogenetic information to be used to explain patterns in community structure, such as niche partitioning and responses to stress, is extensive. Differential distribution of related species with similar functional traits suggests niche partitioning, and local redundancy in functional traits may indicate the potential for interspecific competition. In this study, we investigated phylogenetic and functional diversity as a function of habitat for sites with varying levels of oil contamination in the Northern Gulf of Mexico. Our study was conducted in a shallow benthic community at the Chandeleur Islands, a group of uninhabited barrier islands. Infauna were sampled from seagrass (Halodule wrightii) and bare sediment at three sites along the island chain that experienced variable levels of oil impact from the Deepwater Horizon oil spill. Individuals were preserved and 18S and COI genes sequenced, and a phylogenetic tree was constructed of the local community using maximum likelihood. Phylogenetic diversity and evenness were quantified. Ecologically important functional traits were then compiled into respective distance matrices, evaluated through different functional diversity indices, and assessed for correlation with the phylogeny. This integration of functional and phylogenetic diversity has the potential to provide greater insight into factors driving community structure than either metric alone. Determining relevant metrics of diversity is critical to understanding the ecological effects of major disturbances such as oil spills.

Bayes factors for testing inequality constrained hypotheses: Issues with prior specification.

PubMed

Mulder, Joris

2014-02-01

Several issues are discussed when testing inequality constrained hypotheses using a Bayesian approach. First, the complexity (or size) of the inequality constrained parameter spaces can be ignored. This is the case when using the posterior probability that the inequality constraints of a hypothesis hold, Bayes factors based on non-informative improper priors, and partial Bayes factors based on posterior priors. Second, the Bayes factor may not be invariant for linear one-to-one transformations of the data. This can be observed when using balanced priors which are centred on the boundary of the constrained parameter space with a diagonal covariance structure. Third, the information paradox can be observed. When testing inequality constrained hypotheses, the information paradox occurs when the Bayes factor of an inequality constrained hypothesis against its complement converges to a constant as the evidence for the first hypothesis accumulates while keeping the sample size fixed. This paradox occurs when using Zellner's g prior as a result of too much prior shrinkage. Therefore, two new methods are proposed that avoid these issues. First, partial Bayes factors are proposed based on transformed minimal training samples. These training samples result in posterior priors that are centred on the boundary of the constrained parameter space with the same covariance structure as in the sample. Second, a g prior approach is proposed by letting g go to infinity. This is possible because the Jeffreys-Lindley paradox is not an issue when testing inequality constrained hypotheses. A simulation study indicated that the Bayes factor based on this g prior approach converges fastest to the true inequality constrained hypothesis. © 2013 The British Psychological Society.

A phylogeny of Cichlidogyrus spp. (Monogenea, Dactylogyridea) clarifies a host-switch between fish families and reveals an adaptive component to attachment organ morphology of this parasite genus.

PubMed

Messu Mandeng, Françoise D; Bilong Bilong, Charles F; Pariselle, Antoine; Vanhove, Maarten P M; Bitja Nyom, Arnold R; Agnèse, Jean-François

2015-11-10

Parasite switches to new host species are of fundamental scientific interest and may be considered an important speciation mechanism. For numerous monogenean fish parasites, infecting different hosts is associated with morphological adaptations, in particular of the attachment organ (haptor). However, haptoral morphology in Cichlidogyrus spp. (Monogenea, Dactylogyridea), parasites of African cichlids, has been mainly linked to phylogenetic rather than to host constraints. Here we determined the position of Cichlidogyrus amieti, a parasite of species of Aphyosemion (Cyprinodontiformes, Nothobranchiidae) in the phylogeny of its congeners in order to infer its origin and assess the morphological changes associated with host-switching events. The DNA of specimens of C. amieti isolated from Aphyosemion cameronense in Cameroon was sequenced and analyzed together with that of Cichlidogyrus spp. from cichlid hosts. In order to highlight the influence of the lateral transfer of C. amieti on the haptoral sclerotised parts we performed a Principal Component Analysis (PCA) to compare the attachment organ structure of C. amieti to that of congeners infecting cichlids. Cichlidogyrus amieti was found to be nested within a strongly supported clade of species described from Hemichromis spp. (i.e. C. longicirrus and C. dracolemma). This clade is located at a derived position of the tree, suggesting that C. amieti transferred from cichlids to Cyprinodontiformes and not inversely. The morphological similarity between features of their copulatory organs suggested that C. amieti shares a recent ancestor with C. dracolemma. It also indicates that in this case, these organs do not seem subjected to strong divergent selection pressure. On the other hand, there are substantial differences in haptoral morphology between C. amieti and all of its closely related congeners described from Hemichromis spp.. Our study provides new evidence supporting the hypothesis of the adaptive nature of haptor morphology. It demonstrates this adaptive component for the first time within Cichlidogyrus, the attachment organs of which were usually considered to be mainly phylogenetically constrained.

A new phylogenetic diversity measure generalizing the shannon index and its application to phyllostomid bats.

PubMed

Allen, Benjamin; Kon, Mark; Bar-Yam, Yaneer

2009-08-01

Protecting biodiversity involves preserving the maximum number and abundance of species while giving special attention to species with unique genetic or morphological characteristics. In balancing different priorities, conservation policymakers may consider quantitative measures that compare diversity across ecological communities. To serve this purpose, a measure should increase or decrease with changes in community composition in a way that reflects what is valued, including species richness, evenness, and distinctness. However, counterintuitively, studies have shown that established indices, including those that emphasize average interspecies phylogenetic distance, may increase with the elimination of species. We introduce a new diversity index, the phylogenetic entropy, which generalizes in a natural way the Shannon index to incorporate species relatedness. Phylogenetic entropy favors communities in which highly distinct species are more abundant, but it does not advocate decreasing any species proportion below a community structure-dependent threshold. We contrast the behavior of multiple indices on a community of phyllostomid bats in the Selva Lacandona. The optimal genus distribution for phylogenetic entropy populates all genera in a linear relationship to their total phylogenetic distance to other genera. Two other indices favor eliminating 12 out of the 23 genera.

Phylogenetic diversity of ceftriaxone resistance and the presence of extended-spectrum β-lactamase genes in the culturable soil resistome.

PubMed

Pagaling, Eulyn; Gatica, Joao; Yang, Kun; Cytryn, Eddie; Yan, Tao

2016-09-01

The aim of this study was to determine the phylogenetic diversity of ceftriaxone resistance and the presence of known extended-spectrum β-lactamase (ESBL) genes in culturable soil resistomes. Libraries of soil bacterial isolates resistant to ceftriaxone were established from six physicochemically diverse soils collected in Hawaii (USA) and Israel. The phylogenetic affiliation, ceftriaxone and multidrug resistance levels, and presence of known ESBL genes of the isolates were determined. The soil bacterial isolates were phylogenetically grouped with the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. Ceftriaxone minimum inhibitory concentrations (MICs) largely followed the phylogeny structure and higher levels of ceftriaxone resistance corresponded to higher multidrug resistance. Three distinct blaTEM variants were detected in soil bacterial isolates belonging to nine different genera. In conclusion, the culturable soil resistomes for ceftriaxone exhibited high phylogenetic diversity and multidrug resistance. blaTEM was the only known ESBL detected in the soil resistomes, and its distribution in different phylogenetic groups suggests its ubiquitous presence and/or possible horizontal gene transfer within the soil microbiomes. Copyright © 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Electrode assemblies, plasma generating apparatuses, and methods for generating plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kong, Peter C.; Grandy, Jon D.; Detering, Brent A.

Electrode assemblies for plasma reactors include a structure or device for constraining an arc endpoint to a selected area or region on an electrode. In some embodiments, the structure or device may comprise one or more insulating members covering a portion of an electrode. In additional embodiments, the structure or device may provide a magnetic field configured to control a location of an arc endpoint on the electrode. Plasma generating modules, apparatus, and systems include such electrode assemblies. Methods for generating a plasma include covering at least a portion of a surface of an electrode with an electrically insulating membermore » to constrain a location of an arc endpoint on the electrode. Additional methods for generating a plasma include generating a magnetic field to constrain a location of an arc endpoint on an electrode.« less

Electrode assemblies, plasma apparatuses and systems including electrode assemblies, and methods for generating plasma

DOEpatents

Kong, Peter C; Grandy, Jon D; Detering, Brent A; Zuck, Larry D

2013-09-17

Electrode assemblies for plasma reactors include a structure or device for constraining an arc endpoint to a selected area or region on an electrode. In some embodiments, the structure or device may comprise one or more insulating members covering a portion of an electrode. In additional embodiments, the structure or device may provide a magnetic field configured to control a location of an arc endpoint on the electrode. Plasma generating modules, apparatus, and systems include such electrode assemblies. Methods for generating a plasma include covering at least a portion of a surface of an electrode with an electrically insulating member to constrain a location of an arc endpoint on the electrode. Additional methods for generating a plasma include generating a magnetic field to constrain a location of an arc endpoint on an electrode.

Octocoral Species Assembly and Coexistence in Caribbean Coral Reefs.

PubMed

Velásquez, Johanna; Sánchez, Juan A

2015-01-01

What are the determinant factors of community assemblies in the most diverse ecosystem in the ocean? Coral reefs can be divided in continental (i.e., reefs that develop on the continental shelf, including siliciclastic reefs) and oceanic (i.e., far off the continental shelf, usually on volcanic substratum); whether or not these habitat differences impose community-wide ecological divergence or species exclusion/coexistence with evolutionary consequences, is unknown. Studying Caribbean octocorals as model system, we determined the phylogenetic community structure in a coral reef community, making emphasis on species coexistence evidenced on trait evolution and environmental feedbacks. Forty-nine species represented in five families constituted the species pool from which a phylogenetic tree was reconstructed using mtDNA. We included data from 11 localities in the Western Caribbean (Colombia) including most reef types. To test diversity-environment and phenotype-environment relationships, phylogenetic community structure and trait evolution we carried out comparative analyses implementing ecological and evolutionary approaches. Phylogenetic inferences suggest clustering of oceanic reefs (e.g., atolls) contrasting with phylogenetic overdispersion of continental reefs (e.g., reefs banks). Additionally, atolls and barrier reefs had the highest species diversity (Shannon index) whereas phylogenetic diversity was higher in reef banks. The discriminant component analysis supported this differentiation between oceanic and continental reefs, where continental octocoral species tend to have greater calyx apertures, thicker branches, prominent calyces and azooxanthellate species. This analysis also indicated a clear separation between the slope and the remaining habitats, caused by the presence or absence of Symbiodinium. K statistic analysis showed that this trait is conserved as well as the branch shape. There was strong octocoral community structure with opposite diversity and composition patterns between oceanic and continental reefs. Even habitats with similar depths and overall environmental conditions did not share similar communities between oceanic and continental reefs. This indicates a strong regional influence over the local communities, probably due to water transparency differences between major reef types, i.e., oceanic vs. continental shelf-neritic. This was supported by contrasting patterns found in morphology, composition and evolutionary history of the species between atolls and reef banks.

Octocoral Species Assembly and Coexistence in Caribbean Coral Reefs

PubMed Central

Velásquez, Johanna; Sánchez, Juan A.

2015-01-01

Background What are the determinant factors of community assemblies in the most diverse ecosystem in the ocean? Coral reefs can be divided in continental (i.e., reefs that develop on the continental shelf, including siliciclastic reefs) and oceanic (i.e., far off the continental shelf, usually on volcanic substratum); whether or not these habitat differences impose community-wide ecological divergence or species exclusion/coexistence with evolutionary consequences, is unknown. Methods Studying Caribbean octocorals as model system, we determined the phylogenetic community structure in a coral reef community, making emphasis on species coexistence evidenced on trait evolution and environmental feedbacks. Forty-nine species represented in five families constituted the species pool from which a phylogenetic tree was reconstructed using mtDNA. We included data from 11 localities in the Western Caribbean (Colombia) including most reef types. To test diversity-environment and phenotype-environment relationships, phylogenetic community structure and trait evolution we carried out comparative analyses implementing ecological and evolutionary approaches. Results Phylogenetic inferences suggest clustering of oceanic reefs (e.g., atolls) contrasting with phylogenetic overdispersion of continental reefs (e.g., reefs banks). Additionally, atolls and barrier reefs had the highest species diversity (Shannon index) whereas phylogenetic diversity was higher in reef banks. The discriminant component analysis supported this differentiation between oceanic and continental reefs, where continental octocoral species tend to have greater calyx apertures, thicker branches, prominent calyces and azooxanthellate species. This analysis also indicated a clear separation between the slope and the remaining habitats, caused by the presence or absence of Symbiodinium. K statistic analysis showed that this trait is conserved as well as the branch shape. Discussion There was strong octocoral community structure with opposite diversity and composition patterns between oceanic and continental reefs. Even habitats with similar depths and overall environmental conditions did not share similar communities between oceanic and continental reefs. This indicates a strong regional influence over the local communities, probably due to water transparency differences between major reef types, i.e., oceanic vs. continental shelf-neritic. This was supported by contrasting patterns found in morphology, composition and evolutionary history of the species between atolls and reef banks. PMID:26177191

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages.

PubMed

Fukasawa, Yoshinori; Oda, Toshiyuki; Tomii, Kentaro; Imai, Kenichiro

2017-07-01

Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases' evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Spatial diversity of bacterioplankton communities in surface water of northern South China Sea.

PubMed

Li, Jialin; Li, Nan; Li, Fuchao; Zou, Tao; Yu, Shuxian; Wang, Yinchu; Qin, Song; Wang, Guangyi

2014-01-01

The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS). Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones) and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.

Oil-producing flowers within the Iridoideae (Iridaceae): evolutionary trends in the flowers of the New World genera

PubMed Central

Chauveau, Olivier; Eggers, Lilian; Souza-Chies, Tatiana T.; Nadot, Sophie

2012-01-01

Background and Aims Oil-producing flowers related to oil-bee pollination are a major innovation in Neotropical and Mexican Iridaceae. In this study, phylogenetic relationships were investigated among a wide array of New World genera of the tribes Sisyrinchieae, Trimezieae and Tigridieae (Iridaceae: Iridoideae) and the evolution of floral glandular structures, which are predominantly trichomal elaiophores, was examined in relation to the diversification of New World Iridaceae. Methods Phylogenetic analyses based on seven molecular markers obtained from 97 species were conducted to produce the first extensive phylogeny of the New World tribes of subfamily Iridoideae. The resulting phylogenetic hypothesis was used to trace the evolutionary history of glandular structures present in the flowers of numerous species in each tribe. Hypotheses of differential diversification rates among lineages were also investigated using both topological and Binary-State Speciation and Extinction methods. Key Results and Conclusions Floral glandular structures and especially trichomal elaiophores evolved multiple times independently in the American tribes of Iridoideae. The distribution pattern of species displaying glandular trichomes across the phylogeny reveals lability in the pollination system and suggests that these structures may have played a significant role in the diversification of the Iridoideae on the American continent. PMID:22782239

Evolutionary implications of phylogenetic analyses of the gene transfer agent (GTA) of Rhodobacter capsulatus.

PubMed

Lang, Andrew S; Taylor, Terumi A; Beatty, J Thomas

2002-11-01

The gene transfer agent (GTA) of the a-proteobacterium Rhodobacter capsulatus is a cell-controlled genetic exchange vector. Genes that encode the GTA structure are clustered in a 15-kb region of the R. capsulatus chromosome, and some of these genes show sequence similarity to known bacteriophage head and tail genes. However, the production of GTA is controlled at the level of transcription by a cellular two-component signal transduction system. This paper describes homologues of both the GTA structural gene cluster and the GTA regulatory genes in the a-proteobacteria Rhodopseudomonas palustris, Rhodobacter sphaeroides, Caulobacter crescentus, Agrobacterium tumefaciens and Brucella melitensis. These sequences were used in a phylogenetic tree approach to examine the evolutionary relationships of selected GTA proteins to these homologues and (pro)phage proteins, which was compared to a 16S rRNA tree. The data indicate that a GTA-like element was present in a single progenitor of the extant species that contain both GTA structural cluster and regulatory gene homologues. The evolutionary relationships of GTA structural proteins to (pro)phage proteins indicated by the phylogenetic tree patterns suggest a predominantly vertical descent of GTA-like sequences in the a-proteobacteria and little past gene exchange with (pro)phages.

Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

PubMed

Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

2016-01-01

The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp)

PubMed Central

Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

2016-01-01

The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research. PMID:27509049

Trait-based assembly and phylogenetic structure in northeast Pacific rockfish assemblages.

PubMed

Ingram, Travis; Shurin, Jonathan B

2009-09-01

If natural communities are assembled according to deterministic rules, coexisting species will represent a nonrandom subset of the potential species pool. We tested for signatures of assembly rules in the distribution of species' traits in Pacific rockfish (Sebastes spp.) assemblages. We used morphology, dietary niche (estimated with stable nitrogen isotopes), and distribution data to identify traits that relate to local-scale resource use (the alpha-niche) and to environmental gradients (the beta-niche). We showed that gill raker morphology was related to trophic position (an alpha-niche axis), while relative eye size was associated with depth habitat (a beta-niche axis). We therefore hypothesized that, within assemblages of coexisting rockfish species, the gill raker trait would be overdispersed (evenly spaced) due to limiting similarity, while relative eye size would be clustered due to environmental filtering. We examined the evolutionary relatedness of coexisting species to ask whether phylogenetic community structure and trait distributions gave similar indications about the roles of assembly processes. We tested the trait distributions and phylogenetic structure of 30 published rockfish assemblages against a null model of random community assembly. As predicted, the gill raker trait tended to be more evenly spaced than expected by chance, as did overall body size, while relative eye size was more clustered than expected. Phylogenetic community structure appeared to reflect historical dispersal and speciation and did not provide consistent support for assembly rules. Our results indicate that rockfish community assembly is nonrandom with regard to species' traits and show how distinguishing traits related to the alpha- and beta-niches and incorporating functional morphology can provide for powerful tests of assembly rules.

Parallel or convergent evolution in human population genomic data revealed by genotype networks.

PubMed

R Vahdati, Ali; Wagner, Andreas

2016-08-02

Genotype networks are representations of genetic variation data that are complementary to phylogenetic trees. A genotype network is a graph whose nodes are genotypes (DNA sequences) with the same broadly defined phenotype. Two nodes are connected if they differ in some minimal way, e.g., in a single nucleotide. We analyze human genome variation data from the 1,000 genomes project, and construct haploid genotype (haplotype) networks for 12,235 protein coding genes. The structure of these networks varies widely among genes, indicating different patterns of variation despite a shared evolutionary history. We focus on those genes whose genotype networks show many cycles, which can indicate homoplasy, i.e., parallel or convergent evolution, on the sequence level. For 42 genes, the observed number of cycles is so large that it cannot be explained by either chance homoplasy or recombination. When analyzing possible explanations, we discovered evidence for positive selection in 21 of these genes and, in addition, a potential role for constrained variation and purifying selection. Balancing selection plays at most a small role. The 42 genes with excess cycles are enriched in functions related to immunity and response to pathogens. Genotype networks are representations of genetic variation data that can help understand unusual patterns of genomic variation.

Constrained hierarchical least square nonlinear equation solvers. [for indefinite stiffness and large structural deformations

NASA Technical Reports Server (NTRS)

Padovan, J.; Lackney, J.

1986-01-01

The current paper develops a constrained hierarchical least square nonlinear equation solver. The procedure can handle the response behavior of systems which possess indefinite tangent stiffness characteristics. Due to the generality of the scheme, this can be achieved at various hierarchical application levels. For instance, in the case of finite element simulations, various combinations of either degree of freedom, nodal, elemental, substructural, and global level iterations are possible. Overall, this enables a solution methodology which is highly stable and storage efficient. To demonstrate the capability of the constrained hierarchical least square methodology, benchmarking examples are presented which treat structure exhibiting highly nonlinear pre- and postbuckling behavior wherein several indefinite stiffness transitions occur.

Estimating free-body modal parameters from tests of a constrained structure

NASA Technical Reports Server (NTRS)

Cooley, Victor M.

1993-01-01

Hardware advances in suspension technology for ground tests of large space structures provide near on-orbit boundary conditions for modal testing. Further advances in determining free-body modal properties of constrained large space structures have been made, on the analysis side, by using time domain parameter estimation and perturbing the stiffness of the constraints over multiple sub-tests. In this manner, passive suspension constraint forces, which are fully correlated and therefore not usable for spectral averaging techniques, are made effectively uncorrelated. The technique is demonstrated with simulated test data.

Microbial Fingerprints of Community Structure Correlate with Changes in Ecosystem Function Induced by Perturbing the Redox Environment

NASA Astrophysics Data System (ADS)

Mills, A. L.; Ford, R. M.; Vallino, J. J.; Herman, J. S.; Hornberger, G. M.

2001-12-01

Restoration of high-quality groundwater has been an elusive engineering goal. Consequently, natural microbially-mediated reactions are increasingly relied upon to degrade organic contaminants, including hydrocarbons and many synthetic compounds. Of concern is how the introduction of an organic chemical contaminant affects the indigenous microbial communities, the geochemistry of the aquifer, and the function of the ecosystem. The presence of functional redundancy in microbial communities suggests that recovery of the community after a disturbance such as a contamination event could easily result in a community that is similar in function to that which existed prior to the contamination, but which is compositionally quite different. To investigate the relationship between community structure and function we observed the response of a diverse microbial community obtained from raw sewage to a dynamic redox environment using an aerobic/anaerobic/aerobic cycle. To evaluate changes in community function CO2, pH, ammonium and nitrate levels were monitored. A phylogenetically-based DNA technique (tRFLP) was used to assess changes in microbial community structure. Principal component analysis of the tRFLP data revealed significant changes in the composition of the microbial community that correlated well with changes in community function. Results from our experiments will be discussed in the context of a metabolic model based the biogeochemistry of the system. The governing philosophy of this thermodynamically constrained metabolic model is that living systems synthesize and allocate cellular machinery in such a way as to "optimally" utilize available resources in the environment. The robustness of this optimization-based approach provides a powerful tool for studying relationships between microbial diversity and ecosystem function.

Phylogenetic and structural response of heterotrophic bacteria to dissolved organic matter of different chemical composition in a continuous culture study.

PubMed

Landa, M; Cottrell, M T; Kirchman, D L; Kaiser, K; Medeiros, P M; Tremblay, L; Batailler, N; Caparros, J; Catala, P; Escoubeyrou, K; Oriol, L; Blain, S; Obernosterer, I

2014-06-01

Dissolved organic matter (DOM) and heterotrophic bacteria are highly diverse components of the ocean system, and their interactions are key in regulating the biogeochemical cycles of major elements. How chemical and phylogenetic diversity are linked remains largely unexplored to date. To investigate interactions between bacterial diversity and DOM, we followed the response of natural bacterial communities to two sources of phytoplankton-derived DOM over six bacterial generation times in continuous cultures. Analyses of total hydrolysable neutral sugars and amino acids, and ultrahigh resolution mass spectrometry revealed large differences in the chemical composition of the two DOM sources. According to 454 pyrosequences of 16S ribosomal ribonucleic acid genes, diatom-derived DOM sustained higher levels of bacterial richness, evenness and phylogenetic diversity than cyanobacteria-derived DOM. These distinct community structures were, however, not associated with specific taxa. Grazing pressure affected bacterial community composition without changing the overall pattern of bacterial diversity levels set by DOM. Our results demonstrate that resource composition can shape several facets of bacterial diversity without influencing the phylogenetic composition of bacterial communities, suggesting functional redundancy at different taxonomic levels for the degradation of phytoplankton-derived DOM. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods.

PubMed

Duchêne, Sebastián; Geoghegan, Jemma L; Holmes, Edward C; Ho, Simon Y W

2016-11-15

In rapidly evolving pathogens, including viruses and some bacteria, genetic change can accumulate over short time-frames. Accordingly, their sampling times can be used to calibrate molecular clocks, allowing estimation of evolutionary rates. Methods for estimating rates from time-structured data vary in how they treat phylogenetic uncertainty and rate variation among lineages. We compiled 81 virus data sets and estimated nucleotide substitution rates using root-to-tip regression, least-squares dating and Bayesian inference. Although estimates from these three methods were often congruent, this largely relied on the choice of clock model. In particular, relaxed-clock models tended to produce higher rate estimates than methods that assume constant rates. Discrepancies in rate estimates were also associated with high among-lineage rate variation, and phylogenetic and temporal clustering. These results provide insights into the factors that affect the reliability of rate estimates from time-structured sequence data, emphasizing the importance of clock-model testing. sduchene@unimelb.edu.au or garzonsebastian@hotmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Modeling adaptive kernels from probabilistic phylogenetic trees.

PubMed

Nicotra, Luca; Micheli, Alessio

2009-01-01

Modeling phylogenetic interactions is an open issue in many computational biology problems. In the context of gene function prediction we introduce a class of kernels for structured data leveraging on a hierarchical probabilistic modeling of phylogeny among species. We derive three kernels belonging to this setting: a sufficient statistics kernel, a Fisher kernel, and a probability product kernel. The new kernels are used in the context of support vector machine learning. The kernels adaptivity is obtained through the estimation of the parameters of a tree structured model of evolution using as observed data phylogenetic profiles encoding the presence or absence of specific genes in a set of fully sequenced genomes. We report results obtained in the prediction of the functional class of the proteins of the budding yeast Saccharomyces cerevisae which favorably compare to a standard vector based kernel and to a non-adaptive tree kernel function. A further comparative analysis is performed in order to assess the impact of the different components of the proposed approach. We show that the key features of the proposed kernels are the adaptivity to the input domain and the ability to deal with structured data interpreted through a graphical model representation.

Altitude acts as an environmental filter on phylogenetic composition, traits and diversity in bee communities.

PubMed

Hoiss, Bernhard; Krauss, Jochen; Potts, Simon G; Roberts, Stuart; Steffan-Dewenter, Ingolf

2012-11-07

Knowledge about the phylogeny and ecology of communities along environmental gradients helps to disentangle the role of competition-driven processes and environmental filtering for community assembly. In this study, we evaluated patterns in species richness, phylogenetic structure and life-history traits of bee communities along altitudinal gradients in the Alps, Germany. We found a linear decline in species richness and abundance but increasing phylogenetic clustering in communities with increasing altitude. The proportion of social- and ground-nesting species, as well as mean body size and altitudinal range of bee communities, increased with increasing altitude, whereas the mean geographical distribution decreased. Our results suggest that community assembly at high altitudes is dominated by environmental filtering effects, whereas the relative importance of competition increases at low altitudes. We conclude that inherent phylogenetic and ecological species attributes at high altitudes pose a threat for less competitive alpine specialists with ongoing climate change.

Altitude acts as an environmental filter on phylogenetic composition, traits and diversity in bee communities

PubMed Central

Hoiss, Bernhard; Krauss, Jochen; Potts, Simon G.; Roberts, Stuart; Steffan-Dewenter, Ingolf

2012-01-01

Knowledge about the phylogeny and ecology of communities along environmental gradients helps to disentangle the role of competition-driven processes and environmental filtering for community assembly. In this study, we evaluated patterns in species richness, phylogenetic structure and life-history traits of bee communities along altitudinal gradients in the Alps, Germany. We found a linear decline in species richness and abundance but increasing phylogenetic clustering in communities with increasing altitude. The proportion of social- and ground-nesting species, as well as mean body size and altitudinal range of bee communities, increased with increasing altitude, whereas the mean geographical distribution decreased. Our results suggest that community assembly at high altitudes is dominated by environmental filtering effects, whereas the relative importance of competition increases at low altitudes. We conclude that inherent phylogenetic and ecological species attributes at high altitudes pose a threat for less competitive alpine specialists with ongoing climate change. PMID:22933374

The ovary structure and oogenesis in the basal crustaceans and hexapods. Possible phylogenetic significance.

PubMed

Jaglarz, Mariusz K; Kubrakiewicz, Janusz; Bilinski, Szczepan M

2014-07-01

Recent large-scale phylogenetic analyses of exclusively molecular or combined molecular and morphological characters support a close relationship between Crustacea and Hexapoda. The growing consensus on this phylogenetic link is reflected in uniting both taxa under the name Pancrustacea or Tetraconata. Several recent molecular phylogenies have also indicated that the monophyletic hexapods should be nested within paraphyletic crustaceans. However, it is still contentious exactly which crustacean taxon is the sister group to Hexapoda. Among the favored candidates are Branchiopoda, Malacostraca, Remipedia and Xenocarida (Remipedia + Cephalocarida). In this context, we review morphological and ultrastructural features of the ovary architecture and oogenesis in these crustacean groups in search of traits potentially suitable for phylogenetic considerations. We have identified a suite of morphological characters which may prove useful in further comparative studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Delimitation of the Thoracosphaeraceae (Dinophyceae), including the calcareous dinoflagellates, based on large amounts of ribosomal RNA sequence data.

PubMed

Gottschling, Marc; Soehner, Sylvia; Zinssmeister, Carmen; John, Uwe; Plötner, Jörg; Schweikert, Michael; Aligizaki, Katerina; Elbrächter, Malte

2012-01-01

The phylogenetic relationships of the Dinophyceae (Alveolata) are not sufficiently resolved at present. The Thoracosphaeraceae (Peridiniales) are the only group of the Alveolata that include members with calcareous coccoid stages; this trait is considered apomorphic. Although the coccoid stage apparently is not calcareous, Bysmatrum has been assigned to the Thoracosphaeraceae based on thecal morphology. We tested the monophyly of the Thoracosphaeraceae using large sets of ribosomal RNA sequence data of the Alveolata including the Dinophyceae. Phylogenetic analyses were performed using Maximum Likelihood and Bayesian approaches. The Thoracosphaeraceae were monophyletic, but included also a number of non-calcareous dinophytes (such as Pentapharsodinium and Pfiesteria) and even parasites (such as Duboscquodinium and Tintinnophagus). Bysmatrum had an isolated and uncertain phylogenetic position outside the Thoracosphaeraceae. The phylogenetic relationships among calcareous dinophytes appear complex, and the assumption of the single origin of the potential to produce calcareous structures is challenged. The application of concatenated ribosomal RNA sequence data may prove promising for phylogenetic reconstructions of the Dinophyceae in future. Copyright © 2011 Elsevier GmbH. All rights reserved.

Repeated evolution of camouflage in speciose desert rodents.

PubMed

Boratyński, Zbyszek; Brito, José C; Campos, João C; Cunha, José L; Granjon, Laurent; Mappes, Tapio; Ndiaye, Arame; Rzebik-Kowalska, Barbara; Serén, Nina

2017-06-14

There are two main factors explaining variation among species and the evolution of characters along phylogeny: adaptive change, including phenotypic and genetic responses to selective pressures, and phylogenetic inertia, or the resemblance between species due to shared phylogenetic history. Phenotype-habitat colour match, a classic Darwinian example of the evolution of camouflage (crypsis), offers the opportunity to test the importance of historical versus ecological mechanisms in shaping phenotypes among phylogenetically closely related taxa. To assess it, we investigated fur (phenotypic data) and habitat (remote sensing data) colourations, along with phylogenetic information, in the species-rich Gerbillus genus. Overall, we found a strong phenotype-habitat match, once the phylogenetic signal is taken into account. We found that camouflage has been acquired and lost repeatedly in the course of the evolutionary history of Gerbillus. Our results suggest that fur colouration and its covariation with habitat is a relatively labile character in mammals, potentially responding quickly to selection. Relatively unconstrained and substantial genetic basis, as well as structural and functional independence from other fitness traits of mammalian colouration might be responsible for that observation.

Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men.

PubMed

German, Danielle; Grabowski, Mary Kate; Beyrer, Chris

2017-02-01

The multidimensional nature and continued evolution of HIV epidemics among men who have sex with men (MSM) requires innovative intervention approaches. Strategies are needed that recognise the individual, social and structural factors driving HIV transmission; that can pinpoint networks with heightened transmission risk; and that can help target intervention in real time. HIV phylogenetics is a rapidly evolving field with strong promise for informing innovative responses to the HIV epidemic among MSM. Currently, HIV phylogenetic insights are providing new understandings of characteristics of HIV epidemics involving MSM, social networks influencing transmission, characteristics of HIV transmission clusters involving MSM, targets for antiretroviral and other prevention strategies and dynamics of emergent epidemics. Maximising the potential of HIV phylogenetics for HIV responses among MSM will require attention to key methodological challenges and ethical considerations, as well as resolving key implementation and scientific questions. Enhanced and integrated use of HIV surveillance, sociobehavioural and phylogenetic data resources are becoming increasingly critical for informing public health approaches to HIV among MSM.

Fabrication of (PPC/NCC)/PVA composites with inner-outer double constrained structure and improved glass transition temperature.

PubMed

Cui, Shaoying; Li, Li; Wang, Qi

2018-07-01

Improving glass transition temperature (T g ) and mechanical property of the environment-friendly poly(propylene carbonate) via intermacromolecular complexation through hydrogen bonding is attractive and of great importance. A novel and effective strategy to prepare (polypropylene carbonate/nanocrystalline cellulose)/polyvinyl alcohol ((PPC/NCC)/PVA) composites with inner-outer double constrained structure was reported in this work. Outside the PPC phase, PVA, as a strong skeleton at microscale, could constrain the movement of PPC molecular chains by forming hydrogen bonding with PPC at the interface of PPC and PVA phases; inside the PPC phase, the rod-like NCC could restrain the flexible molecular chains of PPC at nanoscale by forming multi-hydrogen bonding with PPC. Under the synergistic effect of this novel inner-outer double constrained structure, T g , mechanical properties and thermal stability of (PPC/NCC)/PVA composite were significantly increased, e.g. T g of the composite researched the maximum value of 49.6 °C, respectively 15.6 °C, 5.7 °C and 4.2 °C higher than that of PPC, PPC/NCC and PPC/PVA composite. Copyright © 2018 Elsevier Ltd. All rights reserved.

Probabilistic Graphical Model Representation in Phylogenetics

PubMed Central

Höhna, Sebastian; Heath, Tracy A.; Boussau, Bastien; Landis, Michael J.; Ronquist, Fredrik; Huelsenbeck, John P.

2014-01-01

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution. [Computation; graphical models; inference; modularization; statistical phylogenetics; tree plate.] PMID:24951559

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison

PubMed Central

Ratmann, Oliver; Hodcroft, Emma B.; Pickles, Michael; Cori, Anne; Hall, Matthew; Lycett, Samantha; Colijn, Caroline; Dearlove, Bethany; Didelot, Xavier; Frost, Simon; Hossain, A.S. Md Mukarram; Joy, Jeffrey B.; Kendall, Michelle; Kühnert, Denise; Leventhal, Gabriel E.; Liang, Richard; Plazzotta, Giacomo; Poon, Art F.Y.; Rasmussen, David A.; Stadler, Tanja; Volz, Erik; Weis, Caroline; Leigh Brown, Andrew J.; Fraser, Christophe

2017-01-01

Viral phylogenetic methods contribute to understanding how HIV spreads in populations, and thereby help guide the design of prevention interventions. So far, most analyses have been applied to well-sampled concentrated HIV-1 epidemics in wealthy countries. To direct the use of phylogenetic tools to where the impact of HIV-1 is greatest, the Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium generates full-genome viral sequences from across sub-Saharan Africa. Analyzing these data presents new challenges, since epidemics are principally driven by heterosexual transmission and a smaller fraction of cases is sampled. Here, we show that viral phylogenetic tools can be adapted and used to estimate epidemiological quantities of central importance to HIV-1 prevention in sub-Saharan Africa. We used a community-wide methods comparison exercise on simulated data, where participants were blinded to the true dynamics they were inferring. Two distinct simulations captured generalized HIV-1 epidemics, before and after a large community-level intervention that reduced infection levels. Five research groups participated. Structured coalescent modeling approaches were most successful: phylogenetic estimates of HIV-1 incidence, incidence reductions, and the proportion of transmissions from individuals in their first 3 months of infection correlated with the true values (Pearson correlation > 90%), with small bias. However, on some simulations, true values were markedly outside reported confidence or credibility intervals. The blinded comparison revealed current limits and strengths in using HIV phylogenetics in challenging settings, provided benchmarks for future methods’ development, and supports using the latest generation of phylogenetic tools to advance HIV surveillance and prevention. PMID:28053012

Life history and biogeographic diversification of an endemic western North American freshwater fish clade using a comparative species tree approach.

PubMed

Baumsteiger, Jason; Kinziger, Andrew P; Aguilar, Andres

2012-12-01

The west coast of North America contains a number of biogeographic freshwater provinces which reflect an ever-changing aquatic landscape. Clues to understanding this complex structure are often encapsulated genetically in the ichthyofauna, though frequently as unresolved evolutionary relationships and putative cryptic species. Advances in molecular phylogenetics through species tree analyses now allow for improved exploration of these relationships. Using a comprehensive approach, we analyzed two mitochondrial and nine nuclear loci for a group of endemic freshwater fish (sculpin-Cottus) known for a wide ranging distribution and complex species structure in this region. Species delimitation techniques identified three novel cryptic lineages, all well supported by phylogenetic analyses. Comparative phylogenetic analyses consistently found five distinct clades reflecting a number of unique biogeographic provinces. Some internal node relationships varied by species tree reconstruction method, and were associated with either Bayesian or maximum likelihood statistical approaches or between mitochondrial, nuclear, and combined datasets. Limited cases of mitochondrial capture were also evident, suggestive of putative ancestral hybridization between species. Biogeographic diversification was associated with four major regions and revealed historical faunal exchanges across regions. Mapping of an important life-history character (amphidromy) revealed two separate instances of trait evolution, a transition that has occurred repeatedly in Cottus. This study demonstrates the power of current phylogenetic methods, the need for a comprehensive phylogenetic approach, and the potential for sculpin to serve as an indicator of biogeographic history for native ichthyofauna in the region. Copyright © 2012 Elsevier Inc. All rights reserved.

Frugivores bias seed-adult tree associations through nonrandom seed dispersal: a phylogenetic approach.

PubMed

Razafindratsima, Onja H; Dunham, Amy E

2016-08-01

Frugivores are the main seed dispersers in many ecosystems, such that behaviorally driven, nonrandom patterns of seed dispersal are a common process; but patterns are poorly understood. Characterizing these patterns may be essential for understanding spatial organization of fruiting trees and drivers of seed-dispersal limitation in biodiverse forests. To address this, we studied resulting spatial associations between dispersed seeds and adult tree neighbors in a diverse rainforest in Madagascar, using a temporal and phylogenetic approach. Data show that by using fruiting trees as seed-dispersal foci, frugivores bias seed dispersal under conspecific adults and under heterospecific trees that share dispersers and fruiting time with the dispersed species. Frugivore-mediated seed dispersal also resulted in nonrandom phylogenetic associations of dispersed seeds with their nearest adult neighbors, in nine out of the 16 months of our study. However, these nonrandom phylogenetic associations fluctuated unpredictably over time, ranging from clustered to overdispersed. The spatial and phylogenetic template of seed dispersal did not translate to similar patterns of association in adult tree neighborhoods, suggesting the importance of post-dispersal processes in structuring plant communities. Results suggest that frugivore-mediated seed dispersal is important for structuring early stages of plant-plant associations, setting the template for post-dispersal processes that influence ultimate patterns of plant recruitment. Importantly, if biased patterns of dispersal are common in other systems, frugivores may promote tree coexistence in biodiverse forests by limiting the frequency and diversity of heterospecific interactions of seeds they disperse. © 2016 by the Ecological Society of America.

MASTtreedist: visualization of tree space based on maximum agreement subtree.

PubMed

Huang, Hong; Li, Yongji

2013-01-01

Phylogenetic tree construction process might produce many candidate trees as the "best estimates." As the number of constructed phylogenetic trees grows, the need to efficiently compare their topological or physical structures arises. One of the tree comparison's software tools, the Mesquite's Tree Set Viz module, allows the rapid and efficient visualization of the tree comparison distances using multidimensional scaling (MDS). Tree-distance measures, such as Robinson-Foulds (RF), for the topological distance among different trees have been implemented in Tree Set Viz. New and sophisticated measures such as Maximum Agreement Subtree (MAST) can be continuously built upon Tree Set Viz. MAST can detect the common substructures among trees and provide more precise information on the similarity of the trees, but it is NP-hard and difficult to implement. In this article, we present a practical tree-distance metric: MASTtreedist, a MAST-based comparison metric in Mesquite's Tree Set Viz module. In this metric, the efficient optimizations for the maximum weight clique problem are applied. The results suggest that the proposed method can efficiently compute the MAST distances among trees, and such tree topological differences can be translated as a scatter of points in two-dimensional (2D) space. We also provide statistical evaluation of provided measures with respect to RF-using experimental data sets. This new comparison module provides a new tree-tree pairwise comparison metric based on the differences of the number of MAST leaves among constructed phylogenetic trees. Such a new phylogenetic tree comparison metric improves the visualization of taxa differences by discriminating small divergences of subtree structures for phylogenetic tree reconstruction.

Evolution of early life inferred from protein and ribonucleic acid sequences

NASA Technical Reports Server (NTRS)

Dayhoff, M. O.; Schwartz, R. M.

1978-01-01

The chemical structures of ferredoxin, 5S ribosomal RNA, and c-type cytochrome sequences have been employed to construct a phylogenetic tree which connects all major photosynthesizing organisms: the three types of bacteria, blue-green algae, and chloroplasts. Anaerobic and aerobic bacteria, eukaryotic cytoplasmic components and mitochondria are also included in the phylogenetic tree. Anaerobic nonphotosynthesizing bacteria similar to Clostridium were the earliest organisms, arising more than 3.2 billion years ago. Bacterial photosynthesis evolved nearly 3.0 billion years ago, while oxygen-evolving photosynthesis, originating in the blue-green algal line, came into being about 2.0 billion years ago. The phylogenetic tree supports the symbiotic theory of the origin of eukaryotes.

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

PubMed

Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

2014-01-01

The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.

Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae)

PubMed Central

2011-01-01

Background The genus Pyrus belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of Pyrus has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of LEAFY and the alcohol dehydrogenase gene (Adh) were selected to investigate their molecular evolution and phylogenetic utility. Results DNA sequence analyses revealed a complex ortholog and paralog structure of Adh genes in Pyrus and Malus, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some Adh homologs are putatively nonfunctional. A partial region of Adh1 was sequenced for 18 Pyrus species and three subparalogs representing Adh1-1 were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of LEAFY, multiple inparalogs were discovered for both LFY1int2 and LFY2int2. LFY1int2 is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs. LFY2int2-N, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of Pyrus using LFY2int2-N. Conclusions Our study represents the first phylogenetic analyses based on LCNGs in Pyrus. Ancient and recent duplications lead to a complex structure of Adh outparalogs and inparalogs in Pyrus and Malus, resulting in neofunctionalization, nonfunctionalization and possible subfunctionalization. Among all investigated orthologs, LFY2int2-N is the best nuclear marker for phylogenetic reconstruction of Pyrus due to suitable sequence divergence and the absence of lineage sorting. PMID:21917170

Phylobetadiversity among forest types in the Brazilian Atlantic Forest complex.

PubMed

Duarte, Leandro Da Silva; Bergamin, Rodrigo Scarton; Marcilio-Silva, Vinícius; Seger, Guilherme Dubal Dos Santos; Marques, Márcia Cristina Mendes

2014-01-01

Phylobetadiversity is defined as the phylogenetic resemblance between communities or biomes. Analyzing phylobetadiversity patterns among different vegetation physiognomies within a single biome is crucial to understand the historical affinities between them. Based on the widely accepted idea that different forest physiognomies within the Southern Brazilian Atlantic Forest constitute different facies of a single biome, we hypothesize that more recent phylogenetic nodes should drive phylobetadiversity gradients between the different forest types within the Atlantic Forest, as the phylogenetic divergence among those forest types is biogeographically recent. We compiled information from 206 checklists describing the occurrence of shrub/tree species across three different forest physiognomies within the Southern Brazilian Atlantic Forest (Dense, Mixed and Seasonal forests). We analyzed intra-site phylogenetic structure (phylogenetic diversity, net relatedness index and nearest taxon index) and phylobetadiversity between plots located at different forest types, using five different methods differing in sensitivity to either basal or terminal nodes (phylogenetic fuzzy weighting, COMDIST, COMDISTNT, UniFrac and Rao's H). Mixed forests showed higher phylogenetic diversity and overdispersion than the other forest types. Furthermore, all forest types differed from each other in relation phylobetadiversity patterns, particularly when phylobetadiversity methods more sensitive to terminal nodes were employed. Mixed forests tended to show higher phylogenetic differentiation to Dense and Seasonal forests than these latter from each other. The higher phylogenetic diversity and phylobetadiversity levels found in Mixed forests when compared to the others likely result from the biogeographical origin of several taxa occurring in these forests. On one hand, Mixed forests shelter several temperate taxa, like the conifers Araucaria and Podocarpus. On the other hand, tropical groups, like Myrtaceae, are also very representative of this forest type. We point out to the need of more attention to Mixed forests as a conservation target within the Brazilian Atlantic Forest given their high phylogenetic uniqueness.

Phylobetadiversity among Forest Types in the Brazilian Atlantic Forest Complex

PubMed Central

Duarte, Leandro Da Silva; Bergamin, Rodrigo Scarton; Marcilio-Silva, Vinícius; Seger, Guilherme Dubal Dos Santos; Marques, Márcia Cristina Mendes

2014-01-01

Phylobetadiversity is defined as the phylogenetic resemblance between communities or biomes. Analyzing phylobetadiversity patterns among different vegetation physiognomies within a single biome is crucial to understand the historical affinities between them. Based on the widely accepted idea that different forest physiognomies within the Southern Brazilian Atlantic Forest constitute different facies of a single biome, we hypothesize that more recent phylogenetic nodes should drive phylobetadiversity gradients between the different forest types within the Atlantic Forest, as the phylogenetic divergence among those forest types is biogeographically recent. We compiled information from 206 checklists describing the occurrence of shrub/tree species across three different forest physiognomies within the Southern Brazilian Atlantic Forest (Dense, Mixed and Seasonal forests). We analyzed intra-site phylogenetic structure (phylogenetic diversity, net relatedness index and nearest taxon index) and phylobetadiversity between plots located at different forest types, using five different methods differing in sensitivity to either basal or terminal nodes (phylogenetic fuzzy weighting, COMDIST, COMDISTNT, UniFrac and Rao’s H). Mixed forests showed higher phylogenetic diversity and overdispersion than the other forest types. Furthermore, all forest types differed from each other in relation phylobetadiversity patterns, particularly when phylobetadiversity methods more sensitive to terminal nodes were employed. Mixed forests tended to show higher phylogenetic differentiation to Dense and Seasonal forests than these latter from each other. The higher phylogenetic diversity and phylobetadiversity levels found in Mixed forests when compared to the others likely result from the biogeographical origin of several taxa occurring in these forests. On one hand, Mixed forests shelter several temperate taxa, like the conifers Araucaria and Podocarpus. On the other hand, tropical groups, like Myrtaceae, are also very representative of this forest type. We point out to the need of more attention to Mixed forests as a conservation target within the Brazilian Atlantic Forest given their high phylogenetic uniqueness. PMID:25121495

Invasions but not extinctions change phylogenetic diversity of angiosperm assemblage on southeastern Pacific Oceanic islands

PubMed Central

2017-01-01

We assessed changes in phylogenetic diversity of angiosperm flora on six oceanic islands located in the southeastern Pacific Ocean, by comparing flora from two periods: the pre-European colonization of islands and current times. We hypothesize that, in the time between these periods, extinction of local plant species and addition of exotic plants modified phylogenetic-α-diversity at different levels (deeper and terminal phylogeny) and increased phylo-β-diversity among islands. Based on floristic studies, we assembled a phylogenetic tree from occurrence data that includes 921 species, of which 165 and 756 were native or exotic in origin, respectively. Then, we studied change in the phylo-α-diversity and phylo-β-diversity (1 –Phylosor) by comparing pre-European and current times. Despite extinction of 18 native angiosperm species, an increase in species richness and phylo-α-diversity was observed for all islands studied, attributed to introduction of exotic plants (between 6 to 477 species per island). We did not observe significant variation of mean phylogenetic distance (MPD), a measure of the ‘deeper’ phylogenetic diversity of assemblages (e.g., orders, families), suggesting that neither extinctions nor introductions altered phylogenetic structure of the angiosperms of these islands. In regard to phylo-β-diversity, we detected temporal turnover (variation in phylogenetic composition) between periods to flora (0.38 ± 0.11). However, when analyses were performed only considering native plants, we did not observe significant temporal turnover between periods (0.07 ± 0.06). These results indicate that introduction of exotic angiosperms has contributed more notably than extinctions to the configuration of plant assemblages and phylogenetic diversity on the studied islands. Because phylogenetic diversity is closely related to functional diversity (species trait variations and roles performed by organisms), our results suggests that the introduction of exotic plants to these islands could have detrimental impacts for ecosystem functions and ecosystem services that islands provide (e.g. productivity). PMID:28763508

Community assembly and diversification in Indo-Pacific coral reef fishes

PubMed Central

Hubert, Nicolas; Paradis, Emmanuel; Bruggemann, Henrich; Planes, Serge

2011-01-01

Theories of species coexistence have played a central role in ecology and evolutionary studies of the origin and maintenance of biodiversity in highly diverse communities. The concept of niche and associated theories predict that competition for available ecological space leads to a ceiling in species richness that influences further diversification patterns. By contrast, the neutral theory supports that speciation is stochastic and diversity independent. We examined the phylogenetic community structure and diversification rates in three families and 14 sites within coral reef fish communities from the Indian and Pacific oceans. Using the phylogenetic relationships among 157 species estimated with 2300 bp of mitochondrial DNA, we tested predictions in terms of species coexistence from the neutral and niche theories. At the regional scale, our findings suggest that phylogenetic community structure shifts during community assembly to a pattern of dispersion as a consequence of allopatric speciation in recent times but overall, variations in diversification rates did not relate with sea level changes. At the local scale, the phylogenetic community structure is consistent with a neutral model of community assembly since no departure from a random sorting of species was observed. The present results support a neutral model of community assembly as a consequence of the stochastic and unpredictable nature of coral reefs favoring generalist and sedentary species competing for living space rather than trophic resources. As a consequence, the observed decrease in diversification rates may be seen as the result of a limited supply of living space as expected in a finite island model. PMID:22393499

Discrimination of acoustically similar conspecific and heterospecific vocalizations by black-capped chickadees (Poecile atricapillus).

PubMed

Hahn, Allison H; Campbell, Kimberley A; Congdon, Jenna V; Hoang, John; McMillan, Neil; Scully, Erin N; Yong, Joshua J H; Elie, Julie E; Sturdy, Christopher B

2017-07-01

Chickadees produce a multi-note chick-a-dee call in multiple socially relevant contexts. One component of this call is the D note, which is a low-frequency and acoustically complex note with a harmonic-like structure. In the current study, we tested black-capped chickadees on a between-category operant discrimination task using vocalizations with acoustic structures similar to black-capped chickadee D notes, but produced by various songbird species, in order to examine the role that phylogenetic distance plays in acoustic perception of vocal signals. We assessed the extent to which discrimination performance was influenced by the phylogenetic relatedness among the species producing the vocalizations and by the phylogenetic relatedness between the subjects' species (black-capped chickadees) and the vocalizers' species. We also conducted a bioacoustic analysis and discriminant function analysis in order to examine the acoustic similarities among the discrimination stimuli. A previous study has shown that neural activation in black-capped chickadee auditory and perceptual brain regions is similar following the presentation of these vocalization categories. However, we found that chickadees had difficulty discriminating between forward and reversed black-capped chickadee D notes, a result that directly corresponded to the bioacoustic analysis indicating that these stimulus categories were acoustically similar. In addition, our results suggest that the discrimination between vocalizations produced by two parid species (chestnut-backed chickadees and tufted titmice) is perceptually difficult for black-capped chickadees, a finding that is likely in part because these vocalizations contain acoustic similarities. Overall, our results provide evidence that black-capped chickadees' perceptual abilities are influenced by both phylogenetic relatedness and acoustic structure.

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

PubMed Central

Sheik, Cody S.; Stevenson, Emily I.; Den Uyl, Paul A.; Arendt, Carli A.; Aciego, Sarah M.; Dick, Gregory J.

2015-01-01

Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical, and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG) in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream, and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time. PMID:26042114

Spatial Structure of Evolutionary Models of Dialects in Contact

PubMed Central

Murawaki, Yugo

2015-01-01

Phylogenetic models, originally developed to demonstrate evolutionary biology, have been applied to a wide range of cultural data including natural language lexicons, manuscripts, folktales, material cultures, and religions. A fundamental question regarding the application of phylogenetic inference is whether trees are an appropriate approximation of cultural evolutionary history. Their validity in cultural applications has been scrutinized, particularly with respect to the lexicons of dialects in contact. Phylogenetic models organize evolutionary data into a series of branching events through time. However, branching events are typically not included in dialectological studies to interpret the distributions of lexical terms. Instead, dialectologists have offered spatial interpretations to represent lexical data. For example, new lexical items that emerge in a politico-cultural center are likely to spread to peripheries, but not vice versa. To explore the question of the tree model’s validity, we present a simple simulation model in which dialects form a spatial network and share lexical items through contact rather than through common ancestors. We input several network topologies to the model to generate synthetic data. We then analyze the synthesized data using conventional phylogenetic techniques. We found that a group of dialects can be considered tree-like even if it has not evolved in a temporally tree-like manner but has a temporally invariant, spatially tree-like structure. In addition, the simulation experiments appear to reproduce unnatural results observed in reconstructed trees for real data. These results motivate further investigation into the spatial structure of the evolutionary history of dialect lexicons as well as other cultural characteristics. PMID:26221958

Structure and phylogenetic diversity of post-fire ectomycorrhizal communities of maritime pine.

PubMed

Rincón, A; Santamaría, B P; Ocaña, L; Verdú, M

2014-02-01

Environmental disturbances define the diversity and assemblage of species, affecting the functioning of ecosystems. Fire is a major disturbance of Mediterranean pine forests. Pines are highly dependent on the ectomycorrhizal (EM) fungal symbiosis, which is critical for tree recruitment under primary succession. To determine the effects of time since fire on the structure and recovery of EM fungal communities, we surveyed the young Pinus pinaster regenerate in three sites differing in the elapsed time after the last fire event. Pine roots were collected, and EM fungi characterized by sequencing the internal transcribed spacer (ITS) and the large subunit (LSU) regions of the nuclear ribosomal (nr)-DNA. The effects of the elapsed time after fire on the EM community structure (richness, presence/absence of fungi, phylogenetic diversity) and on soil properties were analysed.Fungal richness decreased with the elapsed time since the fire; although, the phylogenetic diversity of the EM community increased. Soil properties were different depending on the elapsed time after fire and particularly, the organic matter, carbon-to-nitrogen (C/N) ratio, nitrogen and iron significantly correlated with the assemblage of fungal species. Ascomycetes, particularly Tuberaceae and Pezizales, were significantly over-represented on saplings in the burned site. On seedlings, a significant over-representation of Rhizopogonaceae and Atheliaceae was observed in the most recently burned site, while other fungi (i.e. Cortinariaceae) were significantly under-represented. Our results are consistent with the hypothesis that fire can act as a selective agent by printing a phylogenetic signal on the EM fungal communities associated with naturally regenerated pines, pointing out to some groups as potential fire-adapted fungi.

Considering Future Potential Regarding Structural Diversity in Selection of Forest Reserves.

PubMed

Lundström, Johanna; Öhman, Karin; Rönnqvist, Mikael; Gustafsson, Lena

2016-01-01

A rich structural diversity in forests promotes biodiversity. Forests are dynamic and therefore it is crucial to consider future structural potential when selecting reserves, to make robust conservation decisions. We analyzed forests in boreal Sweden based on 17,599 National Forest Inventory (NFI) plots with the main aim to understand how effectiveness of reserves depends on the time dimension in the selection process, specifically by considering future structural diversity. In the study both the economic value and future values of 15 structural variables were simulated during a 100 year period. To get a net present structural value (NPSV), a single value covering both current and future values, we used four discounting alternatives: (1) only considering present values, (2) giving equal importance to values in each of the 100 years within the planning horizon, (3) applying an annual discount rate considering the risk that values could be lost, and (4) only considering the values in year 100. The four alternatives were evaluated in a reserve selection model under budget-constrained and area-constrained selections. When selecting young forests higher structural richness could be reached at a quarter of the cost over almost twice the area in a budget-constrained selection compared to an area-constrained selection. Our results point to the importance of considering future structural diversity in the selection of forest reserves and not as is done currently to base the selection on existing values. Targeting future values increases structural diversity and implies a relatively lower cost. Further, our results show that a re-orientation from old to young forests would imply savings while offering a more extensive reserve network with high structural qualities in the future. However, caution must be raised against a drastic reorientation of the current old-forest strategy since remnants of ancient forests will need to be prioritized due to their role for disturbance-sensitive species.

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

PubMed

Leontis, N B; Westhof, E

1998-09-01

A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings. Thus, each non-Watson-Crick pair could be characterized by a phylogenetic signature of variations between isosteric-like pairings. In addition to the conservative changes, which form a dictionary of pairings isosterically compatible with those observed in the crystal structure, concerted changes involving several base pairs also occur. The latter covariations may indicate transitions between related but distinctive motifs within the loop E of 5S ribosomal RNA.

On Prophoca and Leptophoca (Pinnipedia, Phocidae) from the Miocene of the North Atlantic realm: redescription, phylogenetic affinities and paleobiogeographic implications

PubMed Central

Louwye, Stephen

2017-01-01

Background Prophoca and Leptophoca represent the oldest known genera of phocine seals, dating from the latest early to middle Miocene. Originally, Prophoca rousseaui and Prophoca proxima were described based on fragmentary remains from the Miocene of Belgium. However, several researchers contested the union of Prophoca rousseaui and Prophoca proxima into one genus, without providing evidence. The stratigraphic context of Prophoca remained poorly constrained due to the lack of precise data associated with the original specimens collected in the area of Antwerp (north of Belgium). Methods Prophoca and Leptophoca are redescribed and their phylogenetic position among Phocidae is reassessed using PAUP. Dinoflagellate biostratigraphy has been carried out on sediment samples associated with specimens from Prophoca and Leptophoca to elucidate their approximate ages. Results Whereas the species Prophoca rousseaui is redescribed, Prophoca proxima is considered synonymous to Leptophoca lenis, with the proposal of a new combination Leptophoca proxima (Van Beneden, 1877). Sediment samples from specimens of both taxa have been dated to the late Langhian–early Serravallian (middle Miocene). Following a reinvestigation of Leptophoca amphiatlantica, characters from the original diagnosis are questioned and the specimens of Leptophoca amphiatlantica are considered Leptophoca cf. L. proxima. In a phylogenetic analysis, Prophoca rousseaui and Leptophoca proxima constitute early branching stem-phocines. Discussion Leptophoca proxima from the North Sea Basin is younger than the oldest known find of Leptophoca proxima from North America, which does not contradict the hypothesis that Phocinae originated along the east coast of North America during the late early Miocene, followed by dispersal to Europe shortly after. Morphological features of the appendicular skeleton indicate that Prophoca rousseaui and Leptophoca proxima have archaic locomotory modes, retaining a more prominent use of the fore flipper for aquatic propulsion than extant Phocidae. PMID:28243538

Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

PubMed

Pyron, R Alexander; Costa, Gabriel C; Patten, Michael A; Burbrink, Frank T

2015-11-01

Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species-richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population-genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well-defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species. © 2014 Cambridge Philosophical Society.

Studying the evolutionary significance of thermal adaptation in ectotherms: The diversification of amphibians' energetics.

PubMed

Nespolo, Roberto F; Figueroa, Julio; Solano-Iguaran, Jaiber J

2017-08-01

A fundamental problem in evolutionary biology is the understanding of the factors that promote or constrain adaptive evolution, and assessing the role of natural selection in this process. Here, comparative phylogenetics, that is, using phylogenetic information and traits to infer evolutionary processes has been a major paradigm . In this study, we discuss Ornstein-Uhlenbeck models (OU) in the context of thermal adaptation in ectotherms. We specifically applied this approach to study amphibians's evolution and energy metabolism. It has been hypothesized that amphibians exploit adaptive zones characterized by low energy expenditure, which generate specific predictions in terms of the patterns of diversification in standard metabolic rate (SMR). We complied whole-animal metabolic rates for 122 species of amphibians, and adjusted several models of diversification. According to the adaptive zone hypothesis, we expected: (1) to find "accelerated evolution" in SMR (i.e., diversification above Brownian Motion expectations, BM), (2) that a model assuming evolutionary optima (i.e., an OU model) fits better than a white-noise model and (3) that a model assuming multiple optima (according to the three amphibians's orders) fits better than a model assuming a single optimum. As predicted, we found that the diversification of SMR occurred most of the time, above BM expectations. Also, we found that a model assuming an optimum explained the data in a better way than a white-noise model. However, we did not find evidence that an OU model with multiple optima fits the data better, suggesting a single optimum in SMR for Anura, Caudata and Gymnophiona. These results show how comparative phylogenetics could be applied for testing adaptive hypotheses regarding history and physiological performance in ectotherms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Towards a Phylogenetic Approach to the Composition of Species Complexes in the North and Central American Triatoma, Vectors of Chagas Disease

PubMed Central

de la Rúa, Nicholas M.; Bustamante, Dulce M.; Menes, Marianela; Stevens, Lori; Monroy, Carlota; Kilpatrick, William; Rizzo, Donna; Klotz, Stephen A.; Schmidt, Justin; Axen, Heather J.; Dorn, Patricia L.

2014-01-01

Phylogenetic relationships of insect vectors of parasitic diseases are important for understanding the evolution of epidemiologically relevant traits, and may be useful in vector control. The subfamily Triatominae (Hemiptera:Reduviidae) includes ~140 extant species arranged in five tribes comprised of 15 genera. The genus Triatoma is the most species-rich and contains important vectors of Trypanosoma cruzi, the causative agent of Chagas disease. Triatoma species were grouped into complexes originally by morphology and more recently with the addition of information from molecular phylogenetics (the four-complex hypothesis); however, without a strict adherence to monophyly. To date, the validity of proposed species complexes has not been tested by statistical tests of topology. The goal of this study was to clarify the systematics of 19 Triatoma species from North and Central America. We inferred their evolutionary relatedness using two independent data sets: the complete nuclear Internal Transcribed Spacer-2 ribosomal DNA (ITS-2 rDNA) and head morphometrics. In addition, we used the Shimodaira-Hasegawa statistical test of topology to assess the fit of the data to a set of competing systematic hypotheses (topologies). An unconstrained topology inferred from the ITS-2 data was compared to topologies constrained based on the four-complex hypothesis or one inferred from our morphometry results. The unconstrained topology represents a statistically significant better fit of the molecular data than either the four-complex or the morphometric topology. We propose an update to the composition of species complexes in the North and Central American Triatoma, based on a phylogeny inferred from ITS-2 as a first step towards updating the phylogeny of the complexes based on monophyly and statistical tests of topologies. PMID:24681261

Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica.

PubMed

Hurtado, Luis A; Mateos, Mariana; Wang, Chang; Santamaria, Carlos A; Jung, Jongwoo; Khalaji-Pirbalouty, Valiallah; Kim, Won

2018-01-01

The native ranges and invasion histories of many marine species remain elusive due to a dynamic dispersal process via marine vessels. Molecular markers can aid in identification of native ranges and elucidation of the introduction and establishment process. The supralittoral isopod Ligia exotica has a wide tropical and subtropical distribution, frequently found in harbors and ports around the globe. This isopod is hypothesized to have an Old World origin, from where it was unintentionally introduced to other regions via wooden ships and solid ballast. Its native range, however, remains uncertain. Recent molecular studies uncovered the presence of two highly divergent lineages of L. exotica in East Asia, and suggest this region is a source of nonindigenous populations. In this study, we conducted phylogenetic analyses (Maximum Likelihood and Bayesian) of a fragment of the mitochondrial 16S ribosomal (r)DNA gene using a dataset of this isopod that greatly expanded previous representation from Asia and putative nonindigenous populations around the world. For a subset of samples, sequences of 12S rDNA and NaK were also obtained and analyzed together with 16S rDNA. Our results show that L. exotica is comprised of several highly divergent genetic lineages, which probably represent different species. Most of the 16S rDNA genetic diversity (48 haplotypes) was detected in East and Southeast Asia. Only seven haplotypes were observed outside this region (in the Americas, Hawai'i, Africa and India), which were identical or closely related to haplotypes found in East and Southeast Asia. Phylogenetic patterns indicate the L. exotica clade originated and diversified in East and Southeast Asia, and only members of one of the divergent lineages have spread out of this region, recently, suggesting the potential to become invasive is phylogenetically constrained.

A Fluorescent Protein Scaffold for Presenting Structurally Constrained Peptides Provides an Effective Screening System to Identify High Affinity Target-Binding Peptides

PubMed Central

Kadonosono, Tetsuya; Yabe, Etsuri; Furuta, Tadaomi; Yamano, Akihiro; Tsubaki, Takuya; Sekine, Takuya; Kuchimaru, Takahiro; Sakurai, Minoru; Kizaka-Kondoh, Shinae

2014-01-01

Peptides that have high affinity for target molecules on the surface of cancer cells are crucial for the development of targeted cancer therapies. However, unstructured peptides often fail to bind their target molecules with high affinity. To efficiently identify high-affinity target-binding peptides, we have constructed a fluorescent protein scaffold, designated gFPS, in which structurally constrained peptides are integrated at residues K131–L137 of superfolder green fluorescent protein. Molecular dynamics simulation supported the suitability of this site for presentation of exogenous peptides with a constrained structure. gFPS can present 4 to 12 exogenous amino acids without a loss of fluorescence. When gFPSs presenting human epidermal growth factor receptor type 2 (HER2)-targeting peptides were added to the culture medium of HER2-expressing cells, we could easily identify the peptides with high HER2-affinity and -specificity based on gFPS fluorescence. In addition, gFPS could be expressed on the yeast cell surface and applied for a high-throughput screening. These results demonstrate that gFPS has the potential to serve as a powerful tool to improve screening of structurally constrained peptides that have a high target affinity, and suggest that it could expedite the one-step identification of clinically applicable cancer cell-binding peptides. PMID:25084350

Does aquatic foraging impact head shape evolution in snakes?

PubMed

Segall, Marion; Cornette, Raphaël; Fabre, Anne-Claire; Godoy-Diana, Ramiro; Herrel, Anthony

2016-08-31

Evolutionary trajectories are often biased by developmental and historical factors. However, environmental factors can also impose constraints on the evolutionary trajectories of organisms leading to convergence of morphology in similar ecological contexts. The physical properties of water impose strong constraints on aquatic feeding animals by generating pressure waves that can alert prey and potentially push them away from the mouth. These hydrodynamic constraints have resulted in the independent evolution of suction feeding in most groups of secondarily aquatic tetrapods. Despite the fact that snakes cannot use suction, they have invaded the aquatic milieu many times independently. Here, we test whether the aquatic environment has constrained head shape evolution in snakes and whether shape converges on that predicted by biomechanical models. To do so, we used three-dimensional geometric morphometrics and comparative, phylogenetically informed analyses on a large sample of aquatic snake species. Our results show that aquatic snakes partially conform to our predictions and have a narrower anterior part of the head and dorsally positioned eyes and nostrils. This morphology is observed, irrespective of the phylogenetic relationships among species, suggesting that the aquatic environment does indeed drive the evolution of head shape in snakes, thus biasing the evolutionary trajectory of this group of animals. © 2016 The Author(s).

The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life.

PubMed

Zhou, Xin; Frandsen, Paul B; Holzenthal, Ralph W; Beet, Clare R; Bennett, Kristi R; Blahnik, Roger J; Bonada, Núria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V; Collins, Gemma E; deWaard, Jeremy; Dean, John; Flint, Oliver S; Hausmann, Axel; Hendrich, Lars; Hess, Monika; Hogg, Ian D; Kondratieff, Boris C; Malicky, Hans; Milton, Megan A; Morinière, Jérôme; Morse, John C; Mwangi, François Ngera; Pauls, Steffen U; Gonzalez, María Razo; Rinne, Aki; Robinson, Jason L; Salokannel, Juha; Shackleton, Michael; Smith, Brian; Stamatakis, Alexandros; StClair, Ros; Thomas, Jessica A; Zamora-Muñoz, Carmen; Ziesmann, Tanja; Kjer, Karl M

2016-09-05

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

Digestive capacity predicts diet diversity in Neotropical frugivorous bats.

PubMed

Saldaña-Vázquez, Romeo A; Ruiz-Sanchez, Eduardo; Herrera-Alsina, Leonel; Schondube, Jorge E

2015-09-01

1. Predicting the diet diversity of animals is important to basic and applied ecology. Knowledge of diet diversity in animals helps us understand niche partitioning, functional diversity and ecosystem services such as pollination, pest control and seed dispersal. 2. There is a negative relationship between the length of the digestive tract and diet diversity in animals; however, the role of digestive physiology in determining diet diversity has been ignored. This is especially important in vertebrates with powered flight because, unlike non-flying vertebrates, they have limitations that may constrain gut size. 3. Here, we evaluate the relationship between digestive capacity and diet diversity in Carollinae and Stenodermatinae frugivorous bats. These bats disperse the seeds of plants that are key to Neotropical forest regeneration. 4. Our results show that digestive capacity is a good predictor of diet diversity in Carollinae and Stenodermatinae frugivorous bats (R(2) = 0·77). 5. Surprisingly, the most phylogenetically closely related species were not similar in their digestive capacity or diet diversity. The lack of a phylogenetic signal for the traits evaluated implies differences in digestive physiology and diet in closely related species. 6. Our results highlight the predictive usefulness of digestive physiology for understanding the feeding ecology of animals. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Ecological Trait Composition of Freshwater Fish Across Gradients of Environmental Variability in North-Eastern Australia

NASA Astrophysics Data System (ADS)

Kennard, M. J.; Pusey, B. J.; Arthington, A. H.

2005-05-01

North-eastern Australia encompasses 18o of latitude, monsoonal/tropical to sub-tropical/temperate climates, geomorphologically diverse rivers, and flow regimes with markedly varied seasonality, constancy and predictability. Fish assemblages in the region vary in relation to the predictability of aquatic habitat availability and other topographic, climatic and/or biogeographic factors. This paper examines how environmental, biogeographic and phylogenetic factors may constrain ecological trait composition at local and regional scales. We derived 17 categories of ecological traits to describe the morphology, behaviour, habitat, life history and trophic characteristics of 114 fish species from 64 river basins. Trait composition varied substantially across the region. The number of riffle dwelling species, maximum size and longevity of fishes was greater in the hydrologically predictable and constant rivers of the Wet Tropics region than in more unpredictable or seasonal environments. The importance of herbivory was also greater in the tropics. Historical biogeographic and phylogenetic factors may confound our ability to understand the role of environmental factors in determining spatial variation in ecological trait composition. Understanding the functional linkages between environmental drivers of fish species distributions via their ecological characteristics should provide a foundation for predicting future impacts of environmental change in a region of Australia subject to increasing human pressures.

Phylogeny and Bayesian divergence time estimations of small-headed flies (Diptera: Acroceridae) using multiple molecular markers.

PubMed

Winterton, Shaun L; Wiegmann, Brian M; Schlinger, Evert I

2007-06-01

The first formal analysis of phylogenetic relationships among small-headed flies (Acroceridae) is presented based on DNA sequence data from two ribosomal (16S and 28S) and two protein-encoding genes: carbomoylphosphate synthase (CPS) domain of CAD (i.e., rudimentary locus) and cytochrome oxidase I (COI). DNA sequences from 40 species in 22 genera of Acroceridae (representing all three subfamilies) were compared with outgroup exemplars from Nemestrinidae, Stratiomyidae, Tabanidae, and Xylophagidae. Parsimony and Bayesian simultaneous analyses of the full data set recover a well-resolved and strongly supported hypothesis of phylogenetic relationships for major lineages within the family. Molecular evidence supports the monophyly of traditionally recognised subfamilies Philopotinae and Panopinae, but Acrocerinae are polyphyletic. Panopinae, sometimes considered "primitive" based on morphology and host-use, are always placed in a more derived position in the current study. Furthermore, these data support emerging morphological evidence that the type genus Acrocera Meigen, and its sister genus Sphaerops, are atypical acrocerids, comprising a sister lineage to all other Acroceridae. Based on the phylogeny generated in the simultaneous analysis, historical divergence times were estimated using Bayesian methodology constrained with fossil data. These estimates indicate Acroceridae likely evolved during the late Triassic but did not diversify greatly until the Cretaceous.

[Short interspersed repetitive sequences (SINEs) and their use as a phylogenetic tool].

PubMed

Kramerov, D A; Vasetskiĭ, N S

2009-01-01

The data on one of the most common repetitive elements of eukaryotic genomes, short interspersed elements (SINEs), are reviewed. Their structure, origin, and functioning in the genome are discussed. The variation and abundance of these neutral genomic markers makes them a convenient and reliable tool for phylogenetic analysis. The main methods of such analysis are presented, and the potential and limitations of this approach are discussed using specific examples.

Adaptive Constrained Optimal Control Design for Data-Based Nonlinear Discrete-Time Systems With Critic-Only Structure.

PubMed

Luo, Biao; Liu, Derong; Wu, Huai-Ning

2018-06-01

Reinforcement learning has proved to be a powerful tool to solve optimal control problems over the past few years. However, the data-based constrained optimal control problem of nonaffine nonlinear discrete-time systems has rarely been studied yet. To solve this problem, an adaptive optimal control approach is developed by using the value iteration-based Q-learning (VIQL) with the critic-only structure. Most of the existing constrained control methods require the use of a certain performance index and only suit for linear or affine nonlinear systems, which is unreasonable in practice. To overcome this problem, the system transformation is first introduced with the general performance index. Then, the constrained optimal control problem is converted to an unconstrained optimal control problem. By introducing the action-state value function, i.e., Q-function, the VIQL algorithm is proposed to learn the optimal Q-function of the data-based unconstrained optimal control problem. The convergence results of the VIQL algorithm are established with an easy-to-realize initial condition . To implement the VIQL algorithm, the critic-only structure is developed, where only one neural network is required to approximate the Q-function. The converged Q-function obtained from the critic-only VIQL method is employed to design the adaptive constrained optimal controller based on the gradient descent scheme. Finally, the effectiveness of the developed adaptive control method is tested on three examples with computer simulation.

Comparative Analysis of Type IV Pilin in Desulfuromonadales

PubMed Central

Shu, Chuanjun; Xiao, Ke; Yan, Qin; Sun, Xiao

2016-01-01

During anaerobic respiration, the bacteria Geobacter sulfurreducens can transfer electrons to extracellular electron accepters through its pilus. G. sulfurreducens pili have been reported to have metallic-like conductivity that is similar to doped organic semiconductors. To study the characteristics and origin of conductive pilin proteins found in the pilus structure, their genetic, structural, and phylogenetic properties were analyzed. The genetic relationships, and conserved structures and sequences that were obtained were used to predict the evolution of the pilins. Homologous genes that encode conductive pilin were found using PilFind and Cluster. Sequence characteristics and protein tertiary structures were analyzed with MAFFT and QUARK, respectively. The origin of conductive pilins was explored by building a phylogenetic tree. Truncation is a characteristic of conductive pilin. The structures of truncated pilins and their accompanying proteins were found to be similar to the N-terminal and C-terminal ends of full-length pilins respectively. The emergence of the truncated pilins can probably be ascribed to the evolutionary pressure of their extracellular electron transporting function. Genes encoding truncated pilins and proteins similar to the C-terminal of full-length pilins, which contain a group of consecutive anti-parallel beta-sheets, are adjacent in bacterial genomes. According to the genetic, structure, and phylogenetic analyses performed in this study, we inferred that the truncated pilins and their accompanying proteins probably evolved from full-length pilins by gene fission through duplication, degeneration, and separation. These findings provide new insights about the molecular mechanisms involved in long-range electron transport along the conductive pili of Geobacter species. PMID:28066394

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis

PubMed Central

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence. PMID:11833653

Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications

NASA Astrophysics Data System (ADS)

Humpula, James F.; Ostrom, Peggy H.; Gandhi, Hasand; Strahler, John R.; Walker, Angela K.; Stafford, Thomas W.; Smith, James J.; Voorhies, Michael R.; George Corner, R.; Andrews, Phillip C.

2007-12-01

Ancient DNA sequences offer an extraordinary opportunity to unravel the evolutionary history of ancient organisms. Protein sequences offer another reservoir of genetic information that has recently become tractable through the application of mass spectrometric techniques. The extent to which ancient protein sequences resolve phylogenetic relationships, however, has not been explored. We determined the osteocalcin amino acid sequence from the bone of an extinct Camelid (21 ka, Camelops hesternus) excavated from Isleta Cave, New Mexico and three bones of extant camelids: bactrian camel ( Camelus bactrianus); dromedary camel ( Camelus dromedarius) and guanaco ( Llama guanacoe) for a diagenetic and phylogenetic assessment. There was no difference in sequence among the four taxa. Structural attributes observed in both modern and ancient osteocalcin include a post-translation modification, Hyp 9, deamidation of Gln 35 and Gln 39, and oxidation of Met 36. Carbamylation of the N-terminus in ancient osteocalcin may result in blockage and explain previous difficulties in sequencing ancient proteins via Edman degradation. A phylogenetic analysis using osteocalcin sequences of 25 vertebrate taxa was conducted to explore osteocalcin protein evolution and the utility of osteocalcin sequences for delineating phylogenetic relationships. The maximum likelihood tree closely reflected generally recognized taxonomic relationships. For example, maximum likelihood analysis recovered rodents, birds and, within hominins, the Homo-Pan-Gorilla trichotomy. Within Artiodactyla, character state analysis showed that a substitution of Pro 4 for His 4 defines the Capra-Ovis clade within Artiodactyla. Homoplasy in our analysis indicated that osteocalcin evolution is not a perfect indicator of species evolution. Limited sequence availability prevented assigning functional significance to sequence changes. Our preliminary analysis of osteocalcin evolution represents an initial step towards a complete character analysis aimed at determining the evolutionary history of this functionally significant protein. We emphasize that ancient protein sequencing and phylogenetic analyses using amino acid sequences must pay close attention to post-translational modifications, amino acid substitutions due to diagenetic alteration and the impacts of isobaric amino acids on mass shifts and sequence alignments.

Genetic structure and domestication of carrot (Daucus carota subsp. sativus L.) (Apiaceae)

USDA-ARS?s Scientific Manuscript database

Analyses of genetic structure and phylogenetic relationships illuminate the origin and domestication of modern crops. Despite being an important world-wide vegetable, the genetic structure and domestication of carrot (Daucus carota L.) is poorly understood. We provide the first such study using a la...

Integrating Stand and Soil Properties to Understand Foliar Nutrient Dynamics during Forest Succession Following Slash-and-Burn Agriculture in the Bolivian Amazon

PubMed Central

Broadbent, Eben N.; Almeyda Zambrano, Angélica M.; Asner, Gregory P.; Soriano, Marlene; Field, Christopher B.; de Souza, Harrison Ramos; Peña-Claros, Marielos; Adams, Rachel I.; Dirzo, Rodolfo; Giles, Larry

2014-01-01

Secondary forests cover large areas of the tropics and play an important role in the global carbon cycle. During secondary forest succession, simultaneous changes occur among stand structural attributes, soil properties, and species composition. Most studies classify tree species into categories based on their regeneration requirements. We use a high-resolution secondary forest chronosequence to assign trees to a continuous gradient in species successional status assigned according to their distribution across the chronosequence. Species successional status, not stand age or differences in stand structure or soil properties, was found to be the best predictor of leaf trait variation. Foliar δ13C had a significant positive relationship with species successional status, indicating changes in foliar physiology related to growth and competitive strategy, but was not correlated with stand age, whereas soil δ13C dynamics were largely constrained by plant species composition. Foliar δ15N had a significant negative correlation with both stand age and species successional status, – most likely resulting from a large initial biomass-burning enrichment in soil 15N and 13C and not closure of the nitrogen cycle. Foliar %C was neither correlated with stand age nor species successional status but was found to display significant phylogenetic signal. Results from this study are relevant to understanding the dynamics of tree species growth and competition during forest succession and highlight possibilities of, and potentially confounding signals affecting, the utility of leaf traits to understand community and species dynamics during secondary forest succession. PMID:24516525

Integrating stand and soil properties to understand foliar nutrient dynamics during forest succession following slash-and-burn agriculture in the Bolivian Amazon.

PubMed

Broadbent, Eben N; Almeyda Zambrano, Angélica M; Asner, Gregory P; Soriano, Marlene; Field, Christopher B; de Souza, Harrison Ramos; Peña-Claros, Marielos; Adams, Rachel I; Dirzo, Rodolfo; Giles, Larry

2014-01-01

Secondary forests cover large areas of the tropics and play an important role in the global carbon cycle. During secondary forest succession, simultaneous changes occur among stand structural attributes, soil properties, and species composition. Most studies classify tree species into categories based on their regeneration requirements. We use a high-resolution secondary forest chronosequence to assign trees to a continuous gradient in species successional status assigned according to their distribution across the chronosequence. Species successional status, not stand age or differences in stand structure or soil properties, was found to be the best predictor of leaf trait variation. Foliar δ(13)C had a significant positive relationship with species successional status, indicating changes in foliar physiology related to growth and competitive strategy, but was not correlated with stand age, whereas soil δ(13)C dynamics were largely constrained by plant species composition. Foliar δ(15)N had a significant negative correlation with both stand age and species successional status, - most likely resulting from a large initial biomass-burning enrichment in soil (15)N and (13)C and not closure of the nitrogen cycle. Foliar %C was neither correlated with stand age nor species successional status but was found to display significant phylogenetic signal. Results from this study are relevant to understanding the dynamics of tree species growth and competition during forest succession and highlight possibilities of, and potentially confounding signals affecting, the utility of leaf traits to understand community and species dynamics during secondary forest succession.

An RNA Element That Facilitates Programmed Ribosomal Readthrough in Turnip Crinkle Virus Adopts Multiple Conformations

PubMed Central

Kuhlmann, Micki M.; Chattopadhyay, Maitreyi; Stupina, Vera A.; Gao, Feng

2016-01-01

ABSTRACT Ribosome recoding is used by RNA viruses for translational readthrough or frameshifting past termination codons for the synthesis of extension products. Recoding sites, along with downstream recoding stimulatory elements (RSEs), have long been studied in reporter constructs, because these fragments alone mediate customary levels of recoding and are thus assumed to contain complete instructions for establishment of the proper ratio of termination to recoding. RSEs from the Tombusviridae and Luteoviridae are thought to be exceptions, since they contain a long-distance RNA-RNA connection with the 3′ end. This interaction has been suggested to substitute for pseudoknots, thought to be missing in tombusvirid RSEs. We provide evidence that the phylogenetically conserved RSE of the carmovirus Turnip crinkle virus (TCV) adopts an alternative, smaller structure that extends an upstream conserved hairpin and that this alternative structure is the predominant form of the RSE within nascent viral RNA in plant cells and when RNA is synthesized in vitro. The TCV RSE also contains an internal pseudoknot along with the long-distance interaction, and the pseudoknot is not compatible with the phylogenetically conserved structure. Conserved residues just past the recoding site are important for recoding, and these residues are also conserved in the RSEs of gammaretroviruses. Our data demonstrate the dynamic nature of the TCV RSE and suggest that studies using reporter constructs may not be effectively recapitulating RSE-mediated recoding within viral genomes. IMPORTANCE Ribosome recoding is used by RNA viruses to enable ribosomes to extend translation past termination codons for the synthesis of longer products. Recoding sites and a downstream recoding stimulatory element (RSE) mediate expected levels of recoding when excised and placed in reporter constructs and thus are assumed to contain complete instructions for the establishment of the proper ratio of termination to recoding. We provide evidence that most of the TCV RSE adopts an alternative structure that extends an upstream conserved hairpin and that this alternative structure, and not the phylogenetically conserved structure, is the predominant form of the RSE in RNA synthesized in vitro and in plant cells. The TCV RSE also contains an internal pseudoknot that is not compatible with the phylogenetically conserved structure and an RNA bridge to the 3′ end. These data suggest that the TCV RSE is structurally dynamic and that multiple conformations are likely required to regulate ribosomal readthrough. PMID:27440887

Constrained Principal Component Analysis: Various Applications.

ERIC Educational Resources Information Center

Hunter, Michael; Takane, Yoshio

2002-01-01

Provides example applications of constrained principal component analysis (CPCA) that illustrate the method on a variety of contexts common to psychological research. Two new analyses, decompositions into finer components and fitting higher order structures, are presented, followed by an illustration of CPCA on contingency tables and the CPCA of…

Structural optimization: Status and promise

NASA Astrophysics Data System (ADS)

Kamat, Manohar P.

Chapters contained in this book include fundamental concepts of optimum design, mathematical programming methods for constrained optimization, function approximations, approximate reanalysis methods, dual mathematical programming methods for constrained optimization, a generalized optimality criteria method, and a tutorial and survey of multicriteria optimization in engineering. Also included are chapters on the compromise decision support problem and the adaptive linear programming algorithm, sensitivity analyses of discrete and distributed systems, the design sensitivity analysis of nonlinear structures, optimization by decomposition, mixed elements in shape sensitivity analysis of structures based on local criteria, and optimization of stiffened cylindrical shells subjected to destabilizing loads. Other chapters are on applications to fixed-wing aircraft and spacecraft, integrated optimum structural and control design, modeling concurrency in the design of composite structures, and tools for structural optimization. (No individual items are abstracted in this volume)

Genetic diversity and structure of elite cotton germplasm (Gossypium hirsutum L.) using genome-wide SNP data.

PubMed

Ai, XianTao; Liang, YaJun; Wang, JunDuo; Zheng, JuYun; Gong, ZhaoLong; Guo, JiangPing; Li, XueYuan; Qu, YanYing

2017-10-01

Cotton (Gossypium spp.) is the most important natural textile fiber crop, and Gossypium hirsutum L. is responsible for 90% of the annual cotton crop in the world. Information on cotton genetic diversity and population structure is essential for new breeding lines. In this study, we analyzed population structure and genetic diversity of 288 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China, using genome-wide single nucleotide polymorphisms (SNP) markers. The average polymorphsim information content (PIC) was 0.25, indicating a relatively low degree of genetic diversity. Population structure analysis revealed extensive admixture and identified three subgroups. Phylogenetic analysis supported the subgroups identified by STRUCTURE. The results from both population structure and phylogenetic analysis were, for the most part, in agreement with pedigree information. Analysis of molecular variance revealed a larger amount of variation was due to diversity within the groups. Establishment of genetic diversity and population structure from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in upland cotton.

Using magma flow indicators to infer flow dynamics in sills

NASA Astrophysics Data System (ADS)

Hoyer, Lauren; Watkeys, Michael K.

2017-03-01

Fabrics from Anisotropy of Magnetic Susceptibility (AMS) analyses and Shape Preferred Orientation (SPO) of plagioclase are compared with field structures (such as bridge structures, intrusive steps and magma lobes) formed during magma intrusion in Jurassic sills. This is to constrain magma flow directions in the sills of the Karoo Igneous Province along the KwaZulu-Natal North Coast and to show how accurately certain structures predict a magma flow sense, thus improving the understanding of the Karoo sub-volcanic dynamics. The AMS fabrics are derived from magnetite grains and are well constrained, however the SPO results are commonly steeply inclined, poorly constrained and differ to the AMS fabrics. Both techniques resulted in asymmetrical fabrics. Successful relationships were established between the AMS fabric and the long axes of the magma flow indicators, implying adequate magma flow prediction. However, where numerous sill segments merge, either in the form of magma lobes or bridge structures, the coalescence process creates a new fabric between the segments preserving late-stage magma migration between the merged segments, overprinting the initial magma flow direction.

Rearrangement moves on rooted phylogenetic networks

PubMed Central

Gambette, Philippe; van Iersel, Leo; Jones, Mark; Scornavacca, Celine

2017-01-01

Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network—that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose “horizontal” moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and “vertical” moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves—named rNNI and rSPR—reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results—separating the contributions of horizontal and vertical moves—we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a solid basis for practical phylogenetic network reconstruction. PMID:28763439

Phylogenetic patterns of climatic, habitat and trophic niches in a European avian assemblage

PubMed Central

Pearman, Peter B; Lavergne, Sébastien; Roquet, Cristina; Wüest, Rafael; Zimmermann, Niklaus E; Thuiller, Wilfried

2014-01-01

Aim The origins of ecological diversity in continental species assemblages have long intrigued biogeographers. We apply phylogenetic comparative analyses to disentangle the evolutionary patterns of ecological niches in an assemblage of European birds. We compare phylogenetic patterns in trophic, habitat and climatic niche components. Location Europe. Methods From polygon range maps and handbook data we inferred the realized climatic, habitat and trophic niches of 405 species of breeding birds in Europe. We fitted Pagel's lambda and kappa statistics, and conducted analyses of disparity through time to compare temporal patterns of ecological diversification on all niche axes together. All observed patterns were compared with expectations based on neutral (Brownian) models of niche divergence. Results In this assemblage, patterns of phylogenetic signal (lambda) suggest that related species resemble each other less in regard to their climatic and habitat niches than they do in their trophic niche. Kappa estimates show that ecological divergence does not gradually increase with divergence time, and that this punctualism is stronger in climatic niches than in habitat and trophic niches. Observed niche disparity markedly exceeds levels expected from a Brownian model of ecological diversification, thus providing no evidence for past phylogenetic niche conservatism in these multivariate niches. Levels of multivariate disparity are greatest for the climatic niche, followed by disparity of the habitat and the trophic niches. Main conclusions Phylogenetic patterns in the three niche components differ within this avian assemblage. Variation in evolutionary rates (degree of gradualism, constancy through the tree) and/or non-random macroecological sampling probably lead here to differences in the phylogenetic structure of niche components. Testing hypotheses on the origin of these patterns requires more complete phylogenetic trees of the birds, and extended ecological data on different niche components for all bird species. PMID:24790525

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

PubMed

Ratmann, Oliver; Hodcroft, Emma B; Pickles, Michael; Cori, Anne; Hall, Matthew; Lycett, Samantha; Colijn, Caroline; Dearlove, Bethany; Didelot, Xavier; Frost, Simon; Hossain, A S Md Mukarram; Joy, Jeffrey B; Kendall, Michelle; Kühnert, Denise; Leventhal, Gabriel E; Liang, Richard; Plazzotta, Giacomo; Poon, Art F Y; Rasmussen, David A; Stadler, Tanja; Volz, Erik; Weis, Caroline; Leigh Brown, Andrew J; Fraser, Christophe

2017-01-01

Viral phylogenetic methods contribute to understanding how HIV spreads in populations, and thereby help guide the design of prevention interventions. So far, most analyses have been applied to well-sampled concentrated HIV-1 epidemics in wealthy countries. To direct the use of phylogenetic tools to where the impact of HIV-1 is greatest, the Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium generates full-genome viral sequences from across sub-Saharan Africa. Analyzing these data presents new challenges, since epidemics are principally driven by heterosexual transmission and a smaller fraction of cases is sampled. Here, we show that viral phylogenetic tools can be adapted and used to estimate epidemiological quantities of central importance to HIV-1 prevention in sub-Saharan Africa. We used a community-wide methods comparison exercise on simulated data, where participants were blinded to the true dynamics they were inferring. Two distinct simulations captured generalized HIV-1 epidemics, before and after a large community-level intervention that reduced infection levels. Five research groups participated. Structured coalescent modeling approaches were most successful: phylogenetic estimates of HIV-1 incidence, incidence reductions, and the proportion of transmissions from individuals in their first 3 months of infection correlated with the true values (Pearson correlation > 90%), with small bias. However, on some simulations, true values were markedly outside reported confidence or credibility intervals. The blinded comparison revealed current limits and strengths in using HIV phylogenetics in challenging settings, provided benchmarks for future methods' development, and supports using the latest generation of phylogenetic tools to advance HIV surveillance and prevention. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The drug:H+ antiporters of family 2 (DHA2), siderophore transporters (ARN) and glutathione:H+ antiporters (GEX) have a common evolutionary origin in hemiascomycete yeasts

PubMed Central

2013-01-01

Background The Saccharomyces cerevisiae 14-spanner Drug:H+ Antiporter family 2 (DHA2) are transporters of the Major Facilitator Superfamily (MFS) involved in multidrug resistance (MDR). Although poorly characterized, DHA2 family members were found to participate in the export of structurally and functionally unrelated compounds or in the uptake of amino acids into the vacuole or the cell. In S. cerevisiae, the four ARN/SIT family members encode siderophore transporters and the two GEX family members encode glutathione extrusion pumps. The evolutionary history of DHA2, ARN and GEX genes, encoding 14-spanner MFS transporters, is reconstructed in this study. Results The translated ORFs of 31 strains from 25 hemiascomycetous species, including 10 pathogenic Candida species, were compared using a local sequence similarity algorithm. The constraining and traversing of a network representing the pairwise similarity data gathered 355 full size proteins and retrieved ARN and GEX family members together with DHA2 transporters, suggesting the existence of a close phylogenetic relationship among these 14-spanner major facilitators. Gene neighbourhood analysis was combined with tree construction methodologies to reconstruct their evolutionary history and 7 DHA2 gene lineages, 5 ARN gene lineages, and 1 GEX gene lineage, were identified. The S. cerevisiae DHA2 proteins Sge1, Azr1, Vba3 and Vba5 co-clustered in a large phylogenetic branch, the ATR1 and YMR279C genes were proposed to be paralogs formed during the Whole Genome Duplication (WGD) whereas the closely related ORF YOR378W resides in its own lineage. Homologs of S. cerevisiae DHA2 vacuolar proteins Vba1, Vba2 and Vba4 occur widespread in the Hemiascomycetes. Arn1/Arn2 homologs were only found in species belonging to the Saccharomyces complex and are more abundant in the pre-WGD species. Arn4 homologs were only found in sub-telomeric regions of species belonging to the Sacharomyces sensu strictu group (SSSG). Arn3 type siderophore transporters are abundant in the Hemiascomycetes and form an ancient gene lineage extending to the filamentous fungi. Conclusions The evolutionary history of DHA2, ARN and GEX genes was reconstructed and a common evolutionary root shared by the encoded proteins is hypothesized. A new protein family, denominated DAG, is proposed to span these three phylogenetic subfamilies of 14-spanner MFS transporters. PMID:24345006

Global mammal beta diversity shows parallel assemblage structure in similar but isolated environments

PubMed Central

Graham, Catherine H.; Brooks, Thomas M.; Rondinini, Carlo; Hedges, S. Blair; Davidson, Ana D.; Costa, Gabriel C.

2016-01-01

The taxonomic, phylogenetic and trait dimensions of beta diversity each provide us unique insights into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait beta diversity. Conversely, we expect lower phylogenetic diversity, but higher trait biodiversity among assemblages that are connected but are in differing environmental conditions. We calculated all pairwise comparisons of approximately 110 × 110 km grid cells across the globe for more than 5000 mammal species (approx. 70 million comparisons). We considered realms as units representing geographical distance and historical isolation and biomes as units with similar environmental conditions. While beta diversity dimensions were generally correlated, we highlight geographical regions of decoupling among beta diversity dimensions. Our analysis shows that assemblages from tropical forests in different realms had low trait dissimilarity while phylogenetic beta diversity was significantly higher than expected, suggesting potential convergent evolution. Low trait beta diversity was surprisingly not found between isolated deserts, despite harsh environmental conditions. Overall, our results provide evidence for parallel assemblage structure of mammal assemblages driven by environmental conditions at a global scale. PMID:27559061

Radiating despite a Lack of Character: Ecological Divergence among Closely Related, Morphologically Similar Honeyeaters (Aves: Meliphagidae) Co-occurring in Arid Australian Environments.

PubMed

Miller, Eliot T; Wagner, Sarah K; Harmon, Luke J; Ricklefs, Robert E

2017-02-01

Quantifying the relationship between form and function can inform use of morphology as a surrogate for ecology. How the strength of this relationship varies continentally can inform understanding of evolutionary radiations; for example, does the relationship break down when certain lineages invade and diversify in novel habitats? The 75 species of Australian honeyeaters (Meliphagidae) are morphologically and ecologically diverse, with species feeding on nectar, insects, fruit, and other resources. We investigated Meliphagidae ecomorphology and community structure by (1) quantifying the concordance between morphology and ecology (foraging behavior), (2) estimating rates of trait evolution in relation to the packing of ecological space, and (3) comparing phylogenetic and trait community structure across the broad environmental gradients of the continent. We found that morphology explained 37% of the variance in ecology (and 62% vice versa), and we uncovered well-known bivariate relationships among the multivariate ecomorphological data. Ecological trait diversity declined less rapidly than phylogenetic diversity along a gradient of decreasing precipitation. We employ a new method (trait fields) and extend another (phylogenetic fields) to show that while species in phylogenetically clustered, arid-environment assemblages are similar morphologically, they are as varied in foraging behavior as those from more diverse assemblages. Thus, although closely related and similar morphologically, these arid-adapted species have diverged in ecological space to a similar degree as their mesic counterparts.

Echinococcus granulosus: Evidence of a heterodimeric glutathione transferase built up by phylogenetically distant subunits.

PubMed

Arbildi, Paula; La-Rocca, Silvana; Lopez, Veronica; Da-Costa, Natalia; Fernandez, Veronica

2017-01-01

In the cestode parasite Echinococcus granulosus, three phylogenetically distant cytosolic glutathione transferases (GSTs) (EgGST1, 2 and 3) were identified. Interestingly, the C-terminal domains of EgGST3 and EgGST2 but not EgGST1, exhibit all amino acids involved in Sigma-class GST dimerization. Here, we provide evidence indicating that EgGST2 and EgGST3 naturally form a heterodimeric structure (EgGST2-3), and also we report the enzymatic activity of the recombinant heterodimer. EgGST2-3 might display novel properties able to influence the infection establishment. This is the first report of a stable heterodimeric GST built up by phylogenetically distant subunits. Copyright © 2016 Elsevier B.V. All rights reserved.

Design and Analysis of the Measurement Characteristics of a Bidirectional-Decoupling Over-Constrained Six-Dimensional Parallel-Mechanism Force Sensor

PubMed Central

Zhao, Tieshi; Zhao, Yanzhi; Hu, Qiangqiang; Ding, Shixing

2017-01-01

The measurement of large forces and the presence of errors due to dimensional coupling are significant challenges for multi-dimensional force sensors. To address these challenges, this paper proposes an over-constrained six-dimensional force sensor based on a parallel mechanism of steel ball structures as a measurement module. The steel ball structure can be subject to rolling friction instead of sliding friction, thus reducing the influence of friction. However, because the structure can only withstand unidirectional pressure, the application of steel balls in a six-dimensional force sensor is difficult. Accordingly, a new design of the sensor measurement structure was designed in this study. The static equilibrium and displacement compatibility equations of the sensor prototype’s over-constrained structure were established to obtain the transformation function, from which the forces in the measurement branches of the proposed sensor were then analytically derived. The sensor’s measurement characteristics were then analysed through numerical examples. Finally, these measurement characteristics were confirmed through calibration and application experiments. The measurement accuracy of the proposed sensor was determined to be 1.28%, with a maximum coupling error of 1.98%, indicating that the proposed sensor successfully overcomes the issues related to steel ball structures and provides sufficient accuracy. PMID:28867812

The evolutionary roots of human decision making.

PubMed

Santos, Laurie R; Rosati, Alexandra G

2015-01-03

Humans exhibit a suite of biases when making economic decisions. We review recent research on the origins of human decision making by examining whether similar choice biases are seen in nonhuman primates, our closest phylogenetic relatives. We propose that comparative studies can provide insight into four major questions about the nature of human choice biases that cannot be addressed by studies of our species alone. First, research with other primates can address the evolution of human choice biases and identify shared versus human-unique tendencies in decision making. Second, primate studies can constrain hypotheses about the psychological mechanisms underlying such biases. Third, comparisons of closely related species can identify when distinct mechanisms underlie related biases by examining evolutionary dissociations in choice strategies. Finally, comparative work can provide insight into the biological rationality of economically irrational preferences.

Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists.

PubMed

Lentendu, Guillaume; Mahé, Frédéric; Bass, David; Rueckert, Sonja; Stoeck, Thorsten; Dunthorn, Micah

2018-05-30

Tropical animals and plants are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown whether microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of tropical protists, we used metabarcoding data of species sampled in the soils of three lowland Neotropical rainforests. Taxa-area and distance-decay relationships for three of the dominant protist taxa and their subtaxa were estimated at both the OTU and phylogenetic levels, with presence-absence and abundance-based measures. These estimates were compared to null models. High local alpha and low regional beta diversity patterns were consistently found for both the parasitic Apicomplexa and the largely free-living Cercozoa and Ciliophora. Similar to animals and plants, the protists showed spatial structures between forests at the OTU and phylogenetic levels, and only at the phylogenetic level within forests. These results suggest that the biogeographies of macro- and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. However, and unlike the animals and plants, the protist OTUs did not exhibit spatial structures within forests, which hinders our ability to estimate the local and regional diversity of protists in tropical forests. © 2018 John Wiley & Sons Ltd.

Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau

PubMed Central

Li, Yuntao; Adams, Jonathan; Shi, Yu; Wang, Hao; He, Jin-Sheng; Chu, Haiyan

2017-01-01

Global change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community. Bacterial and eukaryotic diversity was quite stable among different soil water availability, but archaeal diversity was dramatically different between the habitats. The auxotype of methanogens also varied significantly among different habitats. The co-varying soil properties among habitats shaped the community structure of soil microbes, with archaea being particularly sensitive in terms of community composition, diversity and functional groups. Bacterial and archaeal phylogenetic community turnover was mainly driven by deterministic processes while stochastic processes had stronger effects on eukaryotic phylogenetic community turnover. Our work provides insight into microbial community, functional group and phylogenetic turnover under different soil conditions in low-latitude alpine ecosystem. PMID:28401921

Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Li, Yuntao; Adams, Jonathan; Shi, Yu; Wang, Hao; He, Jin-Sheng; Chu, Haiyan

2017-04-01

Global change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community. Bacterial and eukaryotic diversity was quite stable among different soil water availability, but archaeal diversity was dramatically different between the habitats. The auxotype of methanogens also varied significantly among different habitats. The co-varying soil properties among habitats shaped the community structure of soil microbes, with archaea being particularly sensitive in terms of community composition, diversity and functional groups. Bacterial and archaeal phylogenetic community turnover was mainly driven by deterministic processes while stochastic processes had stronger effects on eukaryotic phylogenetic community turnover. Our work provides insight into microbial community, functional group and phylogenetic turnover under different soil conditions in low-latitude alpine ecosystem.

Environmental filtering structures tree functional traits combination and lineages across space in tropical tree assemblages.

PubMed

Asefa, Mengesha; Cao, Min; Zhang, Guocheng; Ci, Xiuqin; Li, Jie; Yang, Jie

2017-03-09

Environmental filtering consistently shapes the functional and phylogenetic structure of species across space within diverse forests. However, poor descriptions of community functional and lineage distributions across space hamper the accurate understanding of coexistence mechanisms. We combined environmental variables and geographic space to explore how traits and lineages are filtered by environmental factors using extended RLQ and fourth-corner analyses across different spatial scales. The dispersion patterns of traits and lineages were also examined in a 20-ha tropical rainforest dynamics plot in southwest China. We found that environmental filtering was detected across all spatial scales except the largest scale (100 × 100 m). Generally, the associations between functional traits and environmental variables were more or less consistent across spatial scales. Species with high resource acquisition-related traits were associated with the resource-rich part of the plot across the different spatial scales, whereas resource-conserving functional traits were distributed in limited-resource environments. Furthermore, we found phylogenetic and functional clustering at all spatial scales. Similar functional strategies were also detected among distantly related species, suggesting that phylogenetic distance is not necessarily a proxy for functional distance. In summary, environmental filtering considerably structured the trait and lineage assemblages in this species-rich tropical rainforest.

Bioinformatics analysis of the oxidosqualene cyclase gene and the amino acid sequence in mangrove plants

NASA Astrophysics Data System (ADS)

Basyuni, M.; Wati, R.

2017-01-01

This study described the bioinformatics methods to analyze seven oxidosqualene cyclase (OSC) genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, similarity, subcellular localization and phylogenetic. The physical and chemical properties of seven mangrove OSC showed variation among the genes. The percentage of the secondary structure of seven mangrove OSC genes followed the order of a helix > random coil > extended chain structure. The values of chloroplast or signal peptide were too low, indicated that no chloroplast transit peptide or signal peptide of secretion pathway in mangrove OSC genes. The target peptide value of mitochondria varied from 0.163 to 0.430, indicated it was possible to exist. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove OSC genes. To clarify the relationship among the mangrove OSC gene, a phylogenetic tree was constructed. The phylogenetic tree shows that there are three clusters, Kandelia KcMS join with Bruguiera BgLUS, Rhizophora RsM1 was close to Bruguiera BgbAS, and Rhizophora RcCAS join with Kandelia KcCAS. The present study, therefore, supported the previous results that plant OSC genes form distinct clusters in the tree.

Investigating the link between fish community structure and environmental state in deep-time

NASA Astrophysics Data System (ADS)

Sibert, E. C.

2017-12-01

In the modern ocean, a bottom-up ecological viewpoint posits that the composition of plankton communities is often a function of ambient oceanographic conditions, including nutrient concentrations and water temperature. Thus, certain plankton species or communities can be associated with specific oceanographic conditions, giving them potential as carriers of paleoceanographic information. Furthermore, consumer groups, such as fish, depend on the structure and composition of these plankton, and therefore different plankton communities will support different types of fish. In addition, fish have their own physiological constraints for surviving in particular environments, such as oxygen demand, and metabolic rate, causing certain clades to be selectively associated with different water mass characteristics. Thus, the relative or absolute abundances of different fish species or groups could shed light on shifting oxygen concentrations, temperature, or primary productivity in the past. To assess whether fish communities have sufficient environmental control to provide paleoceanographic insights, I use a variety of morphological, phylogenetic, and ecological statistical approaches, to correlate modern fish communities from around the world with environmental variables. I then apply these principles to a series of ichthyolith assemblages from the Cretaceous and Cenozoic, across both space and time, to assess whether fish community composition, abundance, or other characteristics can be predictive of ocean temperature or export productivity. I find that while the abundance of fish fossils in deep-sea cores is often, though not always, correlated with certain export production and temperature proxies, community composition appears to vary independently of these variables on long timescales, driven more by evolutionary processes. However, there are distinct differences in contemporary communities in different locations, suggesting that there is potential in using fish community composition in well-constrained systems. Furthermore, when fish community structure or abundance diverges from the expected state, this may provide significant insight into the structure and functioning of marine ecosystems.

A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters

PubMed Central

Saier, Milton H.

2000-01-01

A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects. PMID:10839820

Thioredoxin and evolution

NASA Technical Reports Server (NTRS)

Buchanan, B. B.

1991-01-01

Comparisons of primary structure have revealed significant homology between the m type thioredoxins of chloroplasts and the thioredoxins from a variety of bacteria. Chloroplast thioredoxin f, by comparison, remains an enigma: certain residues are invariant with those of the other thioredoxins, but a phylogenetic relationship to bacterial or m thioredoxins seems distant. Knowledge of the evolutionary history of thioredoxin f is, nevertheless, of interest because of its role in photosynthesis. Therefore, we have attempted to gain information on the evolutionary history of chloroplast thioredoxin f, as well as m. Our goal was first to establish the utility of thioredoxin as a phylogenetic marker, and, if found suitable, to deduce the evolutionary histories of the chloroplast thioredoxins. To this end, we have constructed phylogenetic (minimal replacement) trees using computer analysis. The results show that the thioredoxins of bacteria and animals fall into distinct phylogenetic groups - the bacterial group resembling that derived from earlier 16s RNA analysis and the animal group showing a cluster consistent with known relationships. The chloroplast thioredoxins show a novel type of phylogenetic arrangement: one m type aligns with its counterpart of eukaryotic algae, cyanobacteria and other bacteria, whereas the second type (f type) tracks with animal thioredoxin. The results give new insight into the evolution of photosynthesis.

Single-cell analysis of uncultured magnetotactic bacteria via fluorescence-coupled electron microscopy approach

NASA Astrophysics Data System (ADS)

LI, J.; Zhang, H.; Liu, P.; Menguy, N.; Pan, Y.

2017-12-01

Magnetotactic bacteria (MTB) are phylogenetically diverse and can biomineralize magnetic nanocrystals of magnetite or greigite in intracellular structures termed magnetosomes. Their remains within sediments or sedimentary rocks, i.e. magnetofossils, have been used to retrieve paleomagnetic and paleoenvironmental information of deposition time, as well as to trace the origin and evolution of life on Earth and even perhaps Mars. A precise identification of magnetofossils heavily depends on our knowledge of phylogenetic diversity and magnetosomal biomineralization within natural MTB. In this paper, we will present a novel method which can rapidly characterize both the phylogenetic and biomineralogical properties of uncultured MTB at the single-cell level by coupling fluorescence and electron microscopy. Using this method, we have successfully identified several uncultured MTB strains from natural environments in China. These MTB are phylogenetically affiliated with the Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria and Nitrospirae phylum, and form octahedral, cuboctahedral, prismatic, tooth-like and bullet-shaped magnetite magnetosomes. A corresponding analysis of magnetosome morphology and bacterial phylogenetics on each MTB strain has shown a species/strain-specific magnetosome biomineralization. The new method is not only promising for better understanding the correlation between magnetosome mineral habits and MTB phylogenies, but also crucial for unambiguously identifying magnetofossils.

Phylogenetic and functional traits of ectomycorrhizal assemblages in top soil from different biogeographic regions and forest types.

PubMed

Pena, Rodica; Lang, Christa; Lohaus, Gertrud; Boch, Steffen; Schall, Peter; Schöning, Ingo; Ammer, Christian; Fischer, Markus; Polle, Andrea

2017-04-01

Ectomycorrhizal (EM) fungal taxonomic, phylogenetic, and trait diversity (exploration types) were analyzed in beech and conifer forests along a north-to-south gradient in three biogeographic regions in Germany. The taxonomic community structures of the ectomycorrhizal assemblages in top soil were influenced by stand density and forest type, by biogeographic environmental factors (soil physical properties, temperature, and precipitation), and by nitrogen forms (amino acids, ammonium, and nitrate). While α-diversity did not differ between forest types, β-diversity increased, leading to higher γ-diversity on the landscape level when both forest types were present. The highest taxonomic diversity of EM was found in forests in cool, moist climate on clay and silty soils and the lowest in the forests in warm, dry climate on sandy soils. In the region with higher taxonomic diversity, phylogenetic clustering was found, but not trait clustering. In the warm region, trait clustering occurred despite neutral phylogenetic effects. These results suggest that different forest types and favorable environmental conditions in forests promote high EM species richness in top soil presumably with both high functional diversity and phylogenetic redundancy, while stressful environmental conditions lead to lower species richness and functional redundancy.

The building of a biodiversity hotspot across a land-bridge in the Mediterranean

PubMed Central

Molina-Venegas, Rafael; Aparicio, Abelardo; Lavergne, Sébastien; Arroyo, Juan

2015-01-01

Many of the macroevolutionary processes that have shaped present-day phylogenetic patterns were caused by geological events such as plate tectonics and temporary land-bridges. The study of spatial patterns of phylogenetic diversity can provide insights into these past events. Here we focus on a western Mediterranean biodiversity hotspot located in the southern Iberian Peninsula and northwest Africa, two regions that are separated by the Strait of Gibraltar. We explore the spatial structure of the phylogenetic relationships within and across large-scale plant assemblages. Significant turnover in terminal lineages tends to occur between landmasses, whereas turnover in deep lineages tends to occur within landmasses. Plant assemblages in the western ecoregions of this hotspot tend to be phylogenetically overdispersed but are phylogenetically clustered on its eastern margins. We discuss our results in the light of potential scenarios of niche evolution (or conservatism) and lineage diversification. The significant turnover between landmasses suggests a common scenario of allopatric speciation that could have been facilitated by the intermittent joining of the two continents. This may have constituted an important stimulus for diversification and the emergence of this western Mediterranean biodiversity hotspot. PMID:26246551

The building of a biodiversity hotspot across a land-bridge in the Mediterranean.

PubMed

Molina-Venegas, Rafael; Aparicio, Abelardo; Lavergne, Sébastien; Arroyo, Juan

2015-08-22

Many of the macroevolutionary processes that have shaped present-day phylogenetic patterns were caused by geological events such as plate tectonics and temporary land-bridges. The study of spatial patterns of phylogenetic diversity can provide insights into these past events. Here we focus on a western Mediterranean biodiversity hotspot located in the southern Iberian Peninsula and northwest Africa, two regions that are separated by the Strait of Gibraltar. We explore the spatial structure of the phylogenetic relationships within and across large-scale plant assemblages. Significant turnover in terminal lineages tends to occur between landmasses, whereas turnover in deep lineages tends to occur within landmasses. Plant assemblages in the western ecoregions of this hotspot tend to be phylogenetically overdispersed but are phylogenetically clustered on its eastern margins. We discuss our results in the light of potential scenarios of niche evolution (or conservatism) and lineage diversification. The significant turnover between landmasses suggests a common scenario of allopatric speciation that could have been facilitated by the intermittent joining of the two continents. This may have constituted an important stimulus for diversification and the emergence of this western Mediterranean biodiversity hotspot. © 2015 The Author(s).

Prioritizing Populations for Conservation Using Phylogenetic Networks

PubMed Central

Volkmann, Logan; Martyn, Iain; Moulton, Vincent; Spillner, Andreas; Mooers, Arne O.

2014-01-01

In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations. PMID:24586451

Evolution of oil-producing trichomes in Sisyrinchium (Iridaceae): insights from the first comprehensive phylogenetic analysis of the genus

PubMed Central

Chauveau, Olivier; Eggers, Lilian; Raquin, Christian; Silvério, Adriano; Brown, Spencer; Couloux, Arnaud; Cruaud, Corine; Kaltchuk-Santos, Eliane; Yockteng, Roxana; Souza-Chies, Tatiana T.; Nadot, Sophie

2011-01-01

Background and Aims Sisyrinchium (Iridaceae: Iridoideae: Sisyrinchieae) is one of the largest, most widespread and most taxonomically complex genera in Iridaceae, with all species except one native to the American continent. Phylogenetic relationships within the genus were investigated and the evolution of oil-producing structures related to specialized oil-bee pollination examined. Methods Phylogenetic analyses based on eight molecular markers obtained from 101 Sisyrinchium accessions representing 85 species were conducted in the first extensive phylogenetic analysis of the genus. Total evidence analyses confirmed the monophyly of the genus and retrieved nine major clades weakly connected to the subdivisions previously recognized. The resulting phylogenetic hypothesis was used to reconstruct biogeographical patterns, and to trace the evolutionary origin of glandular trichomes present in the flowers of several species. Key Results and Conclusions Glandular trichomes evolved three times independently in the genus. In two cases, these glandular trichomes are oil-secreting, suggesting that the corresponding flowers might be pollinated by oil-bees. Biogeographical patterns indicate expansions from Central America and the northern Andes to the subandean ranges between Chile and Argentina and to the extended area of the Paraná river basin. The distribution of oil-flower species across the phylogenetic trees suggests that oil-producing trichomes may have played a key role in the diversification of the genus, a hypothesis that requires future testing. PMID:21527419

Assessing the influence of biogeographical region and phylogenetic history on chemical defences and herbivory in Quercus species.

PubMed

Moreira, Xoaquín; Abdala-Roberts, Luis; Galmán, Andrea; Francisco, Marta; Fuente, María de la; Butrón, Ana; Rasmann, Sergio

2018-06-07

Biogeographical factors and phylogenetic history are key determinants of inter-specific variation in plant defences. However, few studies have conducted broad-scale geographical comparisons of plant defences while controlling for phylogenetic relationships, and, in doing so, none have separated constitutive from induced defences. This gap has limited our understanding of how historical or large-scale processes mediate biogeographical patterns in plant defences since these may be contingent upon shared evolutionary history and phylogenetic constraints. We conducted a phylogenetically-controlled experiment testing for differences in constitutive leaf chemical defences and their inducibility between Palearctic and Nearctic oak species (Quercus, total 18 species). We induced defences in one-year old plants by inflicting damage by gypsy moth larvae (Lymantria dispar), estimated the amount of leaf area consumed, and quantified various groups of phenolic compounds. There was no detectable phylogenetic signal for constitutive or induced levels of most defensive traits except for constitutive condensed tannins, as well as no phylogenetic signal in leaf herbivory. We did, however, find marked differences in defence levels between oak species from each region: Palearctic species had higher levels of constitutive condensed tannins, but less constitutive lignins and less constitutive and induced hydrolysable tannins compared with Nearctic species. Additionally, Palearctic species had lower levels of leaf damage compared with Nearctic species. These differences in leaf damage, lignins and hydrolysable (but not condensed) tannins were lost after accounting for phylogeny, suggesting that geographical structuring of phylogenetic relationships mediated biogeographical differences in defences and herbivore resistance. Together, these findings suggest that historical processes and large-scale drivers have shaped differences in allocation to constitutive defences (and in turn resistance) between Palearctic and Nearctic oaks. Moreover, although evidence of phylogenetic conservatism in the studied traits is rather weak, shared evolutionary history appears to mediate some of these biogeographical patterns in allocation to chemical defences. Copyright © 2018 Elsevier Ltd. All rights reserved.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

DOE PAGES

Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J.; ...

2017-06-12

We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster withmore » potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.« less

Basic Helix-Loop-Helix Transcription Factor Gene Family Phylogenetics and Nomenclature

PubMed Central

Skinner, Michael K.; Rawls, Alan; Wilson-Rawls, Jeanne; Roalson, Eric H.

2010-01-01

A phylogenetic analysis of the basic helix-loop-helix (bHLH) gene superfamily was performed using seven different species (human, mouse, rat, worm, fly, yeast, and plant Arabidopsis) and involving over 600 bHLH genes [1]. All bHLH genes were identified in the genomes of the various species, including expressed sequence tags, and the entire coding sequence was used in the analysis. Nearly 15% of the gene family has been updated or added since the original publication. A super-tree involving six clades and all structural relationships was established and is now presented for four of the species. The wealth of functional data available for members of the bHLH gene superfamily provides us with the opportunity to use this exhaustive phylogenetic tree to predict potential functions of uncharacterized members of the family. This phylogenetic and genomic analysis of the bHLH gene family has revealed unique elements of the evolution and functional relationships of the different genes in the bHLH gene family. PMID:20219281

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J.

We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster withmore » potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.« less

Alpine cushion plants inhibit the loss of phylogenetic diversity in severe environments.

PubMed

Butterfield, B J; Cavieres, L A; Callaway, R M; Cook, B J; Kikvidze, Z; Lortie, C J; Michalet, R; Pugnaire, F I; Schöb, C; Xiao, S; Zaitchek, B; Anthelme, F; Björk, R G; Dickinson, K; Gavilán, R; Kanka, R; Maalouf, J-P; Noroozi, J; Parajuli, R; Phoenix, G K; Reid, A; Ridenour, W; Rixen, C; Wipf, S; Zhao, L; Brooker, R W

2013-04-01

Biotic interactions can shape phylogenetic community structure (PCS). However, we do not know how the asymmetric effects of foundation species on communities extend to effects on PCS. We assessed PCS of alpine plant communities around the world, both within cushion plant foundation species and adjacent open ground, and compared the effects of foundation species and climate on alpha (within-microsite), beta (between open and cushion) and gamma (open and cushion combined) PCS. In the open, alpha PCS shifted from highly related to distantly related with increasing potential productivity. However, we found no relationship between gamma PCS and climate, due to divergence in phylogenetic composition between cushion and open sub-communities in severe environments, as demonstrated by increasing phylo-beta diversity. Thus, foundation species functioned as micro-refugia by facilitating less stress-tolerant lineages in severe environments, erasing a global productivity - phylogenetic diversity relationship that would go undetected without accounting for this important biotic interaction. © 2013 Blackwell Publishing Ltd/CNRS.

Phylogenetic diversity of a microbialite reef in a cold alkaline freshwater lake.

PubMed

Chan, Olivia W; Bugler-Lacap, Donnabella C; Biddle, Jennifer F; Lim, Darlene S; McKay, Christopher P; Pointing, Stephen B

2014-06-01

A culture-independent multidomain survey of biodiversity in microbialite structures within the cold alkaline Pavilion Lake (British Columbia, Canada) revealed a largely homogenous community at depths from 10 to 30 m. Real-time quantitative PCR was used to demonstrate that bacteria comprised approximately 80%-95% of recoverable phylotypes. Archaeal phylotypes accounted for <5% of the community in microbialites exposed to the water column, while structures in sediment contact supported 4- to 5-fold higher archaeal abundance. Eukaryal phylotypes were rare and indicated common aquatic diatoms that were concluded not to be part of the microbialite community. Phylogenetic analysis of rRNA genes from clone libraries (N = 491) revealed that alphaproteobacterial phylotypes were most abundant. Cyanobacterial phylotypes were highly diverse but resolved into 4 dominant genera: Acaryochloris, Leptolyngbya, Microcoleus, and Pseudanabaena. Interestingly, microbialite cyanobacteria generally affiliated phylogenetically with aquatic and coral cyanobacterial groups rather than those from stromatolites. Other commonly encountered bacterial phylotypes were from members of the Acidobacteria, with relatively low abundance of the Betaproteobacteria, Chloroflexi, Nitrospirae, and Planctomycetes. Archaeal diversity (N = 53) was largely accounted for by Euryarchaeota, with most phylotypes affiliated with freshwater methanogenic taxa.

Functional and phylogenetic structure of island bird communities.

PubMed

Si, Xingfeng; Cadotte, Marc W; Zeng, Di; Baselga, Andrés; Zhao, Yuhao; Li, Jiaqi; Wu, Yiru; Wang, Siyu; Ding, Ping

2017-05-01

Biodiversity change in anthropogenically transformed habitats is often nonrandom, yet the nature and importance of the different mechanisms shaping community structure are unclear. Here, we extend the classic Theory of Island Biogeography (TIB) to account for nonrandom processes by incorporating species traits and phylogenetic relationships into a study of faunal relaxation following habitat loss and fragmentation. Two possible mechanisms can create nonrandom community patterns on fragment islands. First, small and isolated islands might consist of similar or closely related species because they are environmentally homogeneous or select for certain shared traits, such as dispersal ability. Alternatively, communities on small islands might contain more dissimilar or distantly related species than on large islands because limited space and resource availability result in greater competitive exclusion among species with high niche overlap. Breeding birds were surveyed on 36 islands and two mainland sites annually from 2010 to 2014 in the Thousand Island Lake region, China. We assessed community structure of breeding birds on these subtropical land-bridge islands by integrating species' trait and evolutionary distances. We additionally analysed habitat heterogeneity and variance in size ratios to distinguish biotic and abiotic processes of community assembly. Results showed that functional-phylogenetic diversity increased with island area, and decreased with isolation. Bird communities on the mainland were more diverse and generally less clustered than island bird communities and not different than randomly assembled communities. Bird communities on islands tend to be functionally similar and phylogenetically clustered, especially on small and isolated islands. The nonrandom decline in species diversity and change in bird community structure with island area and isolation, along with the relatively homogeneous habitats on small islands, support the environmental filtering hypothesis. Our study demonstrates the importance of integrating multiple forms of diversity for understanding the effects of habitat loss and fragmentation, and further reveals that TIB could be extended to community measures by moving beyond assumptions of species equivalency in colonisation rates and extinction susceptibilities. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Redescription of two species of Thaparocleidus (Monogenea: Dactylogyridae), with the description of T. armillatus sp. n. from Wallago attu and a phylogenetic analysis based on 18S rDNA sequences.

PubMed

Verma, Chandni; Chaudhary, Anshu; Shanker Singh, Hridaya

2017-09-26

The phylogenetic studies on monogeneans of the genus Thaparocleidus parasitizing W. attu in India was inferred from 18S rDNA gene data. Out of species of Thaparocleidus, one new, T. armillatus sp. n., is described herein which distinguished from its congener species in the shapes and sizes of sclerotized structures and rest of the two species, T. indicus and T. wallagonius are redescribed morphologically as well as validated and confirmed by molecular means also. Besides the above, T. gangus was also included in the molecular analysis as it is recently described on the basis of morphology only. The phylogenetic tree was also reconstructed in order to elucidate the taxonomic status of Thaparocleidus armillatus sp. n., T. indicus, T. wallagonius and T. gangus. This research reports for the first time, the molecular phylogenetic analysis of 18S rDNA gene for four species belonging to the genus Thaparocleidus from W. attu collected off the River Ganga in India. In phylogram, all four species of Thapaocleidus come in a single clade that confirmed their monophyletic status. A very low interspecific variability was observed in T. armillatus sp. n. and T. wallagonius suggesting that these species are highly similar in morphology. Correspondingly, T. indicus and T. gangus also showed low interspecific variability which too signifies their morphological similarities in their sclerotized structures. Our result suggested that all four species taken in the present investigation from India are monophyletic and it is also observed that morphological similarities in the sclerotized structures are well correlated with phylogeny.

Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution.

PubMed

Slater, Graham J

2015-04-21

A long-standing hypothesis in adaptive radiation theory is that ecological opportunity constrains rates of phenotypic evolution, generating a burst of morphological disparity early in clade history. Empirical support for the early burst model is rare in comparative data, however. One possible reason for this lack of support is that most phylogenetic tests have focused on extant clades, neglecting information from fossil taxa. Here, I test for the expected signature of adaptive radiation using the outstanding 40-My fossil record of North American canids. Models implying time- and diversity-dependent rates of morphological evolution are strongly rejected for two ecologically important traits, body size and grinding area of the molar teeth. Instead, Ornstein-Uhlenbeck processes implying repeated, and sometimes rapid, attraction to distinct dietary adaptive peaks receive substantial support. Diversity-dependent rates of morphological evolution seem uncommon in clades, such as canids, that exhibit a pattern of replicated adaptive radiation. Instead, these clades might best be thought of as deterministic radiations in constrained Simpsonian subzones of a major adaptive zone. Support for adaptive peak models may be diagnostic of subzonal radiations. It remains to be seen whether early burst or ecological opportunity models can explain broader adaptive radiations, such as the evolution of higher taxa.

Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution

NASA Astrophysics Data System (ADS)

Slater, Graham J.

2015-04-01

A long-standing hypothesis in adaptive radiation theory is that ecological opportunity constrains rates of phenotypic evolution, generating a burst of morphological disparity early in clade history. Empirical support for the early burst model is rare in comparative data, however. One possible reason for this lack of support is that most phylogenetic tests have focused on extant clades, neglecting information from fossil taxa. Here, I test for the expected signature of adaptive radiation using the outstanding 40-My fossil record of North American canids. Models implying time- and diversity-dependent rates of morphological evolution are strongly rejected for two ecologically important traits, body size and grinding area of the molar teeth. Instead, Ornstein-Uhlenbeck processes implying repeated, and sometimes rapid, attraction to distinct dietary adaptive peaks receive substantial support. Diversity-dependent rates of morphological evolution seem uncommon in clades, such as canids, that exhibit a pattern of replicated adaptive radiation. Instead, these clades might best be thought of as deterministic radiations in constrained Simpsonian subzones of a major adaptive zone. Support for adaptive peak models may be diagnostic of subzonal radiations. It remains to be seen whether early burst or ecological opportunity models can explain broader adaptive radiations, such as the evolution of higher taxa.

Compartments in a marine food web associated with phylogeny, body mass, and habitat structure.

PubMed

Rezende, Enrico L; Albert, Eva M; Fortuna, Miguel A; Bascompte, Jordi

2009-08-01

A long-standing question in community ecology is whether food webs are organized in compartments, where species within the same compartment interact frequently among themselves, but show fewer interactions with species from other compartments. Finding evidence for this community organization is important since compartmentalization may strongly affect food web robustness to perturbation. However, few studies have found unequivocal evidence of compartments, and none has quantified the suite of mechanisms generating such a structure. Here, we combine computational tools from the physics of complex networks with phylogenetic statistical methods to show that a large marine food web is organized in compartments, and that body size, phylogeny, and spatial structure are jointly associated with such a compartmentalized structure. Sharks account for the majority of predatory interactions within their compartments. Phylogenetically closely related shark species tend to occupy different compartments and have divergent trophic levels, suggesting that competition may play an important role structuring some of these compartments. Current overfishing of sharks has the potential to change the structural properties, which might eventually affect the stability of the food web.

Hydrologic consistency as a basis for assessing complexity of monthly water balance models for the continental United States

NASA Astrophysics Data System (ADS)

Martinez, Guillermo F.; Gupta, Hoshin V.

2011-12-01

Methods to select parsimonious and hydrologically consistent model structures are useful for evaluating dominance of hydrologic processes and representativeness of data. While information criteria (appropriately constrained to obey underlying statistical assumptions) can provide a basis for evaluating appropriate model complexity, it is not sufficient to rely upon the principle of maximum likelihood (ML) alone. We suggest that one must also call upon a "principle of hydrologic consistency," meaning that selected ML structures and parameter estimates must be constrained (as well as possible) to reproduce desired hydrological characteristics of the processes under investigation. This argument is demonstrated in the context of evaluating the suitability of candidate model structures for lumped water balance modeling across the continental United States, using data from 307 snow-free catchments. The models are constrained to satisfy several tests of hydrologic consistency, a flow space transformation is used to ensure better consistency with underlying statistical assumptions, and information criteria are used to evaluate model complexity relative to the data. The results clearly demonstrate that the principle of consistency provides a sensible basis for guiding selection of model structures and indicate strong spatial persistence of certain model structures across the continental United States. Further work to untangle reasons for model structure predominance can help to relate conceptual model structures to physical characteristics of the catchments, facilitating the task of prediction in ungaged basins.

A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

PubMed

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

Combined constraints on the structure and physical properties of the East Antarctic lithosphere from geology and geophysics.

NASA Astrophysics Data System (ADS)

Reading, A. M.; Staal, T.; Halpin, J.; Whittaker, J. M.; Morse, P. E.

2017-12-01

The lithosphere of East Antarctica is one of the least explored regions of the planet, yet it is gaining in importance in global scientific research. Continental heat flux density and 3D glacial isostatic adjustment studies, for example, rely on a good knowledge of the deep structure in constraining model inputs.In this contribution, we use a multidisciplinary approach to constrain lithospheric domains. To seismic tomography models, we add constraints from magnetic studies and also new geological constraints. Geological knowledge exists around the periphery of East Antarctica and is reinforced in the knowledge of plate tectonic reconstructions. The subglacial geology of the Antarctic hinterland is largely unknown but the plate reconstructions allow the well-posed extrapolation of major terranes into the interior of the continent, guided by the seismic tomography and magnetic images. We find that the northern boundary of the lithospheric domain centred on the Gamburtsev Subglacial Mountains has a possible trend that runs south of the Lambert Glacier region, turning coastward through Wilkes Land. Other periphery-to-interior connections are less well constrained and the possibility of lithospheric domains that are entirely sub-glacial is high. We develop this framework to include a probabilistic method of handling alternate models and quantifiable uncertainties. We also show first results in using a Bayesian approach to predicting lithospheric boundaries from multivariate data.Within the newly constrained domains, we constrain heat flux (density) as the sum of basal heat flux and upper crustal heat flux. The basal heat flux is constrained by geophysical methods while the upper crustal heat flux is constrained by geology or predicted geology. In addition to heat flux constraints, we also consider the variations in friction experienced by moving ice sheets due to varying geology.

An Algorithmic, Pie-Crusting Medial Soft Tissue Release Reduces the Need for Constrained Inserts Patients With Severe Varus Deformity Undergoing Total Knee Arthroplasty.

PubMed

Goudarz Mehdikhani, Kaveh; Morales Moreno, Beatriz; Reid, Jeremy J; de Paz Nieves, Ana; Lee, Yuo-Yu; González Della Valle, Alejandro

2016-07-01

We studied the need to use a constrained insert for residual intraoperative instability and the 1-year result of patients undergoing total knee arthroplasty (TKA) for a varus deformity. In a control group, a "classic" subperiosteal release of the medial soft tissue sleeve was performed as popularized by pioneers of TKA. In the study group, an algorithmic approach that selectively releases and pie-crusts posteromedial structures in extension and anteromedial structures in flexion was used. All surgeries were performed by a single surgeon using measured resection technique, and posterior-stabilized, cemented implants. There were 228 TKAs in the control group and 188 in the study group. Outcome variables included the use of a constrained insert, and the Knee Society Score at 6 weeks, 4 months, and 1 year postoperatively. The effect of the release technique on use of constrained inserts and clinical outcomes were analyzed in a multivariate model controlling for age, sex, body mass index, and severity of deformity. The use of constrained inserts was significantly lower in study than in control patients (8% vs 18%; P = .002). There was no difference in the Knee Society Score and range of motion between the groups at last follow-up. No patient developed postoperative medial instability. This algorithmic, pie-crusting release technique resulted in a significant reduction in the use of constrained inserts with no detrimental effects in clinical results, joint function, and stability. As constrained TKA implants are more costly than nonconstrained ones, if the adopted technique proves to be safe in the long term, it may cause a positive shift in value for hospitals and cost savings in the health care system. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakraborty, Sandeep; Rao, Basuthkar J.; Baker, Nathan A.

2013-04-01

Phylogenetic analysis of proteins using multiple sequence alignment (MSA) assumes an underlying evolutionary relationship in these proteins which occasionally remains undetected due to considerable sequence divergence. Structural alignment programs have been developed to unravel such fuzzy relationships. However, none of these structure based methods have used electrostatic properties to discriminate between spatially equivalent residues. We present a methodology for MSA of a set of related proteins with known structures using electrostatic properties as an additional discriminator (STEEP). STEEP first extracts a profile, then generates a multiple structural superimposition providing a consolidated spatial framework for comparing residues and finally emits themore » MSA. Residues that are aligned differently by including or excluding electrostatic properties can be targeted by directed evolution experiments to transform the enzymatic properties of one protein into another. We have compared STEEP results to those obtained from a MSA program (ClustalW) and a structural alignment method (MUSTANG) for chymotrypsin serine proteases. Subsequently, we used PhyML to generate phylogenetic trees for the serine and metallo-β-lactamase superfamilies from the STEEP generated MSA, and corroborated the accepted relationships in these superfamilies. We have observed that STEEP acts as a functional classifier when electrostatic congruence is used as a discriminator, and thus identifies potential targets for directed evolution experiments. In summary, STEEP is unique among phylogenetic methods for its ability to use electrostatic congruence to specify mutations that might be the source of the functional divergence in a protein family. Based on our results, we also hypothesize that the active site and its close vicinity contains enough information to infer the correct phylogeny for related proteins.« less

[Dominant structural and functional adaptations of distant chemosensory systems in phylogenesis of Gastropoda].

PubMed

Zaĭtseva, O V

2000-08-01

The invasion of land by gastropods independent and repeated in the course of their evolution, was shown to be accompanied by appearance of organisationally similar olfactory tentacular organs and special integrative centres. The majority of primary and secondary water gastropods in different phylogenetic groups had a different, more primitive organisation of the tentacular sensory system as compared to the terrestrial species. Regularities of the phylogenetic adaptations of mollusks to the habitat media and lifestyle are discussed.

Slip-Sliding-Away: A Review of the Literature on the Constraining Qualities of PowerPoint

ERIC Educational Resources Information Center

Kernbach, Sebastian; Bresciani, Sabrina; Eppler, Martin J.

2015-01-01

PowerPoint is a dominant communication tool in business and education. It allows for creating professional-looking presentations easily, but without understanding its constraining qualities it can be used inappropriately. Therefore we conducted a systematic literature review structuring the literature on PowerPoint in three chronological phases…

Stance and strategy: post-structural perspective and post-colonial engagement to develop nursing knowledge.

PubMed

Sochan, Anne M

2011-07-01

How should nursing knowledge advance? This exploration contextualizes its evolution past and present. In addressing how it evolved in the past, a probable historical evolution of its development draws on the perspectives of Frank & Gills's World System Theory, Kuhn's treatise on Scientific Revolutions, and Foucault's notions of Discontinuities in scientific knowledge development. By describing plausible scenarios of how nursing knowledge evolved, I create a case for why nursing knowledge developers should adopt a post-structural stance in prioritizing their research agenda(s). Further, by adopting a post-structural stance, I create a case on how nurses can advance their disciplinary knowledge using an engaging post-colonial strategy. Given an interrupted history caused by influence(s) constraining nursing's knowledge development by power structures external, and internal, to nursing, knowledge development can evolve in the future by drawing on post-structural interpretation, and post-colonial strategy. The post-structural writings of Deleuze & Guattari's understanding of 'Nomadology' as a subtle means to resist being constrained by existing knowledge development structures, might be a useful stance to understanding the urgency of why nursing knowledge should advance addressing the structural influences on its development. Furthermore, Bhabha's post-colonial elucidation of 'Hybridity' as an equally discreet means to change the culture of those constraining structures is an appropriate strategy to enact how nursing knowledge developers can engage with existing power structures, and simultaneously influence that engagement. Taken together, 'post-structural stance' and 'post-colonial strategy' can refocus nursing scholarship to learn from its past, in order to develop relevant disciplinary knowledge in its future. © 2011 Blackwell Publishing Ltd.

Variation in the shape and mechanical performance of the lower jaws in ceratopsid dinosaurs (Ornithischia, Ceratopsia).

PubMed

Maiorino, Leonardo; Farke, Andrew A; Kotsakis, Tassos; Teresi, Luciano; Piras, Paolo

2015-11-01

Ceratopsidae represents a group of quadrupedal herbivorous dinosaurs that inhabited western North America and eastern Asia during the Late Cretaceous. Although horns and frills of the cranium are highly variable across species, the lower jaw historically has been considered to be relatively conservative in morphology. Here, the lower jaws from 58 specimens representing 21 ceratopsoid taxa were sampled, using geometric morphometrics and 2D finite element analysis (FEA) to explore differences in morphology and mechanical performance across Ceratopsoidea (the clade including Ceratopsidae, Turanoceratops and Zuniceratops). Principal component analyses and non-parametric permuted manovas highlight Triceratopsini as a morphologically distinct clade within the sample. A relatively robust and elongate dentary, a larger and more elongated coronoid process, and a small and dorso-ventrally compressed angular characterize this clade, as well as the absolutely larger size. By contrast, non-triceratopsin chasmosaurines, Centrosaurini and Pachyrhinosaurini have similar morphologies to each other. Zuniceratops and Avaceratops are distinct from other taxa. No differences in size between Pachyrhinosaurini and Centrosaurini are recovered using non-parametric permuted anovas. Structural performance, as evaluated using a 2D FEA, is similar across all groups as measured by overall stress, with the exception of Triceratopsini. Shape, size and stress are phylogenetically constrained. A longer dentary as well as a long coronoid process result in a lower jaw that is reconstructed as relatively much more stressed in triceratopsins. © 2015 Anatomical Society.

The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation.

PubMed

Cardillo, Marcel; Weston, Peter H; Reynolds, Zoe K M; Olde, Peter M; Mast, Austin R; Lemmon, Emily M; Lemmon, Alan R; Bromham, Lindell

2017-08-01

The frequency of evolutionary biome shifts during diversification has important implications for our ability to explain geographic patterns of plant diversity. Recent studies present several examples of biome shifts, but whether frequencies of biome shifts closely reflect geographic proximity or environmental similarity of biomes remains poorly known. We explore this question by using phylogenomic methods to estimate the phylogeny of Hakea, a diverse Australian genus occupying a wide range of biomes. Model-based estimation of ancestral regions indicates that Hakea began diversifying in the Mediterranean biome of southern Australia in the Middle Eocene-Early Oligocene, and dispersed repeatedly into other biomes across the continent. We infer around 47 shifts between biomes. Frequencies of shifts between pairs of biomes are usually similar to those expected from their geographic connectedness or climatic similarity, but in some cases are substantially higher or lower than expected, perhaps reflecting how readily key physiological traits can be modified to adapt lineages to new environments. The history of frequent biome-shifting is reflected in the structure of present-day assemblages, which tend to be more phylogenetically diverse than null-model expectations. The case of Hakea demonstrates that the radiation of large plant clades across wide geographic areas need not be constrained by dispersal limitation or conserved adaptations to particular environments. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

PubMed

Xu, Weijia; Ozer, Stuart; Gutell, Robin R

2009-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA

PubMed Central

Xu, Weijia; Ozer, Stuart; Gutell, Robin R.

2010-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

Blue reflectance in tarantulas is evolutionarily conserved despite nanostructural diversity

PubMed Central

Hsiung, Bor-Kai; Deheyn, Dimitri D.; Shawkey, Matthew D.; Blackledge, Todd A.

2015-01-01

Slight shifts in arrangement within biological photonic nanostructures can produce large color differences, and sexual selection often leads to high color diversity in clades with structural colors. We use phylogenetic reconstruction, electron microscopy, spectrophotometry, and optical modeling to show an opposing pattern of nanostructural diversification accompanied by unusual conservation of blue color in tarantulas (Araneae: Theraphosidae). In contrast to other clades, blue coloration in phylogenetically distant tarantulas peaks within a narrow 20-nm region around 450 nm. Both quasi-ordered and multilayer nanostructures found in different tarantulas produce this blue color. Thus, even within monophyletic lineages, tarantulas have evolved strikingly similar blue coloration through divergent mechanisms. The poor color perception and lack of conspicuous display during courtship of tarantulas argue that these colors are not sexually selected. Therefore, our data contrast with sexual selection that typically produces a diverse array of colors with a single structural mechanism by showing that natural selection on structural color in tarantulas resulted in convergence on similar color through diverse structural mechanisms. PMID:26702433

Phase-field model of domain structures in ferroelectric thin films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Y. L.; Hu, S. Y.; Liu, Z. K.

A phase-field model for predicting the coherent microstructure evolution in constrained thin films is developed. It employs an analytical elastic solution derived for a constrained film with arbitrary eigenstrain distributions. The domain structure evolution during a cubic{r_arrow}tetragonal proper ferroelectric phase transition is studied. It is shown that the model is able to simultaneously predict the effects of substrate constraint and temperature on the volume fractions of domain variants, domain-wall orientations, domain shapes, and their temporal evolution. {copyright} 2001 American Institute of Physics.

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.

PubMed

Speiser, Daniel I; Pankey, M Sabrina; Zaharoff, Alexander K; Battelle, Barbara A; Bracken-Grissom, Heather D; Breinholt, Jesse W; Bybee, Seth M; Cronin, Thomas W; Garm, Anders; Lindgren, Annie R; Patel, Nipam H; Porter, Megan L; Protas, Meredith E; Rivera, Ajna S; Serb, Jeanne M; Zigler, Kirk S; Crandall, Keith A; Oakley, Todd H

2014-11-19

Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository ( http://bitbucket.org/osiris_phylogenetics/pia/ ) and we demonstrate PIA on a publicly-accessible web server ( http://galaxy-dev.cnsi.ucsb.edu/pia/ ). Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa.

Universal artifacts affect the branching of phylogenetic trees, not universal scaling laws.

PubMed

Altaba, Cristian R

2009-01-01

The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny? In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods. All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees. There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1.

Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboreum.

PubMed

Wang, Wei; Xia, Minxuan; Chen, Jie; Deng, Fenni; Yuan, Rui; Zhang, Xiaopei; Shen, Fafu

2016-12-01

The data presented in this paper is supporting the research article "Genome-Wide Analysis of Superoxide Dismutase Gene Family in Gossypium raimondii and G. arboreum" [1]. In this data article, we present phylogenetic tree showing dichotomy with two different clusters of SODs inferred by the Bayesian method of MrBayes (version 3.2.4), "Bayesian phylogenetic inference under mixed models" [2], Ramachandran plots of G. raimondii and G. arboreum SODs, the protein sequence used to generate 3D sructure of proteins and the template accession via SWISS-MODEL server, "SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information." [3] and motif sequences of SODs identified by InterProScan (version 4.8) with the Pfam database, "Pfam: the protein families database" [4].

Solving the Secondary Structure Matching Problem in Cryo-EM De Novo Modeling Using a Constrained K-Shortest Path Graph Algorithm.

PubMed

Al Nasr, Kamal; Ranjan, Desh; Zubair, Mohammad; Chen, Lin; He, Jing

2014-01-01

Electron cryomicroscopy is becoming a major experimental technique in solving the structures of large molecular assemblies. More and more three-dimensional images have been obtained at the medium resolutions between 5 and 10 Å. At this resolution range, major α-helices can be detected as cylindrical sticks and β-sheets can be detected as plain-like regions. A critical question in de novo modeling from cryo-EM images is to determine the match between the detected secondary structures from the image and those on the protein sequence. We formulate this matching problem into a constrained graph problem and present an O(Δ(2)N(2)2(N)) algorithm to this NP-Hard problem. The algorithm incorporates the dynamic programming approach into a constrained K-shortest path algorithm. Our method, DP-TOSS, has been tested using α-proteins with maximum 33 helices and α-β proteins up to five helices and 12 β-strands. The correct match was ranked within the top 35 for 19 of the 20 α-proteins and all nine α-β proteins tested. The results demonstrate that DP-TOSS improves accuracy, time and memory space in deriving the topologies of the secondary structure elements for proteins with a large number of secondary structures and a complex skeleton.

Mantle viscosity structure constrained by joint inversions of seismic velocities and density

NASA Astrophysics Data System (ADS)

Rudolph, M. L.; Moulik, P.; Lekic, V.

2017-12-01

The viscosity structure of Earth's deep mantle affects the thermal evolution of Earth, the ascent of mantle upwellings, sinking of subducted oceanic lithosphere, and the mixing of compositional heterogeneities in the mantle. Modeling the long-wavelength dynamic geoid allows us to constrain the radial viscosity profile of the mantle. Typically, in inversions for the mantle viscosity structure, wavespeed variations are mapped into density variations using a constant- or depth-dependent scaling factor. Here, we use a newly developed joint model of anisotropic Vs, Vp, density and transition zone topographies to generate a suite of solutions for the mantle viscosity structure directly from the seismologically constrained density structure. The density structure used to drive our forward models includes contributions from both thermal and compositional variations, including important contributions from compositionally dense material in the Large Low Velocity Provinces at the base of the mantle. These compositional variations have been neglected in the forward models used in most previous inversions and have the potential to significantly affect large-scale flow and thus the inferred viscosity structure. We use a transdimensional, hierarchical, Bayesian approach to solve the inverse problem, and our solutions for viscosity structure include an increase in viscosity below the base of the transition zone, in the shallow lower mantle. Using geoid dynamic response functions and an analysis of the correlation between the observed geoid and mantle structure, we demonstrate the underlying reason for this inference. Finally, we present a new family of solutions in which the data uncertainty is accounted for using covariance matrices associated with the mantle structure models.

The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses

PubMed Central

Zhang, Yanjun; Du, Liuwen; Liu, Ao; Chen, Jianjun; Wu, Li; Hu, Weiming; Zhang, Wei; Kim, Kyunghee; Lee, Sang-Choon; Yang, Tae-Jin; Wang, Ying

2016-01-01

Epimedium L. is a phylogenetically and economically important genus in the family Berberidaceae. We here sequenced the complete chloroplast (cp) genomes of four Epimedium species using Illumina sequencing technology via a combination of de novo and reference-guided assembly, which was also the first comprehensive cp genome analysis on Epimedium combining the cp genome sequence of E. koreanum previously reported. The five Epimedium cp genomes exhibited typical quadripartite and circular structure that was rather conserved in genomic structure and the synteny of gene order. However, these cp genomes presented obvious variations at the boundaries of the four regions because of the expansion and contraction of the inverted repeat (IR) region and the single-copy (SC) boundary regions. The trnQ-UUG duplication occurred in the five Epimedium cp genomes, which was not found in the other basal eudicotyledons. The rapidly evolving cp genome regions were detected among the five cp genomes, as well as the difference of simple sequence repeats (SSR) and repeat sequence were identified. Phylogenetic relationships among the five Epimedium species based on their cp genomes showed accordance with the updated system of the genus on the whole, but reminded that the evolutionary relationships and the divisions of the genus need further investigation applying more evidences. The availability of these cp genomes provided valuable genetic information for accurately identifying species, taxonomy and phylogenetic resolution and evolution of Epimedium, and assist in exploration and utilization of Epimedium plants. PMID:27014326

Discrete and morphometric traits reveal contrasting patterns and processes in the macroevolutionary history of a clade of scorpions.

PubMed

Mongiardino Koch, N; Ceccarelli, F S; Ojanguren-Affilastro, A A; Ramírez, M J

2017-04-01

Many palaeontological studies have investigated the evolution of entire body plans, generally relying on discrete character-taxon matrices. In contrast, macroevolutionary studies performed by neontologists have mostly focused on morphometric traits. Although these data types are very different, some studies have suggested that they capture common patterns. Nonetheless, the tests employed to support this claim have not explicitly incorporated a phylogenetic framework and may therefore be susceptible to confounding effects due to the presence of common phylogenetic structure. We address this question using the scorpion genus Brachistosternus Pocock 1893 as case study. We make use of a time-calibrated multilocus molecular phylogeny, and compile discrete and traditional morphometric data sets, both capturing the overall morphology of the organisms. We find that morphospaces derived from these matrices are significantly different, and that the degree of discordance cannot be replicated by simulations of random character evolution. Moreover, we find strong support for contrasting modes of evolution, with discrete characters being congruent with an 'early burst' scenario whereas morphometric traits suggest species-specific adaptations to have driven morphological evolution. The inferred macroevolutionary dynamics are therefore contingent on the choice of character type. Finally, we confirm that metrics of correlation fail to detect these profound differences given common phylogenetic structure in both data sets, and that methods incorporating a phylogenetic framework and accounting for expected covariance should be favoured. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees.

PubMed

Nye, Tom M W; Tang, Xiaoxian; Weyenberg, Grady; Yoshida, Ruriko

2017-12-01

Evolutionary relationships are represented by phylogenetic trees, and a phylogenetic analysis of gene sequences typically produces a collection of these trees, one for each gene in the analysis. Analysis of samples of trees is difficult due to the multi-dimensionality of the space of possible trees. In Euclidean spaces, principal component analysis is a popular method of reducing high-dimensional data to a low-dimensional representation that preserves much of the sample's structure. However, the space of all phylogenetic trees on a fixed set of species does not form a Euclidean vector space, and methods adapted to tree space are needed. Previous work introduced the notion of a principal geodesic in this space, analogous to the first principal component. Here we propose a geometric object for tree space similar to the [Formula: see text]th principal component in Euclidean space: the locus of the weighted Fréchet mean of [Formula: see text] vertex trees when the weights vary over the [Formula: see text]-simplex. We establish some basic properties of these objects, in particular showing that they have dimension [Formula: see text], and propose algorithms for projection onto these surfaces and for finding the principal locus associated with a sample of trees. Simulation studies demonstrate that these algorithms perform well, and analyses of two datasets, containing Apicomplexa and African coelacanth genomes respectively, reveal important structure from the second principal components.

Heritable Bovine Rumen Bacteria Are Phylogenetically Related and Correlated with the Cow’s Capacity To Harvest Energy from Its Feed

PubMed Central

Sasson, Goor; Kruger Ben-Shabat, Sheerli; Seroussi, Eyal; Doron-Faigenboim, Adi; Shterzer, Naama; Yaacoby, Shamay; Berg Miller, Margret E.; White, Bryan A.; Halperin, Eran

2017-01-01

ABSTRACT Ruminants sustain a long-lasting obligatory relationship with their rumen microbiome dating back 50 million years. In this unique host-microbiome relationship, the host’s ability to digest its feed is completely dependent on its coevolved microbiome. This extraordinary alliance raises questions regarding the dependent relationship between ruminants’ genetics and physiology and the rumen microbiome structure, composition, and metabolism. To elucidate this relationship, we examined the association of host genetics with the phylogenetic and functional composition of the rumen microbiome. We accomplished this by studying a population of 78 Holstein-Friesian dairy cows, using a combination of rumen microbiota data and other phenotypes from each animal with genotypic data from a subset of 47 animals. We identified 22 operational taxonomic units (OTUs) whose abundances were associated with rumen metabolic traits and host physiological traits and which showed measurable heritability. The abundance patterns of these microbes can explain high proportions of variance in rumen metabolism and many of the host physiological attributes such as its energy-harvesting efficiency. Interestingly, these OTUs shared higher phylogenetic similarity between themselves than expected by chance, suggesting occupation of a specific ecological niche within the rumen ecosystem. The findings presented here suggest that ruminant genetics and physiology are correlated with microbiome structure and that host genetics may shape the microbiome landscape by enriching for phylogenetically related taxa that may occupy a unique niche. PMID:28811339

Thysanophora penicillioides includes multiple genetically diverged groups that coexist respectively in Abies mariesii forests in Japan.

PubMed

Iwamoto, Susumu; Tokumasu, Seiji; Suyama, Yoshihisa; Kakishima, Makoto

2005-01-01

We investigated intraspecific diversity and genetic structures of a saprotrophic fungus--Thysanophora penicillioides--based on sequences of nuclear ribosomal internal transcribed spacer (ITS) in 15 discontinuous Abies mariesii forests of Japan. In such a well-defined morphological species, numerous unexpected ITS variations were revealed: 12 ITS sequence types detected in 254 isolates collected from 15 local populations were classified into five ITS sequence groups. Maximally, four ITS groups consisted of seven ITS types coexisting in one population. However, group 1 was dominant with approximately 65%; in particular, one haplotype, 1a, was most dominant with approximately 60% in respective populations. Therefore, few differences were recognized in genetic structure among local populations, implying that the gene flow of each lineage of the fungus occurs among local populations without geographic limitations. However, minor haplotypes in some ITS groups were found only in restricted areas, suggesting that they might expand steadily from their places of origin to neighboring A. mariesii forests. Aggregating sequence data of seven European strains and four North American strains from various substrates to those of Japanese strains, 18 ITS sequence types and 28 variable sites were recognized. They were clustered into nine lineages by phylogenetic analyses of the beta-tubulin and combined ITS and beta-tubulin datasets. According to phylogenetic species recognition by the concordance of genealogies, respective lineages correspond to phylogenetic species. Plural phylogenetic species coexist in a local population in an A. mariesii forest in Japan.

Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach.

PubMed

Siew, Joyce Phui Yee; Khan, Asif M; Tan, Paul T J; Koh, Judice L Y; Seah, Seng Hong; Koo, Chuay Yeng; Chai, Siaw Ching; Armugam, Arunmozhiarasi; Brusic, Vladimir; Jeyaseelan, Kandiah

2004-12-12

Sequence annotations, functional and structural data on snake venom neurotoxins (svNTXs) are scattered across multiple databases and literature sources. Sequence annotations and structural data are available in the public molecular databases, while functional data are almost exclusively available in the published articles. There is a need for a specialized svNTXs database that contains NTX entries, which are organized, well annotated and classified in a systematic manner. We have systematically analyzed svNTXs and classified them using structure-function groups based on their structural, functional and phylogenetic properties. Using conserved motifs in each phylogenetic group, we built an intelligent module for the prediction of structural and functional properties of unknown NTXs. We also developed an annotation tool to aid the functional prediction of newly identified NTXs as an additional resource for the venom research community. We created a searchable online database of NTX proteins sequences (http://research.i2r.a-star.edu.sg/Templar/DB/snake_neurotoxin). This database can also be found under Swiss-Prot Toxin Annotation Project website (http://www.expasy.org/sprot/).

A phylogenetic perspective on the individual species-area relationship in temperate and tropical tree communities.

PubMed

Yang, Jie; Swenson, Nathan G; Cao, Min; Chuyong, George B; Ewango, Corneille E N; Howe, Robert; Kenfack, David; Thomas, Duncan; Wolf, Amy; Lin, Luxiang

2013-01-01

Ecologists have historically used species-area relationships (SARs) as a tool to understand the spatial distribution of species. Recent work has extended SARs to focus on individual-level distributions to generate individual species area relationships (ISARs). The ISAR approach quantifies whether individuals of a species tend have more or less species richness surrounding them than expected by chance. By identifying richness 'accumulators' and 'repellers', respectively, the ISAR approach has been used to infer the relative importance of abiotic and biotic interactions and neutrality. A clear limitation of the SAR and ISAR approaches is that all species are treated as evolutionarily independent and that a large amount of work has now shown that local tree neighborhoods exhibit non-random phylogenetic structure given the species richness. Here, we use nine tropical and temperate forest dynamics plots to ask: (i) do ISARs change predictably across latitude?; (ii) is the phylogenetic diversity in the neighborhood of species accumulators and repellers higher or lower than that expected given the observed species richness?; and (iii) do species accumulators, repellers distributed non-randomly on the community phylogenetic tree? The results indicate no clear trend in ISARs from the temperate zone to the tropics and that the phylogenetic diversity surrounding the individuals of species is generally only non-random on very local scales. Interestingly the distribution of species accumulators and repellers was non-random on the community phylogenies suggesting the presence of phylogenetic signal in the ISAR across latitude.

The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

PubMed Central

Frandsen, Paul B.; Holzenthal, Ralph W.; Beet, Clare R.; Bennett, Kristi R.; Blahnik, Roger J.; Bonada, Núria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V.; Collins, Gemma E.; deWaard, Jeremy; Dean, John; Flint, Oliver S.; Hausmann, Axel; Hendrich, Lars; Hess, Monika; Hogg, Ian D.; Kondratieff, Boris C.; Malicky, Hans; Milton, Megan A.; Morinière, Jérôme; Morse, John C.; Mwangi, François Ngera; Pauls, Steffen U.; Gonzalez, María Razo; Rinne, Aki; Robinson, Jason L.; Salokannel, Juha; Shackleton, Michael; Smith, Brian; Stamatakis, Alexandros; StClair, Ros; Thomas, Jessica A.; Zamora-Muñoz, Carmen; Ziesmann, Tanja

2016-01-01

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481793

Molecular data do not support a southern hemisphere base of Nothofagus powdery mildews.

PubMed

Niinomi, Seiko; Takamatsu, Susumu; Havrylenko, Maria

2008-01-01

Three powdery mildew species present on Nothofagus (viz. Erysiphe magellanica, E. nothofagi and E. patagoniaca) are endemic to South America and have unique ascomatal appendages that are not found in powdery mildews of the northern hemisphere. We determined the nucleotide sequences of the rDNA internal transcribed spacer regions and D1/D2 domains of the 28S rDNA of these three powdery mildew species to reveal their phylogenetic relationships with powdery mildews of the northern hemisphere. Although the molecular phylogenetic analyses indicated that the three Nothofagus powdery mildews are closely related to each other they did not group into one clade in either the ITS or 28S trees. Kishino-Hasegawa, Shimodaira-Hasegawa and Templeton tests could not significantly reject the constrained trees that were constructed based on the assumption that the Nothofagus powdery mildews would form a single clade. Based on this result and the evidence that all Nothofagus powdery mildews are endemic to South America and have similar morphological characteristics, it is likely that these three species diverged from a single ancestor present on Nothofagus. Calibration of evolutionary events with molecular clocks suggested that the Nothofagus powdery mildews split from the northern hemisphere relatives 22-16 million y ago (Ma) in the middle Miocene, and divergence among the Nothofagus powdery mildews occurred 17-13 Ma. These results do not support a southern hemisphere base of the Nothofagus powdery mildews.

Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences.

PubMed

Zheng, Xiaoyan; Cai, Danying; Potter, Daniel; Postman, Joseph; Liu, Jing; Teng, Yuanwen

2014-11-01

Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence datasets. Phylogenetic trees based on both cpDNA and nuclear LFY2int2-N (LN) data resulted in poor resolution, especially, only five primary species were monophyletic in the LN tree. A phylogenetic network of LN suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Pyrus calleryana and P. regelii were the earliest diverged Pyrus species. Two North African species, P. cordata, P. spinosa and P. betulaefolia were descendent of primitive stock Pyrus species and still share some common molecular characters. Southwestern China, where a large number of P. pashia populations are found, is probably the most important diversification center of Pyrus. More accessions and nuclear genes are needed for further understanding the evolutionary histories of Pyrus. Copyright © 2014 Elsevier Inc. All rights reserved.

Phylogenetic mixtures and linear invariants for equal input models.

PubMed

Casanellas, Marta; Steel, Mike

2017-04-01

The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies becoming indistinguishable from the data, even for infinitely long sequences. However, when the underlying Markov process supports linear phylogenetic invariants, then provided these are sufficiently informative, the identifiability of the tree topology can be restored. In this paper, we investigate a class of processes that support linear invariants once the stationary distribution is fixed, the 'equal input model'. This model generalizes the 'Felsenstein 1981' model (and thereby the Jukes-Cantor model) from four states to an arbitrary number of states (finite or infinite), and it can also be described by a 'random cluster' process. We describe the structure and dimension of the vector spaces of phylogenetic mixtures and of linear invariants for any fixed phylogenetic tree (and for all trees-the so called 'model invariants'), on any number n of leaves. We also provide a precise description of the space of mixtures and linear invariants for the special case of [Formula: see text] leaves. By combining techniques from discrete random processes and (multi-) linear algebra, our results build on a classic result that was first established by James Lake (Mol Biol Evol 4:167-191, 1987).

Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems.

PubMed

Liu, Jingjing; Wu, Weixiang; Chen, Chongjun; Sun, Faqian; Chen, Yingxu

2011-09-01

In order to obtain insight into the prokaryotic diversity and community in leachate sediment, a culture-independent DNA-based molecular phylogenetic approach was performed with archaeal and bacterial 16S rRNA gene clone libraries derived from leachate sediment of an aged landfill. A total of 59 archaeal and 283 bacterial rDNA phylotypes were identified in 425 archaeal and 375 bacterial analyzed clones. All archaeal clones distributed within two archaeal phyla of the Euryarchaeota and Crenarchaeota, and well-defined methanogen lineages, especially Methanosaeta spp., are the most numerically dominant species of the archaeal community. Phylogenetic analysis of the bacterial library revealed a variety of pollutant-degrading and biotransforming microorganisms, including 18 distinct phyla. A substantial fraction of bacterial clones showed low levels of similarity with any previously documented sequences and thus might be taxonomically new. Chemical characteristics and phylogenetic inferences indicated that (1) ammonium-utilizing bacteria might form consortia to alleviate or avoid the negative influence of high ammonium concentration on other microorganisms, and (2) members of the Crenarchaeota found in the sediment might be involved in ammonium oxidation. This study is the first to report the composition of the microbial assemblages and phylogenetic characteristics of prokaryotic populations extant in leachate sediment. Additional work on microbial activity and contaminant biodegradation remains to be explored.

A new version of the RDP (Ribosomal Database Project)

NASA Technical Reports Server (NTRS)

Maidak, B. L.; Cole, J. R.; Parker, C. T. Jr; Garrity, G. M.; Larsen, N.; Li, B.; Lilburn, T. G.; McCaughey, M. J.; Olsen, G. J.; Overbeek, R.;

Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.

PubMed

West, Claire; James, Stephen A; Davey, Robert P; Dicks, Jo; Roberts, Ian N

2014-07-01

The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multilocus rDNA systems. [concerted evolution; genome hydridisation; phylogenetic analysis; ribosomal DNA; whole genome sequencing; yeast]. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

A Phylogenetic Comparative Study of Bantu Kinship Terminology Finds Limited Support for Its Co-Evolution with Social Organisation

PubMed Central

Guillon, Myrtille; Mace, Ruth

2016-01-01

The classification of kin into structured groups is a diverse phenomenon which is ubiquitous in human culture. For populations which are organized into large agropastoral groupings of sedentary residence but not governed within the context of a centralised state, such as our study sample of 83 historical Bantu-speaking groups of sub-Saharan Africa, cultural kinship norms guide all aspects of everyday life and social organization. Such rules operate in part through the use of differing terminological referential systems of familial organization. Although the cross-cultural study of kinship terminology was foundational in Anthropology, few modern studies have made use of statistical advances to further our sparse understanding of the structuring and diversification of terminological systems of kinship over time. In this study we use Bayesian Markov Chain Monte Carlo methods of phylogenetic comparison to investigate the evolution of Bantu kinship terminology and reconstruct the ancestral state and diversification of cousin terminology in this family of sub-Saharan ethnolinguistic groups. Using a phylogenetic tree of Bantu languages, we then test the prominent hypothesis that structured variation in systems of cousin terminology has co-evolved alongside adaptive change in patterns of descent organization, as well as rules of residence. We find limited support for this hypothesis, and argue that the shaping of systems of kinship terminology is a multifactorial process, concluding with possible avenues of future research. PMID:27008364

ODE constrained mixture modelling: a method for unraveling subpopulation structures and dynamics.

PubMed

Hasenauer, Jan; Hasenauer, Christine; Hucho, Tim; Theis, Fabian J

2014-07-01

Functional cell-to-cell variability is ubiquitous in multicellular organisms as well as bacterial populations. Even genetically identical cells of the same cell type can respond differently to identical stimuli. Methods have been developed to analyse heterogeneous populations, e.g., mixture models and stochastic population models. The available methods are, however, either incapable of simultaneously analysing different experimental conditions or are computationally demanding and difficult to apply. Furthermore, they do not account for biological information available in the literature. To overcome disadvantages of existing methods, we combine mixture models and ordinary differential equation (ODE) models. The ODE models provide a mechanistic description of the underlying processes while mixture models provide an easy way to capture variability. In a simulation study, we show that the class of ODE constrained mixture models can unravel the subpopulation structure and determine the sources of cell-to-cell variability. In addition, the method provides reliable estimates for kinetic rates and subpopulation characteristics. We use ODE constrained mixture modelling to study NGF-induced Erk1/2 phosphorylation in primary sensory neurones, a process relevant in inflammatory and neuropathic pain. We propose a mechanistic pathway model for this process and reconstructed static and dynamical subpopulation characteristics across experimental conditions. We validate the model predictions experimentally, which verifies the capabilities of ODE constrained mixture models. These results illustrate that ODE constrained mixture models can reveal novel mechanistic insights and possess a high sensitivity.

CONSTRAINTS ON SPATIAL VARIATIONS IN THE FINE-STRUCTURE CONSTANT FROM PLANCK

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Bryan, Jon; Smidt, Joseph; De Bernardis, Francesco

2015-01-01

We use the cosmic microwave background (CMB) anisotropy data from Planck to constrain the spatial fluctuations of the fine-structure constant α at a redshift of 1100. We use a quadratic estimator to measure the four-point correlation function of the CMB temperature anisotropies and extract the angular power spectrum fine-structure constant spatial variations projected along the line of sight at the last scattering surface. At tens of degree angular scales and above, we constrain the fractional rms fluctuations of the fine-structure constant to be (δα/α){sub rms} < 3.4 × 10{sup –3} at the 68% confidence level. We find no evidence formore » a spatially varying α at a redshift of 10{sup 3}.« less

Stress-Constrained Structural Topology Optimization with Design-Dependent Loads

NASA Astrophysics Data System (ADS)

Lee, Edmund

Topology optimization is commonly used to distribute a given amount of material to obtain the stiffest structure, with predefined fixed loads. The present work investigates the result of applying stress constraints to topology optimization, for problems with design-depending loading, such as self-weight and pressure. In order to apply pressure loading, a material boundary identification scheme is proposed, iteratively connecting points of equal density. In previous research, design-dependent loading problems have been limited to compliance minimization. The present study employs a more practical approach by minimizing mass subject to failure constraints, and uses a stress relaxation technique to avoid stress constraint singularities. The results show that these design dependent loading problems may converge to a local minimum when stress constraints are enforced. Comparisons between compliance minimization solutions and stress-constrained solutions are also given. The resulting topologies of these two solutions are usually vastly different, demonstrating the need for stress-constrained topology optimization.

Accurate de novo design of hyperstable constrained peptides

PubMed Central

Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Bahl, Christopher D.; Gilmore, Jason M.; Harvey, Peta J.; Cheneval, Olivier; Buchko, Garry W.; Pulavarti, Surya V.S.R.K.; Kaas, Quentin; Eletsky, Alexander; Huang, Po-Ssu; Johnsen, William A.; Greisen, Per; Rocklin, Gabriel J.; Song, Yifan; Linsky, Thomas W.; Watkins, Andrew; Rettie, Stephen A.; Xu, Xianzhong; Carter, Lauren P.; Bonneau, Richard; Olson, James M.; Coutsias, Evangelos; Correnti, Colin E.; Szyperski, Thomas; Craik, David J.; Baker, David

2016-01-01

Summary Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for de novo design of conformationally-restricted peptides, and the use of these methods to design 15–50 residue disulfide-crosslinked and heterochiral N-C backbone-cyclized peptides. These peptides are exceptionally stable to thermal and chemical denaturation, and twelve experimentally-determined X-ray and NMR structures are nearly identical to the computational models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs. PMID:27626386

Self-constrained inversion of potential fields

NASA Astrophysics Data System (ADS)

Paoletti, V.; Ialongo, S.; Florio, G.; Fedi, M.; Cella, F.

2013-11-01

We present a potential-field-constrained inversion procedure based on a priori information derived exclusively from the analysis of the gravity and magnetic data (self-constrained inversion). The procedure is designed to be applied to underdetermined problems and involves scenarios where the source distribution can be assumed to be of simple character. To set up effective constraints, we first estimate through the analysis of the gravity or magnetic field some or all of the following source parameters: the source depth-to-the-top, the structural index, the horizontal position of the source body edges and their dip. The second step is incorporating the information related to these constraints in the objective function as depth and spatial weighting functions. We show, through 2-D and 3-D synthetic and real data examples, that potential field-based constraints, for example, structural index, source boundaries and others, are usually enough to obtain substantial improvement in the density and magnetization models.

The Evolutionary Roots of Human Decision Making

PubMed Central

Santos, Laurie R.; Rosati, Alexandra G.

2015-01-01

Humans exhibit a suite of biases when making economic decisions. We review recent research on the origins of human decision making by examining whether similar choice biases are seen in nonhuman primates, our closest phylogenetic relatives. We propose that comparative studies can provide insight into four major questions about the nature of human choice biases that cannot be addressed by studies of our species alone. First, research with other primates can address the evolution of human choice biases and identify shared versus human-unique tendencies in decision making. Second, primate studies can constrain hypotheses about the psychological mechanisms underlying such biases. Third, comparisons of closely related species can identify when distinct mechanisms underlie related biases by examining evolutionary dissociations in choice strategies. Finally, comparative work can provide insight into the biological rationality of economically irrational preferences. PMID:25559115

MOLECULAR ANALYSIS OF MICROBIAL COMMUNITY STRUCTURES IN PRISTINE AND CONTAMINATED AQUIFERS: FIELD AND LABORATORY MICROCOSM EXPERIMENTS

EPA Science Inventory

This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminted (NC) and (ii) examine alterations in micro...

A network approach to analyzing highly recombinant malaria parasite genes.

PubMed

Larremore, Daniel B; Clauset, Aaron; Buckee, Caroline O

2013-01-01

The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences.

A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes

PubMed Central

Larremore, Daniel B.; Clauset, Aaron; Buckee, Caroline O.

2013-01-01

The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences. PMID:24130474

Arbuscular mycorrhizal fungal communities are phylogenetically clustered at small scales

PubMed Central

Horn, Sebastian; Caruso, Tancredi; Verbruggen, Erik; Rillig, Matthias C; Hempel, Stefan

2014-01-01

Next-generation sequencing technologies with markers covering the full Glomeromycota phylum were used to uncover phylogenetic community structure of arbuscular mycorrhizal fungi (AMF) associated with Festuca brevipila. The study system was a semi-arid grassland with high plant diversity and a steep environmental gradient in pH, C, N, P and soil water content. The AMF community in roots and rhizosphere soil were analyzed separately and consisted of 74 distinct operational taxonomic units (OTUs) in total. Community-level variance partitioning showed that the role of environmental factors in determining AM species composition was marginal when controlling for spatial autocorrelation at multiple scales. Instead, phylogenetic distance and spatial distance were major correlates of AMF communities: OTUs that were more closely related (and which therefore may have similar traits) were more likely to co-occur. This pattern was insensitive to phylogenetic sampling breadth. Given the minor effects of the environment, we propose that at small scales closely related AMF positively associate through biotic factors such as plant-AMF filtering and interactions within the soil biota. PMID:24824667

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza.

PubMed

Cybis, Gabriela B; Sinsheimer, Janet S; Bedford, Trevor; Rambaut, Andrew; Lemey, Philippe; Suchard, Marc A

2018-01-30

Influenza is responsible for up to 500,000 deaths every year, and antigenic variability represents much of its epidemiological burden. To visualize antigenic differences across many viral strains, antigenic cartography methods use multidimensional scaling on binding assay data to map influenza antigenicity onto a low-dimensional space. Analysis of such assay data ideally leads to natural clustering of influenza strains of similar antigenicity that correlate with sequence evolution. To understand the dynamics of these antigenic groups, we present a framework that jointly models genetic and antigenic evolution by combining multidimensional scaling of binding assay data, Bayesian phylogenetic machinery and nonparametric clustering methods. We propose a phylogenetic Chinese restaurant process that extends the current process to incorporate the phylogenetic dependency structure between strains in the modeling of antigenic clusters. With this method, we are able to use the genetic information to better understand the evolution of antigenicity throughout epidemics, as shown in applications of this model to H1N1 influenza. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Phylogenetic origins of the plant mitochondrion based on a comparative analysis of 5S ribosomal RNA sequences

NASA Technical Reports Server (NTRS)

Villanueva, E.; Delihas, N.; Luehrsen, K. R.; Fox, G. E.; Gibson, J.

1985-01-01

The complete nucleotide sequences of 5S ribosomal RNAs from Rhodocyclus gelatinosa, Rhodobacter sphaeroides, and Pseudomonas cepacia were determined. Comparisons of these 5S RNA sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5S RNAs share more sequence and signature homology with the RNAs of two nonphotosynthetic strains. Rhodobacter sphaeroides is specifically related to Paracoccus denitrificans and Rc. gelatinosa is related to Ps. cepacia. These results support earlier 16S ribosomal RNA studies and add two important groups to the 5S RNA data base. Unique 5S RNA structural features previously found in P. denitrificans are present also in the 5S RNA of Rb. sphaeroides; these provide the basis for subdivisional signatures. The immediate consequence of obtaining these new sequences is that it is possible to clarify the phylogenetic origins of the plant mitochondrion. In particular, a close phylogenetic relationship is found between the plant mitochondria and members of the alpha subdivision of the purple photosynthetic bacteria, namely, Rb. sphaeroides, P. denitrificans, and Rhodospirillum rubrum.

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

PubMed

Hagopian, Raffi; Davidson, John R; Datta, Ruchira S; Samad, Bushra; Jarvis, Glen R; Sjölander, Kimmen

2010-07-01

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.

The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology

PubMed Central

Sapp, Jan

2005-01-01

Drawing on documents both published and archival, this paper explains how the prokaryote-eukaryote dichotomy of the 1960s was constructed, the purposes it served, and what it implied in terms of classification and phylogeny. In doing so, I first show how the concept was attributed to Edouard Chatton and the context in which he introduced the terms. Following, I examine the context in which the terms were reintroduced into biology in 1962 by Roger Stanier and C. B. van Niel. I study the discourse over the subsequent decade to understand how the organizational dichotomy took on the form of a natural classification as the kingdom Monera or superkingdom Procaryotae. Stanier and van Niel admitted that, in regard to constructing a natural classification of bacteria, structural characteristics were no more useful than physiological properties. They repeatedly denied that bacterial phylogenetics was possible. I thus examine the great historical irony that the “prokaryote,” in both its organizational and phylogenetic senses, was defined (negatively) on the basis of structure. Finally, we see how phylogenetic research based on 16S rRNA led by Carl Woese and his collaborators confronted the prokaryote concept while moving microbiology to the center of evolutionary biology. PMID:15944457

Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

PubMed Central

Matsen IV, Frederick A.; Evans, Steven N.

2013-01-01

Principal components analysis (PCA) and hierarchical clustering are two of the most heavily used techniques for analyzing the differences between nucleic acid sequence samples taken from a given environment. They have led to many insights regarding the structure of microbial communities. We have developed two new complementary methods that leverage how this microbial community data sits on a phylogenetic tree. Edge principal components analysis enables the detection of important differences between samples that contain closely related taxa. Each principal component axis is a collection of signed weights on the edges of the phylogenetic tree, and these weights are easily visualized by a suitable thickening and coloring of the edges. Squash clustering outputs a (rooted) clustering tree in which each internal node corresponds to an appropriate “average” of the original samples at the leaves below the node. Moreover, the length of an edge is a suitably defined distance between the averaged samples associated with the two incident nodes, rather than the less interpretable average of distances produced by UPGMA, the most widely used hierarchical clustering method in this context. We present these methods and illustrate their use with data from the human microbiome. PMID:23505415

Signatures of microevolutionary processes in phylogenetic patterns.

PubMed

Costa, Carolina L N; Lemos-Costa, Paula; Marquitti, Flavia M D; Fernandes, Lucas D; Ramos, Marlon F; Schneider, David M; Martins, Ayana B; Aguiar, Marcus A M

2018-06-23

Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem we analysed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.

Primary structures of skin antimicrobial peptides indicate a close, but not conspecific, phylogenetic relationship between the leopard frogs Lithobates onca and Lithobates yavapaiensis (Ranidae).

PubMed

Conlon, J Michael; Coquet, Laurent; Leprince, Jérôme; Jouenne, Thierry; Vaudry, Hubert; King, Jay D

2010-04-01

The phylogenetic relationship between the relict leopard frog Lithobates (Rana) onca (Cope, 1875) and the lowland leopard frog Lithobates (Rana) yavapaiensis (Platz and Frost, 1984) is unclear. Chromatographic analysis of norepinephrine-stimulated skin secretions from L. onca led to the identification of six peptides with antimicrobial activity. Determination of their primary structures indicated that four of the peptides were identical to brevinin-1Ya, brevinin-1Yb, brevinin-1Yc and ranatuerin-2Ya previously isolated from skin secretions of L. yavapaiensis. However, a peptide belonging to the temporin family (temporin-ONa: FLPTFGKILSGLF.NH(2)) and an atypical member of the ranatuerin-2 family containing a C-terminal cyclic heptapeptide domain (ranatuerin-2ONa: GLMDTVKNAAKNLAGQMLDKLKCKITGSC) were isolated from the L. onca secretions but were not present in the L. yavapaiensis secretions. Ranatuerin-2ONa inhibited the growth of Escherichia coli (MIC=50muM) and Candida albicans (MIC=100muM ) and showed hemolytic activity (LC(50)=90muM) but was inactive against Staphylococcus aureus. The data indicate a close phylogenetic relationship between L. onca and L. yavapaiensis but suggest that they are not conspecific species.

An evolutionary analysis identifies a conserved pentapeptide stretch containing the two essential lysine residues for rice L-myo-inositol 1-phosphate synthase catalytic activity

PubMed Central

Basak, Papri; Maitra-Majee, Susmita; Das, Jayanta Kumar; Mukherjee, Abhishek; Ghosh Dastidar, Shubhra; Pal Choudhury, Pabitra

2017-01-01

A molecular evolutionary analysis of a well conserved protein helps to determine the essential amino acids in the core catalytic region. Based on the chemical properties of amino acid residues, phylogenetic analysis of a total of 172 homologous sequences of a highly conserved enzyme, L-myo-inositol 1-phosphate synthase or MIPS from evolutionarily diverse organisms was performed. This study revealed the presence of six phylogenetically conserved blocks, out of which four embrace the catalytic core of the functional protein. Further, specific amino acid modifications targeting the lysine residues, known to be important for MIPS catalysis, were performed at the catalytic site of a MIPS from monocotyledonous model plant, Oryza sativa (OsMIPS1). Following this study, OsMIPS mutants with deletion or replacement of lysine residues in the conserved blocks were made. Based on the enzyme kinetics performed on the deletion/replacement mutants, phylogenetic and structural comparison with the already established crystal structures from non-plant sources, an evolutionarily conserved peptide stretch was identified at the active pocket which contains the two most important lysine residues essential for catalytic activity. PMID:28950028

Visual exploration of parameter influence on phylogenetic trees.

PubMed

Hess, Martin; Bremm, Sebastian; Weissgraeber, Stephanie; Hamacher, Kay; Goesele, Michael; Wiemeyer, Josef; von Landesberger, Tatiana

2014-01-01

Evolutionary relationships between organisms are frequently derived as phylogenetic trees inferred from multiple sequence alignments (MSAs). The MSA parameter space is exponentially large, so tens of thousands of potential trees can emerge for each dataset. A proposed visual-analytics approach can reveal the parameters' impact on the trees. Given input trees created with different parameter settings, it hierarchically clusters the trees according to their structural similarity. The most important clusters of similar trees are shown together with their parameters. This view offers interactive parameter exploration and automatic identification of relevant parameters. Biologists applied this approach to real data of 16S ribosomal RNA and protein sequences of ion channels. It revealed which parameters affected the tree structures. This led to a more reliable selection of the best trees.

A taxonomic wish-list for community ecology.

PubMed Central

Gotelli, Nicholas J

2004-01-01

Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists. PMID:15253346

A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data.

PubMed

Adams, Dean C

2014-09-01

Phylogenetic signal is the tendency for closely related species to display similar trait values due to their common ancestry. Several methods have been developed for quantifying phylogenetic signal in univariate traits and for sets of traits treated simultaneously, and the statistical properties of these approaches have been extensively studied. However, methods for assessing phylogenetic signal in high-dimensional multivariate traits like shape are less well developed, and their statistical performance is not well characterized. In this article, I describe a generalization of the K statistic of Blomberg et al. that is useful for quantifying and evaluating phylogenetic signal in highly dimensional multivariate data. The method (K(mult)) is found from the equivalency between statistical methods based on covariance matrices and those based on distance matrices. Using computer simulations based on Brownian motion, I demonstrate that the expected value of K(mult) remains at 1.0 as trait variation among species is increased or decreased, and as the number of trait dimensions is increased. By contrast, estimates of phylogenetic signal found with a squared-change parsimony procedure for multivariate data change with increasing trait variation among species and with increasing numbers of trait dimensions, confounding biological interpretations. I also evaluate the statistical performance of hypothesis testing procedures based on K(mult) and find that the method displays appropriate Type I error and high statistical power for detecting phylogenetic signal in high-dimensional data. Statistical properties of K(mult) were consistent for simulations using bifurcating and random phylogenies, for simulations using different numbers of species, for simulations that varied the number of trait dimensions, and for different underlying models of trait covariance structure. Overall these findings demonstrate that K(mult) provides a useful means of evaluating phylogenetic signal in high-dimensional multivariate traits. Finally, I illustrate the utility of the new approach by evaluating the strength of phylogenetic signal for head shape in a lineage of Plethodon salamanders. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The influence of phylogeny, social style, and sociodemographic factors on macaque social network structure.

PubMed

Balasubramaniam, Krishna N; Beisner, Brianne A; Berman, Carol M; De Marco, Arianna; Duboscq, Julie; Koirala, Sabina; Majolo, Bonaventura; MacIntosh, Andrew J; McFarland, Richard; Molesti, Sandra; Ogawa, Hideshi; Petit, Odile; Schino, Gabriele; Sosa, Sebastian; Sueur, Cédric; Thierry, Bernard; de Waal, Frans B M; McCowan, Brenda

2018-01-01

Among nonhuman primates, the evolutionary underpinnings of variation in social structure remain debated, with both ancestral relationships and adaptation to current conditions hypothesized to play determining roles. Here we assess whether interspecific variation in higher-order aspects of female macaque (genus: Macaca) dominance and grooming social structure show phylogenetic signals, that is, greater similarity among more closely-related species. We use a social network approach to describe higher-order characteristics of social structure, based on both direct interactions and secondary pathways that connect group members. We also ask whether network traits covary with each other, with species-typical social style grades, and/or with sociodemographic characteristics, specifically group size, sex-ratio, and current living condition (captive vs. free-living). We assembled 34-38 datasets of female-female dyadic aggression and allogrooming among captive and free-living macaques representing 10 species. We calculated dominance (transitivity, certainty), and grooming (centrality coefficient, Newman's modularity, clustering coefficient) network traits as aspects of social structure. Computations of K statistics and randomization tests on multiple phylogenies revealed moderate-strong phylogenetic signals in dominance traits, but moderate-weak signals in grooming traits. GLMMs showed that grooming traits did not covary with dominance traits and/or social style grade. Rather, modularity and clustering coefficient, but not centrality coefficient, were strongly predicted by group size and current living condition. Specifically, larger groups showed more modular networks with sparsely-connected clusters than smaller groups. Further, this effect was independent of variation in living condition, and/or sampling effort. In summary, our results reveal that female dominance networks were more phylogenetically conserved across macaque species than grooming networks, which were more labile to sociodemographic factors. Such findings narrow down the processes that influence interspecific variation in two core aspects of macaque social structure. Future directions should include using phylogeographic approaches, and addressing challenges in examining the effects of socioecological factors on primate social structure. © 2017 Wiley Periodicals, Inc.

Extrusomes in ciliates: diversification, distribution, and phylogenetic implications.

PubMed

Rosati, Giovanna; Modeo, Letizia

2003-01-01

Exocytosis is, in all likelihood, an important communication method among microbes. Ciliates are highly differentiated and specialized micro-organisms for which versatile and/or sophisticated exocytotic organelles may represent important adaptive tools. Thus, in ciliates, we find a broad range of different extrusomes, i.e ejectable membrane-bound organelles. Structurally simple extrusomes, like mucocysts and cortical granules, are widespread in different taxa within the phylum. They play the roles in each case required for the ecological needs of the organisms. Then, we find a number of more elaborate extrusomes, whose distribution within the phylum is more limited, and in some way related to phylogenetic affinities. Herein we provide a survey of literature and our data on selected extrusomes in ciliates. Their morphology, distribution, and possible function are discussed. The possible phylogenetic implications of their diversity are considered.

Child-Care Provider Survey Reveals Cost Constrains Quality. Research Brief. Volume 96, Number 5

ERIC Educational Resources Information Center

Public Policy Forum, 2008

2008-01-01

A survey of 414 child care providers in southeastern Wisconsin reveals that cost as well as low wages and lack of benefits for workers can constrain providers from pursuing improvements to child-care quality. Of survey respondents, approximately half of whom are home-based and half center-based, 13% have at least three of five structural factors…

Public health nutrition workforce development in seven European countries: constraining and enabling factors.

PubMed

Kugelberg, Susanna; Jonsdottir, Svandis; Faxelid, Elisabeth; Jönsson, Kristina; Fox, Ann; Thorsdottir, Inga; Yngve, Agneta

2012-11-01

Little is known about current public health nutrition workforce development in Europe. The present study aimed to understand constraining and enabling factors to workforce development in seven European countries. A qualitative study comprised of semi-structured face-to-face interviews was conducted and content analysis was used to analyse the transcribed interview data. The study was carried out in Finland, Iceland, Ireland, Slovenia, Spain, Sweden and the UK. Sixty key informants participated in the study. There are constraining and enabling factors for public health nutrition workforce development. The main constraining factors relate to the lack of a supportive policy environment, fragmented organizational structures and a workforce that is not cohesive enough to implement public health nutrition strategic initiatives. Enabling factors were identified as the presence of skilled and dedicated individuals who assume roles as leaders and change agents. There is a need to strengthen coordination between policy and implementation of programmes which may operate across the national to local spectrum. Public health organizations are advised to further define aims and objectives relevant to public health nutrition. Leaders and agents of change will play important roles in fostering intersectorial partnerships, advocating for policy change, establishing professional competencies and developing education and training programmes.

Constrained Low-Rank Learning Using Least Squares-Based Regularization.

PubMed

Li, Ping; Yu, Jun; Wang, Meng; Zhang, Luming; Cai, Deng; Li, Xuelong

2017-12-01

Low-rank learning has attracted much attention recently due to its efficacy in a rich variety of real-world tasks, e.g., subspace segmentation and image categorization. Most low-rank methods are incapable of capturing low-dimensional subspace for supervised learning tasks, e.g., classification and regression. This paper aims to learn both the discriminant low-rank representation (LRR) and the robust projecting subspace in a supervised manner. To achieve this goal, we cast the problem into a constrained rank minimization framework by adopting the least squares regularization. Naturally, the data label structure tends to resemble that of the corresponding low-dimensional representation, which is derived from the robust subspace projection of clean data by low-rank learning. Moreover, the low-dimensional representation of original data can be paired with some informative structure by imposing an appropriate constraint, e.g., Laplacian regularizer. Therefore, we propose a novel constrained LRR method. The objective function is formulated as a constrained nuclear norm minimization problem, which can be solved by the inexact augmented Lagrange multiplier algorithm. Extensive experiments on image classification, human pose estimation, and robust face recovery have confirmed the superiority of our method.

Fault offsets and lateral crustal movement on Europa - Evidence for a mobile ice shell

NASA Technical Reports Server (NTRS)

Schenk, Paul M.; Mckinnon, William B.

1989-01-01

An examination is conducted of Europa's cross-cutting structural relationships between various lineament types, in order to constrain the type of structure involved in each such case and, where possible, to also constrain the degree of extension across the lineaments. Evidence is adduced for significant lateral crustal movement, allowing alternative models and mechanisms for lineament formation to be discussed, as well as plausible lithospheric and crustal models. The question as to whether any of the water-ice layer has been, or currently is, liquid, is also treated in light of the evidence obtained.

Vertebral microanatomy in squamates: structure, growth and ecological correlates

PubMed Central

Houssaye, Alexandra; Mazurier, Arnaud; Herrel, Anthony; Volpato, Virginie; Tafforeau, Paul; Boistel, Renaud; de Buffrénil, Vivian

2010-01-01

The histological study of vertebrae in extant squamates shows that the internal vertebral structure in this group differs from that of other tetrapods. Squamate vertebrae are lightly built and basically composed of two roughly concentric osseous tubes – one surrounding the neural canal and the other constituting the peripheral cortex of the vertebra – connected by few thin trabeculae. This structure, which characteristically evokes that of a tubular bone, results from a peculiar remodelling process characterised by an imbalance between local bone resorption and redeposition; in both periosteal and endosteo-endochondral territories, bone is extensively resorbed but not reconstructed in the same proportion by secondary deposits. This process is particularly intense in the deep region of the centrum, where originally compact cortices are made cancellous, and where the endochondral spongiosa is very loose. This remodelling process starts at an early stage of development and remains active throughout subsequent growth. The growth of squamate centra is also strongly asymmetrical, with the posterior (condylar) part growing much faster than the anterior (cotylar) part. Preliminary analyses testing for associations between vertebral structure and habitat use suggest that vertebrae of fossorial taxa are denser than those of terrestrial taxa, those in aquatic taxa being of intermediate density. However, phylogenetically informed analyses do not corroborate these findings, thus suggesting a strong phylogenetic signal in the data. As our analyses demonstrate that vertebrae in snakes are generally denser than those of lizards sensu stricto, this may drive the presence of a phylogenetic signal in the data. More comprehensive sampling of fossorial and aquatic lizards is clearly needed to more rigorously evaluate these patterns. PMID:21039477

The design of multirate digital control systems

NASA Technical Reports Server (NTRS)

Berg, M. C.

1986-01-01

The successive loop closures synthesis method is the only method for multirate (MR) synthesis in common use. A new method for MR synthesis is introduced which requires a gradient-search solution to a constrained optimization problem. Some advantages of this method are that the control laws for all control loops are synthesized simultaneously, taking full advantage of all cross-coupling effects, and that simple, low-order compensator structures are easily accomodated. The algorithm and associated computer program for solving the constrained optimization problem are described. The successive loop closures , optimal control, and constrained optimization synthesis methods are applied to two example design problems. A series of compensator pairs are synthesized for each example problem. The succesive loop closure, optimal control, and constrained optimization synthesis methods are compared, in the context of the two design problems.

Strategies for using cellular automata to locate constrained layer damping on vibrating structures

NASA Astrophysics Data System (ADS)

Chia, C. M.; Rongong, J. A.; Worden, K.

2009-01-01

It is often hard to optimise constrained layer damping (CLD) for structures more complicated than simple beams and plates as its performance depends on its location, the shape of the applied patch, the mode shapes of the structure and the material properties. This paper considers the use of cellular automata (CA) in conjunction with finite element analysis to obtain an efficient coverage of CLD on structures. The effectiveness of several different sets of local rules governing the CA are compared against each other for a structure with known optimum coverage—namely a plate. The algorithm which attempts to replicate most closely known optimal configurations is considered the most successful. This algorithm is then used to generate an efficient CLD treatment that targets several modes of a curved composite panel. To validate the modelling approaches used, results are also presented of a comparison between theoretical and experimentally obtained modal properties of the damped curved panel.

A gravity model for the Sudbury Structure along the Lithoprobe seismic line

NASA Astrophysics Data System (ADS)

McGrath, P. H.; Broome, H. J.

1994-05-01

Previous gravity models of the Sudbury Structure (1850 Ma) were constrained by surface geology, and by density measurements of surface and borehole rock samples. Recent high-resolution seismic reflection data provide additional constraints for modeling new gravity observations made along the Sudbury Lithoprobe transect. Results indicate, (1) density distributions constrained by the seismic data yield calculated gravity values matching the Bouguer gravity data, (2) the main sources of gravitational disturbance are external to the Sudbury Structure, (3) the positive gravity anomaly trend south of the Sudbury Structure is associated with mafic rocks of Proterozoic age, and (4) the large, ramplike, gravity anomaly paralleling the northwest margin of the Sudbury Structure is an expression of a northward dipping boundary within the Archean basement. The presence of a hidden mafic layer beneath the Sudbury Structure is not required to model the Bouguer gravity data. An enigma is an 8 mGal, positive, gravity anomaly over the south central Sudbury Structure.

Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae

PubMed Central

Ludeña, Bertha; Chabrillange, Nathalie; Aberlenc-Bertossi, Frédérique; Adam, Hélène; Tregear, James W.; Pintaud, Jean-Christophe

2011-01-01

Background and Aims Molecular phylogenetic studies of palms (Arecaceae) have not yet provided a fully resolved phylogeny of the family. There is a need to increase the current set of markers to resolve difficult groups such as the Neotropical subtribe Bactridinae (Arecoideae: Cocoseae). We propose the use of two single-copy nuclear genes as valuable tools for palm phylogenetics. Methods New primers were developed for the amplification of the AGAMOUS 1 (AG1) and PHYTOCHROME B (PHYB) genes. For the AGAMOUS gene, the paralogue 1 of Elaeis guineensis (EgAG1) was targeted. The region amplified contained coding sequences between the MIKC K and C MADS-box domains. For the PHYB gene, exon 1 (partial sequence) was first amplified in palm species using published degenerate primers for Poaceae, and then specific palm primers were designed. The two gene portions were sequenced in 22 species of palms representing all genera of Bactridinae, with emphasis on Astrocaryum and Hexopetion, the status of the latter genus still being debated. Key Results The new primers designed allow consistent amplification and high-quality sequencing within the palm family. The two loci studied produced more variability than chloroplast loci and equally or less variability than PRK, RPBII and ITS nuclear markers. The phylogenetic structure obtained with AG1 and PHYB genes provides new insights into intergeneric relationships within the Bactridinae and the intrageneric structure of Astrocaryum. The Hexopetion clade was recovered as monophyletic with both markers and was weakly supported as sister to Astrocaryum sensu stricto in the combined analysis. The rare Astrocaryum minus formed a species complex with Astrocaryum gynacanthum. Moreover, both AG1 and PHYB contain a microsatellite that could have further uses in species delimitation and population genetics. Conclusions AG1 and PHYB provide additional phylogenetic information within the palm family, and should prove useful in combination with other genes to improve the resolution of palm phylogenies. PMID:21828068

A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting

PubMed Central

Keremane, Manjunath L.; Lee, Richard F.; Maureira-Butler, Ivan J.; Roose, Mikeal L.

2013-01-01

Background Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4–12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species. Methodology and Principal Findings (1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test. Conclusions We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches–gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus. PMID:23874615

Agency Amidst Formidable Structures: How Girls Perform Gender in Science Class

ERIC Educational Resources Information Center

Carlone, Heidi B.; Johnson, Angela; Scott, Catherine M.

2015-01-01

Larger social structures such as race, class, gender, and sexuality and classroom structures like narrowly defined participation practices constrain individuals' agency to engage in untroubled and sustained science identity work. This article explores the central dilemma of attending to structure and agency in settings where inequities are…

Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function.

PubMed

Zhu, Xinyu; Ma, Hong; Chen, Zhiduan

2011-03-09

Plants contain numerous Su(var)3-9 homologues (SUVH) and related (SUVR) genes, some of which await functional characterization. Although there have been studies on the evolution of plant Su(var)3-9 SET genes, a systematic evolutionary study including major land plant groups has not been reported. Large-scale phylogenetic and evolutionary analyses can help to elucidate the underlying molecular mechanisms and contribute to improve genome annotation. Putative orthologs of plant Su(var)3-9 SET protein sequences were retrieved from major representatives of land plants. A novel clustering that included most members analyzed, henceforth referred to as core Su(var)3-9 homologues and related (cSUVHR) gene clade, was identified as well as all orthologous groups previously identified. Our analysis showed that plant Su(var)3-9 SET proteins possessed a variety of domain organizations, and can be classified into five types and ten subtypes. Plant Su(var)3-9 SET genes also exhibit a wide range of gene structures among different paralogs within a family, even in the regions encoding conserved PreSET and SET domains. We also found that the majority of SUVH members were intronless and formed three subclades within the SUVH clade. A detailed phylogenetic analysis of the plant Su(var)3-9 SET genes was performed. A novel deep phylogenetic relationship including most plant Su(var)3-9 SET genes was identified. Additional domains such as SAR, ZnF_C2H2 and WIYLD were early integrated into primordial PreSET/SET/PostSET domain organization. At least three classes of gene structures had been formed before the divergence of Physcomitrella patens (moss) from other land plants. One or multiple retroposition events might have occurred among SUVH genes with the donor genes leading to the V-2 orthologous group. The structural differences among evolutionary groups of plant Su(var)3-9 SET genes with different functions were described, contributing to the design of further experimental studies.

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean.

PubMed

Allers, Elke; Wright, Jody J; Konwar, Kishori M; Howes, Charles G; Beneze, Erica; Hallam, Steven J; Sullivan, Matthew B

2013-02-01

Marine Group A (MGA) is a candidate phylum of Bacteria that is ubiquitous and abundant in the ocean. Despite being prevalent, the structural and functional properties of MGA populations remain poorly constrained. Here, we quantified MGA diversity and population structure in relation to nutrients and O(2) concentrations in the oxygen minimum zone (OMZ) of the Northeast subarctic Pacific Ocean using a combination of catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and 16S small subunit ribosomal RNA (16S rRNA) gene sequencing (clone libraries and 454-pyrotags). Estimates of MGA abundance as a proportion of total bacteria were similar across all three methods although estimates based on CARD-FISH were consistently lower in the OMZ (5.6%±1.9%) than estimates based on 16S rRNA gene clone libraries (11.0%±3.9%) or pyrotags (9.9%±1.8%). Five previously defined MGA subgroups were recovered in 16S rRNA gene clone libraries and five novel subgroups were defined (HF770D10, P262000D03, P41300E03, P262000N21 and A714018). Rarefaction analysis of pyrotag data indicated that the ultimate richness of MGA was very nearly sampled. Spearman's rank analysis of MGA abundances by CARD-FISH and O(2) concentrations resulted in significant correlation. Analyzed in more detail by 16S rRNA pyrotag sequencing, MGA operational taxonomic units affiliated with subgroups Arctic95A-2 and A714018 comprised 0.3-2.4% of total bacterial sequences and displayed strong correlations with decreasing O(2) concentration. This study is the first comprehensive description of MGA diversity using complementary techniques. These results provide a phylogenetic framework for interpreting future studies on ecotype selection among MGA subgroups, and suggest a potentially important role for MGA in the ecology and biogeochemistry of OMZs.

Predicting structures in the Zone of Avoidance

NASA Astrophysics Data System (ADS)

Sorce, Jenny G.; Colless, Matthew; Kraan-Korteweg, Renée C.; Gottlöber, Stefan

2017-11-01

The Zone of Avoidance (ZOA), whose emptiness is an artefact of our Galaxy dust, has been challenging observers as well as theorists for many years. Multiple attempts have been made on the observational side to map this region in order to better understand the local flows. On the theoretical side, however, this region is often simply statistically populated with structures but no real attempt has been made to confront theoretical and observed matter distributions. This paper takes a step forward using constrained realizations (CRs) of the local Universe shown to be perfect substitutes of local Universe-like simulations for smoothed high-density peak studies. Far from generating completely `random' structures in the ZOA, the reconstruction technique arranges matter according to the surrounding environment of this region. More precisely, the mean distributions of structures in a series of constrained and random realizations (RRs) differ: while densities annihilate each other when averaging over 200 RRs, structures persist when summing 200 CRs. The probability distribution function of ZOA grid cells to be highly overdense is a Gaussian with a 15 per cent mean in the random case, while that of the constrained case exhibits large tails. This implies that areas with the largest probabilities host most likely a structure. Comparisons between these predictions and observations, like those of the Puppis 3 cluster, show a remarkable agreement and allow us to assert the presence of the, recently highlighted by observations, Vela supercluster at about 180 h-1 Mpc, right behind the thickest dust layers of our Galaxy.

Phylogenetic relationships within the cyst-forming nematodes (Nematoda, Heteroderidae) based on analysis of sequences from the ITS regions of ribosomal DNA.

PubMed

Subbotin, S A; Vierstraete, A; De Ley, P; Rowe, J; Waeyenberge, L; Moens, M; Vanfleteren, J R

2001-10-01

The ITS1, ITS2, and 5.8S gene sequences of nuclear ribosomal DNA from 40 taxa of the family Heteroderidae (including the genera Afenestrata, Cactodera, Heterodera, Globodera, Punctodera, Meloidodera, Cryphodera, and Thecavermiculatus) were sequenced and analyzed. The ITS regions displayed high levels of sequence divergence within Heteroderinae and compared to outgroup taxa. Unlike recent findings in root knot nematodes, ITS sequence polymorphism does not appear to complicate phylogenetic analysis of cyst nematodes. Phylogenetic analyses with maximum-parsimony, minimum-evolution, and maximum-likelihood methods were performed with a range of computer alignments, including elision and culled alignments. All multiple alignments and phylogenetic methods yielded similar basic structure for phylogenetic relationships of Heteroderidae. The cyst-forming nematodes are represented by six main clades corresponding to morphological characters and host specialization, with certain clades assuming different positions depending on alignment procedure and/or method of phylogenetic inference. Hypotheses of monophyly of Punctoderinae and Heteroderinae are, respectively, strongly and moderately supported by the ITS data across most alignments. Close relationships were revealed between the Avenae and the Sacchari groups and between the Humuli group and the species H. salixophila within Heteroderinae. The Goettingiana group occupies a basal position within this subfamily. The validity of the genera Afenestrata and Bidera was tested and is discussed based on molecular data. We conclude that ITS sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient speciations within Heteroderidae. Copyright 2001 Academic Press.

Is induction ability of seed germination of Phelipanche ramosa phylogenetically structured among hosts? A case study on Fabaceae species.

PubMed

Perronne, Rémi; Gibot-Leclerc, Stéphanie; Dessaint, Fabrice; Reibel, Carole; Le Corre, Valérie

2017-12-01

Phelipanche ramosa is a major root-holoparasitic damaging weed characterized by a broad host range, including numerous Fabaceae species. In France, the agricultural threat posed by P. ramosa has increased over two decades due to the appearance of a genetically differentiated pathovar presenting a clear host specificity for oilseed rape. The new pathovar has led to a massive expansion of P. ramosa in oilseed rape fields. The germination rate of P. ramosa seeds is currently known to vary among P. ramosa pathovars and host species. However, only a few studies have investigated whether phylogenetic relatedness among potential host species is a predictor of the ability of these species to induce the seed germination of parasitic weeds by testing for phylogenetic signal. We focused on a set of 12 Fabaceae species and we assessed the rate of induction of seed germination by these species for two pathovars based on in vitro co-cultivation experiments. All Fabaceae species tested induced the germination of P. ramosa seeds. The germination rate of P. ramosa seeds varied between Fabaceae species and tribes studied, while pathovars appeared non-influential. Considering oilseed rape as a reference species, we also highlighted a significant phylogenetic signal. Phylogenetically related species therefore showed more similar rates of induction of seed germination than species drawn at random from a phylogenetic tree. In in vitro conditions, only Lotus corniculatus induced a significantly higher germination rate than oilseed rape, and could potentially be used as a catch crop after confirmation of these results under field conditions.

Cultural and Environmental Predictors of Pre-European Deforestation on Pacific Islands

PubMed Central

Coomber, Ties; Passmore, Sam; Greenhill, Simon J.; Kushnick, Geoff

2016-01-01

The varied islands of the Pacific provide an ideal natural experiment for studying the factors shaping human impact on the environment. Previous research into pre-European deforestation across the Pacific indicated a major effect of environment but did not account for cultural variation or control for dependencies in the data due to shared cultural ancestry and geographic proximity. The relative importance of environment and culture on Pacific deforestation and forest replacement and the extent to which environmental impact is constrained by cultural ancestry therefore remain unexplored. Here we use comparative phylogenetic methods to model the effect of nine ecological and two cultural variables on pre-European Pacific forest outcomes at 80 locations across 67 islands. We show that some but not all ecological features remain important predictors of forest outcomes after accounting for cultural covariates and non-independence in the data. Controlling for ecology, cultural variation in agricultural intensification predicts deforestation and forest replacement, and there is some evidence that land tenure norms predict forest replacement. These findings indicate that, alongside ecology, cultural factors also predict pre-European Pacific forest outcomes. Although forest outcomes covary with cultural ancestry, this effect disappears after controlling for geographic proximity and ecology. This suggests that forest outcomes were not tightly constrained by colonists’ cultural ancestry, but instead reflect a combination of ecological constraints and the short-term responses of each culture in the face of those constraints. PMID:27232713

Cultural and Environmental Predictors of Pre-European Deforestation on Pacific Islands.

PubMed

Atkinson, Quentin D; Coomber, Ties; Passmore, Sam; Greenhill, Simon J; Kushnick, Geoff

2016-01-01

The varied islands of the Pacific provide an ideal natural experiment for studying the factors shaping human impact on the environment. Previous research into pre-European deforestation across the Pacific indicated a major effect of environment but did not account for cultural variation or control for dependencies in the data due to shared cultural ancestry and geographic proximity. The relative importance of environment and culture on Pacific deforestation and forest replacement and the extent to which environmental impact is constrained by cultural ancestry therefore remain unexplored. Here we use comparative phylogenetic methods to model the effect of nine ecological and two cultural variables on pre-European Pacific forest outcomes at 80 locations across 67 islands. We show that some but not all ecological features remain important predictors of forest outcomes after accounting for cultural covariates and non-independence in the data. Controlling for ecology, cultural variation in agricultural intensification predicts deforestation and forest replacement, and there is some evidence that land tenure norms predict forest replacement. These findings indicate that, alongside ecology, cultural factors also predict pre-European Pacific forest outcomes. Although forest outcomes covary with cultural ancestry, this effect disappears after controlling for geographic proximity and ecology. This suggests that forest outcomes were not tightly constrained by colonists' cultural ancestry, but instead reflect a combination of ecological constraints and the short-term responses of each culture in the face of those constraints.

Functional and phylogenetic relatedness in temporary wetland invertebrates: current macroecological patterns and implications for future climatic change scenarios.

PubMed

Ruhí, Albert; Boix, Dani; Gascón, Stéphanie; Sala, Jordi; Batzer, Darold P

2013-01-01

In freshwater ecosystems, species compositions are known to be determined hierarchically by large to small‑scale environmental factors, based on the biological traits of the organisms. However, in ephemeral habitats this heuristic framework remains largely untested. Although temporary wetland faunas are constrained by a local filter (i.e., desiccation), we propose its magnitude may still depend on large-scale climate characteristics. If this is true, climate should be related to the degree of functional and taxonomic relatedness of invertebrate communities inhabiting seasonal wetlands. We tested this hypothesis in two ways. First, based on 52 biological traits for invertebrates, we conducted a case study to explore functional trends among temperate seasonal wetlands differing in the harshness (i.e., dryness) of their dry season. After finding evidence of trait filtering, we addressed whether it could be generalized across a broader climatic scale. To this end, a meta-analysis (225 seasonal wetlands spread across broad climatic categories: Arid, Temperate, and Cold) allowed us to identify whether an equivalent climate-dependent pattern of trait richness was consistent between the Nearctic and the Western Palearctic. Functional overlap of invertebrates increased from mild (i.e., Temperate) to harsher climates (i.e., Arid and Cold), and phylogenetic clustering (using taxonomy as a surrogate) was highest in Arid and lowest in Temperate wetlands. We show that, (i) as has been described in streams, higher relatedness than would be expected by chance is generally observed in seasonal wetland invertebrate communities; and (ii) this relatedness is not constant but climate-dependent, with the climate under which a given seasonal wetland is located determining the functional overlap and the phylogenetic clustering of the community. Finally, using a space-for-time substitution approach we suggest our results may anticipate how the invertebrate biodiversity embedded in these vulnerable and often overlooked ecosystems will be affected by long-term climate change.

Functional and Phylogenetic Relatedness in Temporary Wetland Invertebrates: Current Macroecological Patterns and Implications for Future Climatic Change Scenarios

PubMed Central

Ruhí, Albert; Boix, Dani; Gascón, Stéphanie; Sala, Jordi; Batzer, Darold P.

2013-01-01

In freshwater ecosystems, species compositions are known to be determined hierarchically by large to small‑scale environmental factors, based on the biological traits of the organisms. However, in ephemeral habitats this heuristic framework remains largely untested. Although temporary wetland faunas are constrained by a local filter (i.e., desiccation), we propose its magnitude may still depend on large-scale climate characteristics. If this is true, climate should be related to the degree of functional and taxonomic relatedness of invertebrate communities inhabiting seasonal wetlands. We tested this hypothesis in two ways. First, based on 52 biological traits for invertebrates, we conducted a case study to explore functional trends among temperate seasonal wetlands differing in the harshness (i.e., dryness) of their dry season. After finding evidence of trait filtering, we addressed whether it could be generalized across a broader climatic scale. To this end, a meta-analysis (225 seasonal wetlands spread across broad climatic categories: Arid, Temperate, and Cold) allowed us to identify whether an equivalent climate-dependent pattern of trait richness was consistent between the Nearctic and the Western Palearctic. Functional overlap of invertebrates increased from mild (i.e., Temperate) to harsher climates (i.e., Arid and Cold), and phylogenetic clustering (using taxonomy as a surrogate) was highest in Arid and lowest in Temperate wetlands. We show that, (i) as has been described in streams, higher relatedness than would be expected by chance is generally observed in seasonal wetland invertebrate communities; and (ii) this relatedness is not constant but climate-dependent, with the climate under which a given seasonal wetland is located determining the functional overlap and the phylogenetic clustering of the community. Finally, using a space-for-time substitution approach we suggest our results may anticipate how the invertebrate biodiversity embedded in these vulnerable and often overlooked ecosystems will be affected by long-term climate change. PMID:24312347

Assessment of trophic ecomorphology in non-alligatoroid crocodylians and its adaptive and taxonomic implications.

PubMed

Iijima, Masaya

2017-08-01

Although the establishment of trophic ecomorphology in living crocodylians can contribute to estimating feeding habits of extinct large aquatic reptiles, assessment of ecomorphological traits other than the snout shape has scarcely been conducted in crocodylians. Here, I tested the validity of the proposed trophic ecomorphological traits in crocodylians by examining the correlation between those traits and the snout shape (an established trophic ecomorphology), using 10 non-alligatoroid crocodylian species with a wide range of snout shape. I then compared the ontogenetic scaling of trophic ecomorphology to discuss its adaptive and taxonomic significance. The results demonstrated that degree of heterodonty, tooth spacing, size of supratemporal fenestra (STF), ventral extension of pterygoid flange and length of lower jaw symphysis are significantly correlated with snout shape by both non-phylogenetic and phylogenetic regression analyses. Gavialis gangeticus falls outside of 95% prediction intervals for the relationships of some traits and the snout shape, suggesting that piscivorous specialization involves the deviation from the typical transformation axis of skull characters. The comparative snout shape ontogeny revealed a universal trend of snout widening through growth in the sampled crocodylians, implying the existence of a shared size-dependent biomechanical constraint in non-alligatoroid crocodylians. Growth patterns of other traits indicated that G. gangeticus shows atypical trends for degree of heterodonty, size of STF, and symphysis length, whereas the same trends are shared for tooth spacing and ventral extension of pterygoid flange among non-alligatoroid crocodylians. These suggest that some characters are ontogenetically labile in response to prey preference shifts through growth, but other characters are in keeping with the conserved biomechanics among non-alligatoroid crocodylians. Some important taxonomic characters such as the occlusal pattern are likely correlated with ontogeny and trophic ecomorphology rather than are constrained by phylogenetic relationships, and careful reassessment of such characters might be necessary for better reconstructing the morphological phylogeny of crocodylians. © 2017 Anatomical Society.

A New Basal Caniform (Mammalia: Carnivora) from the Middle Eocene of North America and Remarks on the Phylogeny of Early Carnivorans

PubMed Central

Tomiya, Susumu

2011-01-01

Background Despite a long history of research, the phylogenetic origin and initial diversification of the mammalian crown-group Carnivora remain elusive. Well-preserved fossil materials of basal carnivorans are essential for resolving these issues, and for constraining the timing of the carnivoran origin, which constitutes an important time-calibration point in mammalian phylogenetics. Methodology/Principal Findings A new carnivoramorphan from the middle Eocene of southern California, Lycophocyon hutchisoni, is described. The new taxon exhibits stages of dental and basicranial evolution that are intermediate between earlier carnivoramorphans and the earliest representatives of canoid carnivorans. The evolutionary affinity of the new taxon was determined by a cladistic analysis of previously-published and newly-acquired morphological data for 30 Paleogene carnivoramorphans. The most-parsimonious trees identified L. hutchisoni as a basal caniform carnivoran, and placed (1) Tapocyon robustus, Quercygale angustidens, “Miacis” sylvestris, “M.” uintensis, and “M.” gracilis inside or outside the Carnivora, (2) nimravids within the Feliformia, and (3) the amphicyonid Daphoenus outside the crown-group Canoidea. Parsimony reconstructions of ancestral character states suggest that loss of the upper third molars and development of well-ossified entotympanics that are firmly fused to the basicranium (neither condition is observed in L. hutchisoni) are not associated with the origin of the Carnivora as traditionally thought, but instead occurred independently in the Caniformia and the Feliformia. A discriminant analysis of the estimated body weight and dental ecomorphology predicted a mesocarnivorous diet for L. hutchisoni, and the postcranial morphology suggests a scansorial habit. Conclusions/Significance Lycophocyon hutchisoni illuminates the morphological evolution of early caniforms leading to the origin of crown-group canoids. Considerable uncertainty remains with respect to the phylogenetic origin of the Carnivora. The minimum date of caniform-feliform divergence is provisionally suggested to be either 47 million years ago or 38 million years ago, depending on the position of “Miacis” sylvestris within or outside the Carnivora, respectively. PMID:21935380

Preliminary observations on the mandibles of palaemonoid shrimp (Crustacea: Decapoda: Caridea: Palaemonoidea)

PubMed Central

De Grave, Sammy; Johnson, Magnus L.

2015-01-01

The mandibles of caridean shrimps have been widely studied in the taxonomy and functional biology of the group. Within the Palaemonoidea the mandibles reach a high level of structural diversity reflecting the diverse lifestyles within the superfamily. However, the majority of studies have been restricted to light microscopy, with the ultrastructure at finer levels poorly known. This study investigates the mandible of nine species belonging to six of the recognised families of the Palaemonoidea using SEM and analyses the results in a phylogenetic and dietary framework. The results of the study indicate that little phylogenetic information is conveyed by the structure of the mandible, but that its form is influenced by primary food sources of each species. With the exception of Anchistioides antiguensis, all species examined possessed cuticular structures at the distal end of the pars molaris (molar process). Five types of cuticular structures are recognised herein, each with a unique form, but variable in number, placement and arrangement. Each type is presumed to have a different function which is likewise related to diet. PMID:25825676

Phylogenetic and Complementation Analysis of a Single-Stranded DNA Binding Protein Family from Lactococcal Phages Indicates a Non-Bacterial Origin

PubMed Central

Mariadassou, Mahendra; Bardowski, Jacek K.; Bidnenko, Elena

2011-01-01

Background The single-stranded-nucleic acid binding (SSB) protein superfamily includes proteins encoded by different organisms from Bacteria and their phages to Eukaryotes. SSB proteins share common structural characteristics and have been suggested to descend from an ancestor polypeptide. However, as other proteins involved in DNA replication, bacterial SSB proteins are clearly different from those found in Archaea and Eukaryotes. It was proposed that the corresponding genes in the phage genomes were transferred from the bacterial hosts. Recently new SSB proteins encoded by the virulent lactococcal bacteriophages (Orf14bIL67-like proteins) have been identified and characterized structurally and biochemically. Methodology/Principal Findings This study focused on the determination of phylogenetic relationships between Orf14bIL67-like proteins and other SSBs. We have performed a large scale phylogenetic analysis and pairwise sequence comparisons of SSB proteins from different phyla. The results show that, in remarkable contrast to other phage SSBs, the Orf14bIL67–like proteins form a distinct, self-contained and well supported phylogenetic group connected to the archaeal SSBs. Functional studies demonstrated that, despite the structural and amino acid sequence differences from bacterial SSBs, Orf14bIL67 protein complements the conditional lethal ssb-1 mutation of Escherichia coli. Conclusions/Significance Here we identified for the first time a group of phages encoded SSBs which are clearly distinct from their bacterial counterparts. All methods supported the recognition of these phage proteins as a new family within the SSB superfamily. Our findings suggest that unlike other phages, the virulent lactococcal phages carry ssb genes that were not acquired from their hosts, but transferred from an archaeal genome. This represents a unique example of a horizontal gene transfer between Archaea and bacterial phages. PMID:22073223

Phylogeny and Evolutionary Patterns in the Dwarf Crayfish Subfamily (Decapoda: Cambarellinae)

PubMed Central

Pedraza-Lara, Carlos; Doadrio, Ignacio; Breinholt, Jesse W.; Crandall, Keith A.

2012-01-01

The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group) and into Central México (Mexican Group), has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp) using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group) and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047), resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric divergence in freshwater organisms can be promoted through diverse vicariant factors. PMID:23155379

Rapid Slewing of Flexible Space Structures

DTIC Science & Technology

2015-09-01

axis gimbal with elastic joints. The performance of the system can be enhanced by designing antenna maneuvers in which the flexible effects are...the effects of the nonlinearities so the vibrational motion can be constrained for a time-optimal slew. It is shown that by constructing an...joints. The performance of the system can be enhanced by designing antenna maneuvers in which the flexible effects are properly constrained, thus

ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics

PubMed Central

Hasenauer, Jan; Hasenauer, Christine; Hucho, Tim; Theis, Fabian J.

2014-01-01

Functional cell-to-cell variability is ubiquitous in multicellular organisms as well as bacterial populations. Even genetically identical cells of the same cell type can respond differently to identical stimuli. Methods have been developed to analyse heterogeneous populations, e.g., mixture models and stochastic population models. The available methods are, however, either incapable of simultaneously analysing different experimental conditions or are computationally demanding and difficult to apply. Furthermore, they do not account for biological information available in the literature. To overcome disadvantages of existing methods, we combine mixture models and ordinary differential equation (ODE) models. The ODE models provide a mechanistic description of the underlying processes while mixture models provide an easy way to capture variability. In a simulation study, we show that the class of ODE constrained mixture models can unravel the subpopulation structure and determine the sources of cell-to-cell variability. In addition, the method provides reliable estimates for kinetic rates and subpopulation characteristics. We use ODE constrained mixture modelling to study NGF-induced Erk1/2 phosphorylation in primary sensory neurones, a process relevant in inflammatory and neuropathic pain. We propose a mechanistic pathway model for this process and reconstructed static and dynamical subpopulation characteristics across experimental conditions. We validate the model predictions experimentally, which verifies the capabilities of ODE constrained mixture models. These results illustrate that ODE constrained mixture models can reveal novel mechanistic insights and possess a high sensitivity. PMID:24992156

Phylogeny, Traits, and Biodiversity of a Neotropical Bat Assemblage: Close Relatives Show Similar Responses to Local Deforestation.

PubMed

Frank, Hannah K; Frishkoff, Luke O; Mendenhall, Chase D; Daily, Gretchen C; Hadly, Elizabeth A

2017-08-01

If species' evolutionary pasts predetermine their responses to evolutionarily novel stressors, then phylogeny could predict species survival in an increasingly human-dominated world. To understand the role of phylogenetic relatedness in structuring responses to rapid environmental change, we focused on assemblages of Neotropical bats, an ecologically diverse and functionally important group. We examined how taxonomic and phylogenetic diversity shift between tropical forest and farmland. We then explored the importance of evolutionary history by ascertaining whether close relatives share similar responses to environmental change and which species traits might mediate these trends. We analyzed a 5-year data set (5,011 captures) from 18 sites in a countryside landscape in southern Costa Rica using statistical models that account and correct for imperfect detection of species across sites, spatial autocorrelation, and consideration of spatial scale. Taxonomic and phylogenetic diversity decreased with deforestation, and assemblages became more phylogenetically clustered. Species' responses to deforestation were strongly phylogenetically correlated. Body mass and absolute wing loading explained a substantial portion of species variation in species' habitat preferences, likely related to these traits' influence on maneuverability in cluttered forest environments. Our findings highlight the role that evolutionary history plays in determining which species will survive human impacts and the need to consider diversity metrics, evolutionary history, and traits together when making predictions about species persistence for conservation or ecosystem functioning.

Ongoing Horizontal and Vertical Transmission of Virulence Genes and papA Alleles among Escherichia coli Blood Isolates from Patients with Diverse-Source Bacteremia

PubMed Central

Johnson, James R.; O'Bryan, Timothy T.; Kuskowski, Michael; Maslow, Joel N.

2001-01-01

The phylogenetic distributions of multiple putative virulence factors (VFs) and papA (P fimbrial structural subunit) alleles among 182 Escherichia coli blood isolates from patients with diverse-source bacteremia were defined. Phylogenetic correspondence among these strains, the E. coli Reference (ECOR) collection, and other collections of extraintestinal pathogenic E. coli (ExPEC) was assessed. Although among the 182 bacteremia isolates phylogenetic group B2 predominated, exhibited the greatest concentration of individual VFs, and contained the largest number of familiar virulent clones, other phylogenetic groups exhibited greater concentrations of certain VFs than did group B2 and included several additional virulent clones. Certain of the newly detected VF genes, e.g., fyuA (yersiniabactin; 76%) and focG (F1C fimbriae; 25%), were as prevalent or more prevalent than their more familiar traditional counterparts, e.g., iut (aerobactin; 57%) and sfaS (S fimbriae; 14%), thus possibly offering additional useful targets for preventive interventions. Considerable diversity of VF profiles was observed at every level within the phylogenetic tree, including even within individual lineages. This suggested that many different pathways can lead to extraintestinal virulence in E. coli and that the evolution of ExPEC, which involves extensive horizontal transmission of VFs and continuous remodeling of pathogenicity-associated islands, is a highly active, ongoing process. PMID:11500406

Phylogenetic relationships of the ciliate class Heterotrichea (Protista, Ciliophora, Postciliodesmatophora) inferred from multiple molecular markers and multifaceted analysis strategy.

PubMed

Shazib, Shahed Uddin Ahmed; Vd'ačný, Peter; Kim, Ji Hye; Jang, Seok Won; Shin, Mann Kyoon

2014-09-01

The ciliate class Heterotrichea is defined by somatic dikinetids bearing postciliodesmata, by an oral apparatus consisting of a paroral membrane and an adoral zone of membranelles, as well as by features of nuclear division involving extramacronuclear microtubules. Although phylogenetic interrelationships among heterotrichs have been analyzed several times, deeper nodes of the heterotrichean tree of life remain poorly resolved. To cast more light on the evolutionary history of heterotricheans, we performed phylogenetic analyses of multiple loci (18S rRNA gene, ITS1-5.8S rRNA-ITS2 region, and 28S rRNA gene) using traditional tree-building phylogenetic methods and statistical tree topology tests as well as phylogenetic networks, split spectrum analysis and quartet likelihood mapping. This multifaceted approach has shown that (1) Peritromus is very likely an adelphotaxon of all other heterotrichs; (2) Spirostomum and Anigsteinia are sister taxa and their common monophyletic origin is strongly supported by a uniquely posteriorly-thickened paroral membrane; (3) the monotypic family Chattonidiidae should be suppressed because its type genus clusters within the family Condylostomatidae; and (4) new families are needed for Gruberia and Fabrea because their affiliation with Spirostomidae and Climacostomidae, respectively, is not supported by molecular phylogenies nor the fine structure of the paroral membrane. Copyright © 2014 Elsevier Inc. All rights reserved.

Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA

PubMed Central

Ball, R. Martin; Freeman, Scott; James, Frances C.; Bermingham, Eldredge; Avise, John C.

1988-01-01

A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P ≈ 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow. PMID:16593914

A phylogenetic community approach for studying termite communities in a West African savannah.

PubMed

Hausberger, Barbara; Korb, Judith

2015-10-01

Termites play fundamental roles in tropical ecosystems, and mound-building species in particular are crucial in enhancing species diversity, from plants to mammals. However, it is still unclear which factors govern the occurrence and assembly of termite communities. A phylogenetic community approach and null models of species assembly were used to examine structuring processes associated with termite community assembly in a pristine savannah. Overall, we did not find evidence for a strong influence of interspecific competition or environmental filtering in structuring these communities. However, the presence of a single species, the mound-building termite Macrotermes bellicosus, left a strong signal on structuring and led to clustered communities of more closely related species. Hence, this species changes the assembly rules for a whole community. Our results show the fundamental importance of a single insect species for community processes, suggesting that more attention to insect species is warranted when developing conservation strategies. © 2015 The Author(s).

Mitochondrial DNA sequence variation and phylogeography of the scarlet kingsnake (Lampropeltis elapsoides).

PubMed

Friedman, Michael; Schaffer, Les

2011-02-01

BACKGROUND AND AIMS. With the goal of assessing population structure and geographic distribution of haplotype lineages among Lampropeltis elapsoides, we sequenced the ND4 mitochondrial DNA locus from 96 specimens of this snake across its area of distribution. MATERIALS AND METHODS. We relied heavily on formalin-fixed museum specimens to accomplish this analysis. RESULTS. The sequence alignment consisted of 491 bp of the selected gene, with 28% missing data. A simulation used to assess the effect of missing data on population genetic and phylogenetic resolution indicated increased character conflict, but with minimal loss of phylogenetic structure. CONCLUSION. This limited dataset suggests that L. elapsoides constitutes a largely unstructured population, with both widespread haplotypes and large number of private haplotypes, a moderate level of nucleotide diversity, and a low, but significant, degree of north-south population differentiation. Haplotype structure and frequency, nucleotide frequency, and values for Tajima's D and Fu's F(S) indicate a recent range or population expansion following a historic bottleneck.

Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum

PubMed Central

Pei, Haisheng; Chen, Zhou; Tan, Xiaoyan; Hu, Jing; Yang, Bin; Sun, Junshe

2017-01-01

Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1–3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP) site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality control in the Ganoderma industry. PMID:28056060

Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum.

PubMed

Zhang, Xiuqing; Xu, Zhangyang; Pei, Haisheng; Chen, Zhou; Tan, Xiaoyan; Hu, Jing; Yang, Bin; Sun, Junshe

2017-01-01

Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1-3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP) site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality control in the Ganoderma industry.

Effects of rooting via out-groups on in-group topology in phylogeny.

PubMed

Ackerman, Margareta; Brown, Daniel G; Loker, David

2014-01-01

Users of phylogenetic methods require rooted trees, because the direction of time depends on the placement of the root. While phylogenetic trees are typically rooted by using an out-group, this mechanism is inappropriate when the addition of an out-group changes the in-group topology. We perform a formal analysis of phylogenetic algorithms under the inclusion of distant out-groups. It turns out that linkage-based algorithms (including UPGMA) and a class of bisecting methods do not modify the topology of the in-group when an out-group is included. By contrast, the popular neighbour joining algorithm fails this property in a strong sense: every data set can have its structure destroyed by some arbitrarily distant outlier. Furthermore, including multiple outliers can lead to an arbitrary topology on the in-group. The standard rooting approach that uses out-groups may be fundamentally unsuited for neighbour joining.

Solution to the phylogenetic enigma of Tetraplatia, a worm-shaped cnidarian

PubMed Central

Collins, Allen G; Bentlage, Bastian; Matsumoto, George I; Haddock, Steven H.D; Osborn, Karen J; Schierwater, Bernd

2005-01-01

Tetraplatia is a genus containing two species of pelagic cnidarians of curious morphology. Their vermiform shape and four swimming flaps are difficult to relate to the features of other cnidarians, thus obscuring their phylogenetic affinities. Since their discovery in the mid-1800s, a number of prominent cnidarian workers have weighed in on this conundrum, some arguing that they are aberrant hydrozoans and others concluding that they are unusual scyphozoans. Current taxonomic practice conforms to the latter view. However, data presented here from the large and small subunits of the nuclear ribosome leave little doubt that Tetraplatia is in fact a hydrozoan genus. Indeed, its precise phylogenetic position is within Narcomedusae, as some authors had previously deduced based on structural characters. The distinctive body plan of Tetraplatia is remarkable because it appears to have a recent origin, in contrast to the prevailing pattern of metazoan history. PMID:17148343

The origin and evolution of seahorses (genus Hippocampus): a phylogenetic study using the cytochrome b gene of mitochondrial DNA.

PubMed

Casey, Stephen P; Hall, Heather J; Stanley, Helen F; Vincent, Amanda C J

2004-02-01

Phylogenetic relationships among 93 specimens of 22 species of seahorses (genus Hippocampus) from the Atlantic and Indo-Pacific Oceans were analysed using cytochrome b gene sequence data. A maximum sequence divergence of 23.2% (Kimura 2-parameter model) suggests a pre-Tethyan origin for the genus. Despite a greater number of seahorse species in the Indo-Pacific than in the Atlantic Ocean, there was no compelling genetic evidence to support an Indo-Pacific origin for the genus Hippocampus. The phylogenetic data suggest that high diversity in the Indo-Pacific results from speciation events dating from the Pleistocene to the Miocene, or earlier. Both vicariance and dispersal events in structuring the current global distribution of seahorses. The results suggested that several species designations need re-evaluating, and further phylogeographic studies are required to determine patterns and processes of seahorse dispersal.

A phylogenetic transform enhances analysis of compositional microbiota data.

PubMed

Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A

2017-02-15

Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.

Partial 16S rRNA primary structure of five Actinomyces species: phylogenetic implications and development of an Actinomyces israelii-specific oligonucleotide probe.

PubMed

Stackebrandt, E; Charfreitag, O

1990-01-01

The intra- and intergeneric relationships of the genus Actinomyces were determined by comparing long 16S rRNA sequences, generated by reverse transcriptase. All species formed a phylogenetically coherent cluster in which Actinomyces bovis, A. viscosus, A. naeslundii, A. odontolyticus and A. israelii constituted genetically well defined species. A. israelii DSM 43322 (serotype 2) was not closely related to three other strains of this species (serotype 1) and, as judged from phylogenetic distances, could be accommodated within A. naeslundii, or represent a new species. In contrast to previous findings, members of the genus Actinomyces appear to be related to Bifidobacterium bifidum. Sequence information was used to develop an oligonucleotide probe for the A. israelii serotype 1 strains, which did not react with the serotype 2 strain or with rRNA from strains of eight Actinomyces species.

Soil shapes community structure through fire.

PubMed

Ojeda, Fernando; Pausas, Juli G; Verdú, Miguel

2010-07-01

Recurrent wildfires constitute a major selecting force in shaping the structure of plant communities. At the regional scale, fire favours phenotypic and phylogenetic clustering in Mediterranean woody plant communities. Nevertheless, the incidence of fire within a fire-prone region may present strong variations at the local, landscape scale. This study tests the prediction that woody communities on acid, nutrient-poor soils should exhibit more pronounced phenotypic and phylogenetic clustering patterns than woody communities on fertile soils, as a consequence of their higher flammability and, hence, presumably higher propensity to recurrent fire. Results confirm the predictions and show that habitat filtering driven by fire may be detected even in local communities from an already fire-filtered regional flora. They also provide a new perspective from which to consider a preponderant role of fire as a key evolutionary force in acid, infertile Mediterranean heathlands.

Community structures and population dynamics of "Candidatus Accumulibacter" in activated sludges of wastewater treatment plants using ppk1 as phylogenetic marker.

PubMed

Zeng, Wei; Zhang, Limin; Fan, Pengchao; Guo, Jingjing; Peng, Yongzhen

2018-05-01

Candidatus Accumulibacter has been identified as dominant polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus (P) removal (EBPR) from wastewater. This study revealed the relevance of community structure, abundance and seasonal population dynamics of Candidatus Accumulibacter to process operation of wastewater treatment plants (WWTPs) in China using ppk1 gene as phylogenetic marker. All sludge samples had properties of denitrifying P removal using nitrate as an electron acceptor. Accumulibacter abundance in the anaerobic-anoxic-oxic (A 2 O) process was the highest (26% of total bacteria), and higher in winter than in summer with a better EBPR performance. Type-II was the dominant Accumulibacter in all processes, and type-I accounted for a small proportion of total Accumulibacter. The abundance of Clade-IIC as the most dominant clade reached 2.59×10 9 cells/g MLSS and accounted for 87.3% of total Accumulibacter. Clade IIC mainly contributed to denitrifying P removal. Clades IIA, IIC and IID were found in all processes, while clade-IIF was only found in oxidation ditch process through phylogenetic analysis. High proportion of clade IID to total Accumulibacter led to poor performance of aerobic P-uptake in inverted A 2 O process. Therefore, Accumulibacter clades in WWTPs were diverse, and EBPR performance was closely related to the clade-level community structures and abundances of Accumulibacter. Copyright © 2017. Published by Elsevier B.V.

Novel parvoviruses in reptiles and genome sequence of a lizard parvovirus shed light on Dependoparvovirus genus evolution.

PubMed

Pénzes, Judit J; Pham, Hanh T; Benkö, Mária; Tijssen, Peter

2015-09-01

Here, we report the detection and partial genome characterization of two novel reptilian parvoviruses derived from a short-tailed pygmy chameleon (Rampholeon brevicaudatus) and a corn snake (Pantherophis guttatus) along with the complete genome analysis of the first lizard parvovirus, obtained from four bearded dragons (Pogona vitticeps). Both homology searches and phylogenetic tree reconstructions demonstrated that all are members of the genus Dependoparvovirus. Even though most dependoparvoviruses replicate efficiently only in co-infections with large DNA viruses, no such agents could be detected in one of the bearded dragon samples, hence the possibility of autonomous replication was explored. The alternative ORF encoding the full assembly activating protein (AAP), typical for the genus, could be obtained from reptilian parvoviruses for the first time, with a structure that appears to be more ancient than that of avian and mammalian parvoviruses. All three viruses were found to harbour short introns as previously observed for snake adeno-associated virus, shorter than that of any non-reptilian dependoparvovirus. According to the phylogenetic calculations based on full non-structural protein (Rep) and AAP sequences, the monophyletic cluster of reptilian parvoviruses seems to be the most basal out of all lineages of genus Dependoparvovirus. The suspected ability for autonomous replication, results of phylogenetic tree reconstruction, intron lengths and the structure of the AAP suggested that a single Squamata origin instead of the earlier assumed diapsid (common avian-reptilian) origin is more likely for the genus Dependoparvovirus of the family Parvoviridae.

Constrained Self-adaptive Solutions Procedures for Structure Subject to High Temperature Elastic-plastic Creep Effects

NASA Technical Reports Server (NTRS)

Padovan, J.; Tovichakchaikul, S.

1983-01-01

This paper will develop a new solution strategy which can handle elastic-plastic-creep problems in an inherently stable manner. This is achieved by introducing a new constrained time stepping algorithm which will enable the solution of creep initiated pre/postbuckling behavior where indefinite tangent stiffnesses are encountered. Due to the generality of the scheme, both monotone and cyclic loading histories can be handled. The presentation will give a thorough overview of current solution schemes and their short comings, the development of constrained time stepping algorithms as well as illustrate the results of several numerical experiments which benchmark the new procedure.

Constrained inversion as a hypothesis testing tool, what can we learn about the lithosphere?

NASA Astrophysics Data System (ADS)

Moorkamp, Max; Stewart, Fishwick; Jones, Alan G.

2017-04-01

Inversion of geophysical data constrained by a reference model is typically used to guide the inversion of low resolution data towards a geologically plausible solution. For example, a migrated seismic section can provide the location of lithological boundaries for potential field inversions. Here we consider the inversion of long-period magnetotelluric data constrained by models generated through surface wave inversion. In this case, we do not consider the surface wave model inherently better in any sense and want to guide the magnetotelluric inversion towards this model, but we want to test the hypothesis that both datasets can be explained by models with similar structure. If the hypothesis test is successful, i.e. we can fit the observations with a conductivity model with structural similarity to the seismic model, we have found an alternative explanation compared to the individual inversion and can use the differences to learn about the resolution of the magnetotelluric data and can improve our interpretation. Conversely, if the test refutes our hypothesis of coincident structure, we have found features in the models that are sensed fundamentally different by both methods which is potentially instructive on the nature of the anomalies. We use a MT dataset acquired in central Botswana over the Okwa terrane and the adjacent Kaapvaal and Zimbabwe Cratons together with a tomographic model for the region to illustrate and test this approach. Here, various conductive structures have been identified that bridge the Moho. Furthermore, the thickness of the lithosphere inferred from the different methods differs. In both cases the question is in how far this is a result of the ill-posed nature of inversion and in how far these differences can be reconciled. Thus this dataset is an ideal test case for our hypothesis testing approach. Finally, we will demonstrate how we can use the results of the constrained inversion to extract conductivity-velocity relationships in the region and gain further insight into the composition and thermal structure of the lithosphere.

Constraining the Dynamical Formation and the Size of the Primordial Building Blocks for Comet 67P/Churyumov-Gerasimenko Using the CONSERT Observations

NASA Astrophysics Data System (ADS)

Heggy, E.; Palmer, E. M.; Kofman, W. W.; Herique, A.; El Maarry, M. R.

2017-12-01

Rosetta's two-year orbital mission at comet 67P/Churyumov-Gerasimenko significantly improved our understanding of the Radar properties of cometary bodies and how they can be used to constrain the ambiguities associated to the dynamical formation of 67P by setting an upper limit on the size of the comet's initial building blocks using the CONSERT, VIRTIS and OSIRIS observations. We present here in an updated post-rendezvous three-dimensional dielectric, textural and structural model of the comet's surface and subsurface at VHF-, X- and S-band radar frequencies. We assess the radar properties of potential structural heterogeneities observed in the upper meters of the shallow subsurface as well as deeper structures across the comet head. We use CONSERT's bistatic radar sounding measurements of the nucleus `head' interior to constrain the dielectric properties and structure of the interior; VIRTIS' multi-spectral observations to constrain the surface mineralogy and the distribution of water-ice on the surface and the implications of the above on the spatial variability of the surface and shallow subsurface dielectric properties. Surface and shallow subsurface structural elements are derived from the OSIRIS' images of exposed outcrops and pit walls. Our dielectric analysis showing the lack of sufficient dielectric contrast correlated with the lack of signal broadening in the 90-MHz radar echoes observed by CONSERT suggests that the the apparent meter-sized inhomogeneities in the walls of deep pits originally interpreted as cometesimals forming the comet's primordial blocks, could be localized evolutionary features of high centered polygons caused by seasonal modifications to the near-subsurface ice formed through thermal expansion and contraction and may not be continuous through the head. Considering the three-dimensional dielectric variability of 67P as derived from CONSERT, VIRTIS, Arecibo observations and laboratory measurement we set an upper limit on the size of the comet's initial building blocks.

Protein structure and evolution: are they constrained globally by a principle derived from information theory?

PubMed

Hatton, Leslie; Warr, Gregory

2015-01-01

That the physicochemical properties of amino acids constrain the structure, function and evolution of proteins is not in doubt. However, principles derived from information theory may also set bounds on the structure (and thus also the evolution) of proteins. Here we analyze the global properties of the full set of proteins in release 13-11 of the SwissProt database, showing by experimental test of predictions from information theory that their collective structure exhibits properties that are consistent with their being guided by a conservation principle. This principle (Conservation of Information) defines the global properties of systems composed of discrete components each of which is in turn assembled from discrete smaller pieces. In the system of proteins, each protein is a component, and each protein is assembled from amino acids. Central to this principle is the inter-relationship of the unique amino acid count and total length of a protein and its implications for both average protein length and occurrence of proteins with specific unique amino acid counts. The unique amino acid count is simply the number of distinct amino acids (including those that are post-translationally modified) that occur in a protein, and is independent of the number of times that the particular amino acid occurs in the sequence. Conservation of Information does not operate at the local level (it is independent of the physicochemical properties of the amino acids) where the influences of natural selection are manifest in the variety of protein structure and function that is well understood. Rather, this analysis implies that Conservation of Information would define the global bounds within which the whole system of proteins is constrained; thus it appears to be acting to constrain evolution at a level different from natural selection, a conclusion that appears counter-intuitive but is supported by the studies described herein.

Phylogenetic trees and Euclidean embeddings.

PubMed

Layer, Mark; Rhodes, John A

2017-01-01

It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution.

PubMed

Meyer, Matthias; Palkopoulou, Eleftheria; Baleka, Sina; Stiller, Mathias; Penkman, Kirsty E H; Alt, Kurt W; Ishida, Yasuko; Mania, Dietrich; Mallick, Swapan; Meijer, Tom; Meller, Harald; Nagel, Sarah; Nickel, Birgit; Ostritz, Sven; Rohland, Nadin; Schauer, Karol; Schüler, Tim; Roca, Alfred L; Reich, David; Shapiro, Beth; Hofreiter, Michael

2017-06-06

The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants ( Elephas maximus ), and many paleontologists place Palaeoloxodon within Elephas . Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods ~120 and ~244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants ( Loxodonta cyclotis ). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta , indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.

Competition and constraint drove Cope's rule in the evolution of giant flying reptiles.

PubMed

Benson, Roger B J; Frigot, Rachel A; Goswami, Anjali; Andres, Brian; Butler, Richard J

2014-04-02

The pterosaurs, Mesozoic flying reptiles, attained wingspans of more than 10 m that greatly exceed the largest birds and challenge our understanding of size limits in flying animals. Pterosaurs have been used to illustrate Cope's rule, the influential generalization that evolutionary lineages trend to increasingly large body sizes. However, unambiguous examples of Cope's rule operating on extended timescales in large clades remain elusive, and the phylogenetic pattern and possible drivers of pterosaur gigantism are uncertain. Here we show 70 million years of highly constrained early evolution, followed by almost 80 million years of sustained, multi-lineage body size increases in pterosaurs. These results are supported by maximum-likelihood modelling of a comprehensive new pterosaur data set. The transition between these macroevolutionary regimes is coincident with the Early Cretaceous adaptive radiation of birds, supporting controversial hypotheses of bird-pterosaur competition, and suggesting that evolutionary competition can act as a macroevolutionary driver on extended geological timescales.

Correlations between adult mimicry and larval host plants in ithomiine butterflies.

PubMed

Willmott, Keith R; Mallet, James

2004-08-07

The apparent paradox of multiple coexisting wing pattern mimicry 'rings' in tropical butterflies has been explained as a result of microhabitat partitioning in adults. However, very few studies have tested this hypothesis. In neotropical forests, ithomiine butterflies dominate and display the richest diversity of mimicry rings. We show that co-mimetic species occupy the same larval host-plant species significantly more often than expected in two out of five communities that we surveyed; in one of these, the effect remains significant after phylogenetic correction. This relationship is most probably a result of a third correlated variable, such as microhabitat. Host-plant microhabitat may constrain adult movement, or host-plant choice may depend on butterfly microhabitat preferences and mimicry associations. This link between mimicry and host plant could help explain some host-plant and mimicry shifts, which have been important in the radiation of this speciose tropical group.

Structural, functional and evolutionary characterization of major drought transcription factors families in maize

NASA Astrophysics Data System (ADS)

Mittal, Shikha; Banduni, Pooja; Mallikarjuna, Mallana G.; Rao, Atmakuri R.; Jain, Prashant A.; Dash, Prasanta K.; Thirunavukkarasu, Nepolean

2018-05-01

Drought is one of the major threats to maize production. In order to improve the production and to breed tolerant hybrids, understanding the genes and regulatory mechanisms during drought stress is important. Transcription factors (TFs) play a major role in gene regulation and many TFs have been identified in response to drought stress. In our experiment, a set of 15 major TF families comprising 1436 genes was structurally and functionally characterized using in-silico tools and a gene expression assay. All 1436 genes were mapped on 10 chromosome of maize. The functional annotation indicated the involvement of these genes in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed individually for each TF family as well as combined TF families. Phylogenetic analysis grouped the TF family of genes into TF-specific and mixed groups. Phylogenetic analysis of genes belonging to various TF families suggested that the origin of TFs occurred in the lineage of maize evolution. Gene structure analysis revealed that more number of genes were intron-rich as compared to intronless genes. Drought-responsive CRE’s such as ABREA, ABREB, DRE1 and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. We also analyzed protein-protein interaction network of 269 drought-responsive genes belonging to different drought-related TFs. The information generated on structural and functional characteristics, expression and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to derive drought-tolerant genotypes in maize.

Constraints and triggers: situational mechanics of gender in negotiation.

PubMed

Bowles, Hannah Riley; Babcock, Linda; McGinn, Kathleen L

2005-12-01

The authors propose 2 categories of situational moderators of gender in negotiation: situational ambiguity and gender triggers. Reducing the degree of situational ambiguity constrains the influence of gender on negotiation. Gender triggers prompt divergent behavioral responses as a function of gender. Field and lab studies (1 and 2) demonstrated that decreased ambiguity in the economic structure of a negotiation (structural ambiguity) reduces gender effects on negotiation performance. Study 3 showed that representation role (negotiating for self or other) functions as a gender trigger by producing a greater effect on female than male negotiation performance. Study 4 showed that decreased structural ambiguity constrains gender effects of representation role, suggesting that situational ambiguity and gender triggers work in interaction to moderate gender effects on negotiation performance. Copyright 2006 APA, all rights reserved.

New substitution models for rooting phylogenetic trees.

PubMed

Williams, Tom A; Heaps, Sarah E; Cherlin, Svetlana; Nye, Tom M W; Boys, Richard J; Embley, T Martin

2015-09-26

The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made. © 2015 The Authors.

A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions

PubMed Central

Makendi, Carine; Page, Andrew J.; Wren, Brendan W.; Le Thi Phuong, Tu; Clare, Simon; Hale, Christine; Goulding, David; Klemm, Elizabeth J.; Pickard, Derek; Okoro, Chinyere; Hunt, Martin; Thompson, Corinne N.; Phu Huong Lan, Nguyen; Tran Do Hoang, Nhu; Thwaites, Guy E.; Le Hello, Simon; Brisabois, Anne; Weill, François-Xavier; Baker, Stephen; Dougan, Gordon

2016-01-01

Salmonella enterica serovar Weltevreden (S. Weltevreden) is an emerging cause of diarrheal and invasive disease in humans residing in tropical regions. Despite the regional and international emergence of this Salmonella serovar, relatively little is known about its genetic diversity, genomics or virulence potential in model systems. Here we used whole genome sequencing and bioinformatics analyses to define the phylogenetic structure of a diverse global selection of S. Weltevreden. Phylogenetic analysis of more than 100 isolates demonstrated that the population of S. Weltevreden can be segregated into two main phylogenetic clusters, one associated predominantly with continental Southeast Asia and the other more internationally dispersed. Subcluster analysis suggested the local evolution of S. Weltevreden within specific geographical regions. Four of the isolates were sequenced using long read sequencing to produce high quality reference genomes. Phenotypic analysis in Hep-2 cells and in a murine infection model indicated that S. Weltevreden were significantly attenuated in these models compared to the classical S. Typhimurium reference strain SL1344. Our work outlines novel insights into this important emerging pathogen and provides a baseline understanding for future research studies. PMID:26867150

On the relationship between phylogenetic diversity and trait diversity.

PubMed

Tucker, Caroline M; Davies, T Jonathan; Cadotte, Marc W; Pearse, William D

2018-05-21

Niche differences are key to understanding the distribution and structure of biodiversity. To examine niche differences, we must first characterize how species occupy niche space, and two approaches are commonly used in the ecological literature. The first uses species traits to estimate multivariate trait space (so-called functional trait diversity, FD); the second quantifies the amount of time or evolutionary history captured by a group of species (phylogenetic diversity, PD). It is often-but controversially-assumed that these putative measures of niche space are at a minimum correlated and perhaps redundant, since more evolutionary time allows for greater accumulation of trait changes. This theoretical expectation remains surprisingly poorly evaluated, particularly in the context of multivariate measures of trait diversity. We evaluated the relationship between phylogenetic diversity and trait diversity using analytical and simulation-based methods across common models of trait evolution. We show that PD correlates with FD increasingly strongly as more traits are included in the FD measure. Our results indicate that phylogenetic diversity can be a useful surrogate for high-dimensional trait diversity, but we also show that the correlation weakens when the underlying process of trait evolution includes variation in rate and optima. © 2018 by the Ecological Society of America.

Molecular phylogenetic lineage of Plagiopogon and Askenasia (Protozoa, Ciliophora) revealed by their gene sequences

NASA Astrophysics Data System (ADS)

Liu, An; Yi, Zhenzhen; Lin, Xiaofeng; Hu, Xiaozhong; Al-Farraj, Saleh A.; Al-Rasheid, Khaled A. S.

2015-08-01

Prostomates and haptorians are two basal groups of ciliates with limited morphological characteristics available for taxonomy. Morphologically, the structures used to identify prostomates and haptorians are similar or even identical, which generate heavy taxonomic and phylogenetic confusion. In present work, phylogenetic positions lineage of two rare genera, Plagiopogon and Askenasia, were investigated. Three genes including small subunit ribosomal RNA gene (hereafter SSU rDNA), internal transcribed spacer region (ITS region), and large subunit ribosomal RNA gene (LSU rDNA) were analyzed, 10 new sequences five species each. Our findings included 1) class Prostomatea and order Haptorida are multiphyletic; 2) it may not be appropriate to place order Cyclotrichiida in subclass Haptoria, and the systematic lineage of order Cyclotrichiida needs to be verified further; 3) genus Plagiopogon branches consistently within a clade covering most prostomes and is basal of clade Colepidae, implying its close lineage to Prostomatea; and 4) Askenasia is phylogenetically distant from the subclass Haptoria but close to classes Prostomatea, Plagiopylea and Oligohymenophorea. We supposed that the toxicyst of Askenasia may be close to taxa of prostomes instead of haptorians, and the dorsal brush is a more typical morphological characteristics of haptorians than toxicysts.

Westward tilt of low-latitude plasma blobs as observed by the Swarm constellation

NASA Astrophysics Data System (ADS)

Park, Jaeheung; Lühr, Hermann; Michaelis, Ingo; Stolle, Claudia; Rauberg, Jan; Buchert, Stephan; Gill, Reine; Merayo, Jose M. G.; Brauer, Peter

2015-04-01

In this study we investigate the three-dimensional structure of low-latitude plasma blobs using multi-instrument and multisatellite observations of the Swarm constellation. During the early commissioning phase the Swarm satellites were flying at the same altitude with zonal separation of about 0.5∘ in geographic longitude. Electron density data from the three satellites constrain the blob morphology projected onto the horizontal plane. Magnetic field deflections around blobs, which originate from field-aligned currents near the irregularity boundaries, constrain the blob structure projected onto the plane perpendicular to the ambient magnetic field. As the two constraints are given for two noncoplanar surfaces, we can get information on the three-dimensional structure of blobs. Combined observation results suggest that blobs are contained within tilted shells of geomagnetic flux tubes, which are similar to the shell structure of equatorial plasma bubbles suggested by previous studies.

How Many Parasites Species a Frog Might Have? Determinants of Parasite Diversity in South American Anurans

PubMed Central

Campião, Karla Magalhães; Ribas, Augusto Cesar de Aquino; Morais, Drausio Honorio; da Silva, Reinaldo José; Tavares, Luiz Eduardo Roland

2015-01-01

There is an increasing interest in unveiling the dynamics of parasite infection. Understanding the interaction patterns, and determinants of host-parasite association contributes to filling knowledge gaps in both community and disease ecology. Despite being targeted as a relevant group for conservation efforts, determinants of the association of amphibians and their parasites in broad scales are poorly understood. Here we describe parasite biodiversity in South American amphibians, testing the influence of host body size and geographic range in helminth parasites species richness (PSR). We also test whether parasite diversity is related to hosts’ phylogenetic diversity. Results showed that nematodes are the most common anuran parasites. Host-parasite network has a nested pattern, with specialist helminth taxa generally associated with hosts that harbour the richest parasite faunas. Host size is positively correlated with helminth fauna richness, but we found no support for the association of host geographic range and PSR. These results remained consistent after correcting for uneven study effort and hosts’ phylogenic correlation. However, we found no association between host and parasite diversity, indicating that more diversified anuran clades not necessarily support higher parasite diversity. Overall, considering both the structure and the determinants of PRS in anurans, we conclude that specialist parasites are more likely to be associated with large anurans, which are the ones harbouring higher PSR, and that the lack of association of PSR with hosts’ clade diversification suggests it is strongly influenced by ecological and contemporary constrains. PMID:26473593

Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA.

PubMed

Medina, M; Collins, A G; Silberman, J D; Sogin, M L

2001-08-14

We studied the evolutionary relationships among basal metazoan lineages by using complete large subunit (LSU) and small subunit (SSU) ribosomal RNA sequences for 23 taxa. After identifying competing hypotheses, we performed maximum likelihood searches for trees conforming to each hypothesis. Kishino-Hasegawa tests were used to determine whether the data (LSU, SSU, and combined) reject any of the competing hypotheses. We also conducted unconstrained tree searches, compared the resulting topologies, and calculated bootstrap indices. Shimodaira-Hasegawa tests were applied to determine whether the data reject any of the topologies resulting from the constrained and unconstrained tree searches. LSU, SSU, and the combined data strongly contradict two assertions pertaining to sponge phylogeny. Hexactinellid sponges are not likely to be the basal lineage of a monophyletic Porifera or the sister group to all other animals. Instead, Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea. It remains unclear, on the basis of these data alone, whether the calcarean sponges are more closely related to Silicea or to nonsponge animals. The SSU and combined data reject the hypothesis that Bilateria is more closely related to Ctenophora than it is to Cnidaria, whereas LSU data alone do not refute either hypothesis. LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa. LSU sequence data reveal phylogenetic structure in a data set with limited taxon sampling. Continued accumulation of LSU sequences should increase our understanding of animal phylogeny.

Foraging mode affects the evolution of egg size in generalist predators embedded in complex food webs.

PubMed

Verdeny-Vilalta, O; Fox, C W; Wise, D H; Moya-Laraño, J

2015-06-01

Ecological networks incorporate myriad biotic interactions that determine the selection pressures experienced by the embedded populations. We argue that within food webs, the negative scaling of abundance with body mass and foraging theory predict that the selective advantages of larger egg size should be smaller for sit-and-wait than active-hunting generalist predators, leading to the evolution of a difference in egg size between them. Because body mass usually scales negatively with predator abundance and constrains predation rate, slightly increasing egg mass should simultaneously allow offspring to feed on more prey and escape from more predators. However, the benefits of larger offspring would be relatively smaller for sit-and-wait predators because (i) due to their lower mobility, encounters with other predators are less common, and (ii) they usually employ a set of alternative hunting strategies that help to subdue relatively larger prey. On the other hand, for active predators, which need to confront prey as they find them, body-size differences may be more important in subduing prey. This difference in benefits should lead to the evolution of larger egg sizes in active-hunting relative to sit-and-wait predators. This prediction was confirmed by a phylogenetically controlled analysis of 268 spider species, supporting the view that the structure of ecological networks may serve to predict relevant selective pressures acting on key life history traits. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life

PubMed Central

Ivancevic, Atma M.; Kortschak, R. Daniel; Bertozzi, Terry; Adelson, David L.

2016-01-01

LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to ‘jump’ around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active L1, in particular, are often thought of as tightly constrained, homologous and ubiquitous elements with well-characterized domain organization. For the past 30 years, model organisms have been used to define L1s as 6–8 kb sequences containing a 5′-UTR, two open reading frames working harmoniously in cis, and a 3′-UTR with a polyA tail. In this study, we demonstrate the remarkable and overlooked diversity of L1s via a comprehensive phylogenetic analysis of elements from over 500 species from widely divergent branches of the tree of life. The rapid and recent growth of L1 elements in mammalian species is juxtaposed against the diverse lineages found in other metazoans and plants. In fact, some of these previously unexplored mammalian species (e.g. snub-nosed monkey, minke whale) exhibit L1 retrotranspositional ‘hyperactivity’ far surpassing that of human or mouse. In contrast, non-mammalian L1s have become so varied that the current classification system seems to inadequately capture their structural characteristics. Our findings illustrate how both long-term inherited evolutionary patterns and random bursts of activity in individual species can significantly alter genomes, highlighting the importance of L1 dynamics in eukaryotes. PMID:27702814

Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Medina, Monica; Collins, Allen G.; Silberman, Jeffrey

2001-06-21

We studied the evolutionary relationships among basal metazoan lineages by using complete large subunit (LSU) and small subunit (SSU) ribosomal RNA sequences for 23 taxa. After identifying competing hypotheses, we performed maximum likelihood searches for trees conforming to each hypothesis. Kishino-Hasegawa tests were used to determine whether the data (LSU, SSU, and combined) reject any of the competing hypotheses. We also conducted unconstrained tree searches, compared the resulting topologies, and calculated bootstrap indices. Shimodaira-Hasegawa tests were applied to determine whether the data reject any of the topologies resulting from the constrained and unconstrained tree searches. LSU, SSU, and the combinedmore » data strongly contradict two assertions pertaining to sponge phylogeny. Hexactinellid sponges are not likely to be the basal lineage of amonophyletic Porifera or the sister group to all other animals. Instead, Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea. It remains unclear, on the basis of these data alone, whether the calcarean sponges are more closely related to Silicea or to nonsponge animals. The SSU and combined data reject the hypothesis that Bilateria is more closely related to Ctenophora than it is to Cnidaria, whereas LSU data alone do not refute either hypothesis. LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa. LSU sequence data reveal phylogenetic structure in a data set with limited taxon sampling. Continued accumulation of LSU sequences should increase our understanding of animal phylogeny.« less

Identification of Two Novel Amalgaviruses in the Common Eelgrass (Zostera marina) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites.

PubMed

Park, Dongbin; Goh, Chul Jun; Kim, Hyein; Hahn, Yoonsoo

2018-04-01

The genome sequences of two novel monopartite RNA viruses were identified in a common eelgrass ( Zostera marina ) transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these two novel viruses belong to the genus Amalgavirus in the family Amalgaviridae . They were named Zostera marina amalgavirus 1 (ZmAV1) and Zostera marina amalgavirus 2 (ZmAV2). Genomes of both ZmAV1 and ZmAV2 contain two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. The fusion protein (ORF1+2) of ORF1 and ORF2, which mediates RNA replication, was produced using the +1 programmed ribosomal frameshifting (PRF) mechanism. The +1 PRF motif sequence, UUU_CGN, which is highly conserved among known amalgaviruses, was also found in ZmAV1 and ZmAV2. Multiple sequence alignment of the ORF1+2 fusion proteins from 24 amalgaviruses revealed that +1 PRF occurred only at three different positions within the 13-amino acid-long segment, which was surrounded by highly conserved regions on both sides. This suggested that the +1 PRF may be constrained by the structure of fusion proteins. Genome sequences of ZmAV1 and ZmAV2, which are the first viruses to be identified in common eelgrass, will serve as useful resources for studying evolution and diversity of amalgaviruses.

Identification of Two Novel Amalgaviruses in the Common Eelgrass (Zostera marina) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites

PubMed Central

Park, Dongbin; Goh, Chul Jun; Kim, Hyein; Hahn, Yoonsoo

2018-01-01

The genome sequences of two novel monopartite RNA viruses were identified in a common eelgrass (Zostera marina) transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these two novel viruses belong to the genus Amalgavirus in the family Amalgaviridae. They were named Zostera marina amalgavirus 1 (ZmAV1) and Zostera marina amalgavirus 2 (ZmAV2). Genomes of both ZmAV1 and ZmAV2 contain two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. The fusion protein (ORF1+2) of ORF1 and ORF2, which mediates RNA replication, was produced using the +1 programmed ribosomal frameshifting (PRF) mechanism. The +1 PRF motif sequence, UUU_CGN, which is highly conserved among known amalgaviruses, was also found in ZmAV1 and ZmAV2. Multiple sequence alignment of the ORF1+2 fusion proteins from 24 amalgaviruses revealed that +1 PRF occurred only at three different positions within the 13-amino acid-long segment, which was surrounded by highly conserved regions on both sides. This suggested that the +1 PRF may be constrained by the structure of fusion proteins. Genome sequences of ZmAV1 and ZmAV2, which are the first viruses to be identified in common eelgrass, will serve as useful resources for studying evolution and diversity of amalgaviruses. PMID:29628822

How Many Parasites Species a Frog Might Have? Determinants of Parasite Diversity in South American Anurans.

PubMed

Campião, Karla Magalhães; Ribas, Augusto Cesar de Aquino; Morais, Drausio Honorio; da Silva, Reinaldo José; Tavares, Luiz Eduardo Roland

2015-01-01

There is an increasing interest in unveiling the dynamics of parasite infection. Understanding the interaction patterns, and determinants of host-parasite association contributes to filling knowledge gaps in both community and disease ecology. Despite being targeted as a relevant group for conservation efforts, determinants of the association of amphibians and their parasites in broad scales are poorly understood. Here we describe parasite biodiversity in South American amphibians, testing the influence of host body size and geographic range in helminth parasites species richness (PSR). We also test whether parasite diversity is related to hosts' phylogenetic diversity. Results showed that nematodes are the most common anuran parasites. Host-parasite network has a nested pattern, with specialist helminth taxa generally associated with hosts that harbour the richest parasite faunas. Host size is positively correlated with helminth fauna richness, but we found no support for the association of host geographic range and PSR. These results remained consistent after correcting for uneven study effort and hosts' phylogenic correlation. However, we found no association between host and parasite diversity, indicating that more diversified anuran clades not necessarily support higher parasite diversity. Overall, considering both the structure and the determinants of PRS in anurans, we conclude that specialist parasites are more likely to be associated with large anurans, which are the ones harbouring higher PSR, and that the lack of association of PSR with hosts' clade diversification suggests it is strongly influenced by ecological and contemporary constrains.

Process-Based Species Pools Reveal the Hidden Signature of Biotic Interactions Amid the Influence of Temperature Filtering.

PubMed

Lessard, Jean-Philippe; Weinstein, Ben G; Borregaard, Michael K; Marske, Katharine A; Martin, Danny R; McGuire, Jimmy A; Parra, Juan L; Rahbek, Carsten; Graham, Catherine H

2016-01-01

A persistent challenge in ecology is to tease apart the influence of multiple processes acting simultaneously and interacting in complex ways to shape the structure of species assemblages. We implement a heuristic approach that relies on explicitly defining species pools and permits assessment of the relative influence of the main processes thought to shape assemblage structure: environmental filtering, dispersal limitations, and biotic interactions. We illustrate our approach using data on the assemblage composition and geographic distribution of hummingbirds, a comprehensive phylogeny and morphological traits. The implementation of several process-based species pool definitions in null models suggests that temperature-but not precipitation or dispersal limitation-acts as the main regional filter of assemblage structure. Incorporating this environmental filter directly into the definition of assemblage-specific species pools revealed an otherwise hidden pattern of phylogenetic evenness, indicating that biotic interactions might further influence hummingbird assemblage structure. Such hidden patterns of assemblage structure call for a reexamination of a multitude of phylogenetic- and trait-based studies that did not explicitly consider potentially important processes in their definition of the species pool. Our heuristic approach provides a transparent way to explore patterns and refine interpretations of the underlying causes of assemblage structure.

Molecular Diversity of Cyanobacteria Inhabiting Coniform Structures and Surrounding Mat in a Yellowstone Hot Spring

NASA Astrophysics Data System (ADS)

Lau, Evan; Nash, Cody Z.; Vogler, Detlev R.; Cullings, K. W.

2005-02-01

Lithified coniform structures are common within cyanobacterial mats in Yellowstone National Park hot springs. It is unknown whether these structures and the mats from which they develop are inhabited by the same cyanobacterial populations. Denaturing gradient gel electrophoresis and sequencing and phylogenetic analysis of 16S rDNA was used to determine whether (1) three different morphological types of lithified coniform structures are inhabited by different cyanobacterial species, (2) these species are partitioned along a vertical gradient of these structures, and (3) lithified and non-lithified sections of mat are inhabited by different cyanobacterial species. Our results, based on multiple samplings, indicate that the cyanobacterial community compositions in the three lithified morphological types were identical and lacked any vertical differentiation. However, lithified and non-lithified portions of the same mat were inhabited by distinct and different populations of cyanobacteria. Cyanobacteria inhabiting lithified structures included at least one undefined Oscillatorialean taxon, which may represent the dominant cyanobacteria genus in lithified coniform stromatolites, Phormidium, three Synechococcus-like species, and two unknown cyanobacterial taxa. In contrast, the surrounding mats contained four closely related Synechococcus-like species. Our results indicate that the distribution of lithified coniform stromatolites may be dependent on the presence of one or more microorganisms, which are phylogenetically different from those inhabiting surrounding non-lithified mats.

Evolutionary differences in Δ13C detected between spore and seed bearing plants following exposure to a range of atmospheric O2:CO2 ratios; implications for paleoatmosphere reconstruction

NASA Astrophysics Data System (ADS)

Porter, Amanda S.; Yiotis, Charilaos; Montañez, Isabel P.; McElwain, Jennifer C.

2017-09-01

The stable carbon isotopes of fossil plants are a reflection of the atmosphere and environment in which they grew. Fossil plant remains have thus stored information about the isotopic composition and concentration of atmospheric carbon dioxide (pCO2) and possibly pO2 through time. Studies to date, utilizing extant plants, have linked changes in plant stable carbon isotopes (δ13Cp) or carbon isotope discrimination (Δ13C) to changes in pCO2 and/or pO2. These studies have relied heavily on angiosperm representatives, a phylogenetic group only present in the fossil record post-Early Cretaceous (∼140 million years ago (mya)), whereas gymnosperms, monilophytes and lycophytes dominated terrestrial ecosystems prior to this time. The aim of this study was to expand our understanding of carbon isotope discrimination in all vascular plant groups of C3 plants including lycophytes, monilophytes, gymnosperms and angiosperms, under elevated CO2 and sub-ambient O2 to explore their utility as paleo-atmospheric proxies. To achieve this goal, plants were grown in controlled environment chambers under a range of O2:CO2 ratio treatments. Results reveal a strong phylogenetic dependency on Δ13C, where spore-bearing (lycophytes and monilophytes) have significantly higher 13C discrimination than seed plants (gymnosperms and angiosperms) by ∼5‰. We attribute this strong phylogenetic signal to differences in Ci/Ca likely mediated by fundamental differences in how spore and seed bearing plants control stomatal aperture. Decreasing O2:CO2 ratio in general resulted in increased carbon isotope discrimination in all plant groups. Notably, while all plant groups respond unidirectionally to elevated atmospheric CO2 (1900 ppm and ambient O2), they do not respond equally to sub-ambient O2 (16%). We conclude that (1) Δ13C has a strong phylogenetic or 'reproductive grade' bias, whereby Δ13C of spore reproducing plants is significantly different to seed reproducing taxa. (2) Δ13C increases with decreasing O2:CO2 ratios (where significant) but is more likely a result of mechanistically uncoupled responses to elevated pCO2 and sub-ambient O2; and (3) due to this response we find δ13Ca cannot be calculated from δ13Cp unless environmental influences such as O2:CO2 ratio can be independently constrained. Therefore, interpretations of trends in fossil plant δ13Cp to reconstruct paleoatmospheric CO2 concentration should include cross calibration based on a nearest living relative, appropriate nearest living equivalent, or utilizing the phylogenetic corrections produced from this study.

Hedonic price models with omitted variables and measurement errors: a constrained autoregression-structural equation modeling approach with application to urban Indonesia

NASA Astrophysics Data System (ADS)

Suparman, Yusep; Folmer, Henk; Oud, Johan H. L.

2014-01-01

Omitted variables and measurement errors in explanatory variables frequently occur in hedonic price models. Ignoring these problems leads to biased estimators. In this paper, we develop a constrained autoregression-structural equation model (ASEM) to handle both types of problems. Standard panel data models to handle omitted variables bias are based on the assumption that the omitted variables are time-invariant. ASEM allows handling of both time-varying and time-invariant omitted variables by constrained autoregression. In the case of measurement error, standard approaches require additional external information which is usually difficult to obtain. ASEM exploits the fact that panel data are repeatedly measured which allows decomposing the variance of a variable into the true variance and the variance due to measurement error. We apply ASEM to estimate a hedonic housing model for urban Indonesia. To get insight into the consequences of measurement error and omitted variables, we compare the ASEM estimates with the outcomes of (1) a standard SEM, which does not account for omitted variables, (2) a constrained autoregression model, which does not account for measurement error, and (3) a fixed effects hedonic model, which ignores measurement error and time-varying omitted variables. The differences between the ASEM estimates and the outcomes of the three alternative approaches are substantial.

Investigating how students communicate tree-thinking

NASA Astrophysics Data System (ADS)

Boyce, Carrie Jo

Learning is often an active endeavor that requires students work at building conceptual understandings of complex topics. Personal experiences, ideas, and communication all play large roles in developing knowledge of and understanding complex topics. Sometimes these experiences can promote formation of scientifically inaccurate or incomplete ideas. Representations are tools used to help individuals understand complex topics. In biology, one way that educators help people understand evolutionary histories of organisms is by using representations called phylogenetic trees. In order to understand phylogenetics trees, individuals need to understand the conventions associated with phylogenies. My dissertation, supported by the Tree-Thinking Representational Competence and Word Association frameworks, is a mixed-methods study investigating the changes in students' tree-reading, representational competence and mental association of phylogenetic terminology after participation in varied instruction. Participants included 128 introductory biology majors from a mid-sized southern research university. Participants were enrolled in either Introductory Biology I, where they were not taught phylogenetics, or Introductory Biology II, where they were explicitly taught phylogenetics. I collected data using a pre- and post-assessment consisting of a word association task and tree-thinking diagnostic (n=128). Additionally, I recruited a subset of students from both courses (n=37) to complete a computer simulation designed to teach students about phylogenetic trees. I then conducted semi-structured interviews consisting of a word association exercise with card sort task, a retrospective pre-assessment discussion, a post-assessment discussion, and interview questions. I found that students who received explicit lecture instruction had a significantly higher increase in scores on a tree-thinking diagnostic than students who did not receive lecture instruction. Students who received both explicit lecture instruction and the computer simulation had a higher level of representational competence and were better able to understand abstract-style phylogenetic trees than students who only completed the simulation. Students who received explicit lecture instruction had a slightly more scientific association of phylogenetic terms than students who received did not receive lecture instruction. My findings suggest that technological instruction alone is not as beneficial as lecture instruction.

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

PubMed Central

Roger, Andrew J; Hug, Laura A

2006-01-01

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes. PMID:16754613

Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent.

PubMed

Alfonso-Morales, Abdulahi; Rios, Liliam; Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L; Bertran, Kateri; Frías, Maria T; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I; Pérez, Lester J

2015-01-01

Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for molecular epidemiology studies.

Evolutionary conservatism explains increasing relatedness of plant communities along a flooding gradient.

PubMed

Tanentzap, Andrew J; Lee, William G

2017-01-01

Abiotic filters have been found either to increase or reduce evolutionary relatedness in plant communities, making it difficult to generalize responses of this major feature of biodiversity to future environmental change. Here, we hypothesized that the responses of phylogenetic structure to environmental change ultimately depend on how species have evolved traits for tolerating the resulting abiotic changes. Working within ephemeral wetlands, we tested whether species were increasingly related as flooding duration intensified. We also identified the mechanisms underlying increased relatedness by measuring root aerenchyma volume (RAV), a trait which promotes waterlogging tolerance. We found that species-specific responses to flooding explained most of the variation in occurrence for 63 vascular plant species across 5170 plots. For a subset of 22 species, we attributed these responses to variation in RAV. Large RAV specifically increased occurrence when flooding lasted for longer time periods, because large RAV reduced above-ground biomass loss. As large RAV was evolutionarily conserved within obligate wetland species, communities were more phylogenetically related as flooding increased. Our study shows how reconstructing the evolutionary history of traits that influence the responses of species to environmental change can help to predict future patterns in phylogenetic structure. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria).

PubMed Central

Edmonds, C G; Crain, P F; Gupta, R; Hashizume, T; Hocart, C H; Kowalak, J A; Pomerantz, S C; Stetter, K O; McCloskey, J A

1991-01-01

Nucleoside modification has been studied in unfractionated tRNA from 11 thermophilic archaea (archaebacteria), including phylogenetically diverse representatives of thermophilic methanogens and sulfur-metabolizing hyperthermophiles which grow optimally in the temperature range of 56 (Thermoplasma acidophilum) to 105 degrees C (Pyrodictium occultum), and for comparison from the most thermophilic bacterium (eubacterium) known, Thermotoga maritima (80 degrees C). Nine nucleosides are found to be unique to the archaea, six of which are structurally novel in being modified both in the base and by methylation in ribose and occur primarily in tRNA from the extreme thermophiles in the Crenarchaeota of the archaeal phylogenetic tree. 2-Thiothymine occurs in tRNA from Thermococcus sp., and constitutes the only known occurrence of the thymine moiety in archaeal RNA, in contrast to its near-ubiquitous presence in tRNA from bacteria and eukarya. A total of 33 modified nucleosides are rigorously characterized in archaeal tRNA in the present study, demonstrating that the structural range of posttranscriptional modifications in archaeal tRNA is more extensive than previously known. From a phylogenetic standpoint, certain tRNA modifications occur in the archaea which are otherwise unique to either the bacterial or eukaryal domain, although the overall patterns of modification are more typical of eukaryotes than bacteria. PMID:1708763

Phylogenetically conserved resource partitioning in the coastal microbial loop

DOE PAGES

Bryson, Samuel; Li, Zhou; Chavez, Francisco; ...

2017-08-11

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bryson, Samuel; Li, Zhou; Chavez, Francisco

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch.

PubMed

Kaplan, Oktay I; Berber, Burak; Hekim, Nezih; Doluca, Osman

2016-11-02

Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Phylogenetically conserved resource partitioning in the coastal microbial loop

PubMed Central

Bryson, Samuel; Li, Zhou; Chavez, Francisco; Weber, Peter K; Pett-Ridge, Jennifer; Hettich, Robert L; Pan, Chongle; Mayali, Xavier; Mueller, Ryan S

2017-01-01

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone. PMID:28800138

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

PubMed Central

Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

2014-01-01

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology. PMID:25414723

Phylogenetic trait conservatism and the evolution of functional trade-offs in arbuscular mycorrhizal fungi.

PubMed

Powell, Jeff R; Parrent, Jeri L; Hart, Miranda M; Klironomos, John N; Rillig, Matthias C; Maherali, Hafiz

2009-12-07

The diversity of functional and life-history traits of organisms depends on adaptation as well as the legacy of shared ancestry. Although the evolution of traits in macro-organisms is well studied, relatively little is known about character evolution in micro-organisms. Here, we surveyed an ancient and ecologically important group of microbial plant symbionts, the arbuscular mycorrhizal (AM) fungi, and tested hypotheses about the evolution of functional and life-history traits. Variation in the extent of root and soil colonization by AM fungi is constrained to a few nodes basal to the most diverse groups within the phylum, with relatively little variation associated with recent divergences. We found no evidence for a trade-off in biomass allocated to root versus soil colonization in three published glasshouse experiments; rather these traits were positively correlated. Partial support was observed for correlated evolution between fungal colonization strategies and functional benefits of the symbiosis to host plants. The evolution of increased soil colonization was positively correlated with total plant biomass and shoot phosphorus content. Although the effect of AM fungi on infection by root pathogens was phylogenetically conserved, there was no evidence for correlated evolution between the extent of AM fungal root colonization and pathogen infection. Variability in colonization strategies evolved early in the diversification of AM fungi, and we propose that these strategies were influenced by functional interactions with host plants, resulting in an evolutionary stasis resembling trait conservatism.

Late Middle Eocene primate from Myanmar and the initial anthropoid colonization of Africa.

PubMed

Chaimanee, Yaowalak; Chavasseau, Olivier; Beard, K Christopher; Kyaw, Aung Aung; Soe, Aung Naing; Sein, Chit; Lazzari, Vincent; Marivaux, Laurent; Marandat, Bernard; Swe, Myat; Rugbumrung, Mana; Lwin, Thit; Valentin, Xavier; Zin-Maung-Maung-Thein; Jaeger, Jean-Jacques

2012-06-26

Reconstructing the origin and early evolutionary history of anthropoid primates (monkeys, apes, and humans) is a current focus of paleoprimatology. Although earlier hypotheses frequently supported an African origin for anthropoids, recent discoveries of older and phylogenetically more basal fossils in China and Myanmar indicate that the group originated in Asia. Given the Oligocene-Recent history of African anthropoids, the colonization of Africa by early anthropoids hailing from Asia was a decisive event in primate evolution. However, the fossil record has so far failed to constrain the nature and timing of this pivotal event. Here we describe a fossil primate from the late middle Eocene Pondaung Formation of Myanmar, Afrasia djijidae gen. et sp. nov., that is remarkably similar to, yet dentally more primitive than, the roughly contemporaneous North African anthropoid Afrotarsius. Phylogenetic analysis suggests that Afrasia and Afrotarsius are sister taxa within a basal anthropoid clade designated as the infraorder Eosimiiformes. Current knowledge of eosimiiform relationships and their distribution through space and time suggests that members of this clade dispersed from Asia to Africa sometime during the middle Eocene, shortly before their first appearance in the African fossil record. Crown anthropoids and their nearest fossil relatives do not appear to be specially related to Afrotarsius, suggesting one or more additional episodes of dispersal from Asia to Africa. Hystricognathous rodents, anthracotheres, and possibly other Asian mammal groups seem to have colonized Africa at roughly the same time or shortly after anthropoids gained their first toehold there.

Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K-Pg mass extinction.

PubMed

Ksepka, Daniel T; Stidham, Thomas A; Williamson, Thomas E

2017-07-25

Evidence is accumulating for a rapid diversification of birds following the K-Pg extinction. Recent molecular divergence dating studies suggest that birds radiated explosively during the first few million years of the Paleocene; however, fossils from this interval remain poorly represented, hindering our understanding of morphological and ecological specialization in early neoavian birds. Here we report a small fossil bird from the Nacimiento Formation of New Mexico, constrained to 62.221-62.517 Ma. This partial skeleton represents the oldest arboreal crown group bird known. Phylogenetic analyses recovered Tsidiiyazhi abini gen. et sp. nov. as a member of the Sandcoleidae, an extinct basal clade of stem mousebirds (Coliiformes). The discovery of Tsidiiyazhi pushes the minimum divergence ages of as many as nine additional major neoavian lineages into the earliest Paleocene, compressing the duration of the proposed explosive post-K-Pg radiation of modern birds into a very narrow temporal window parallel to that suggested for placental mammals. Simultaneously, Tsidiiyazhi provides evidence for the rapid morphological (and likely ecological) diversification of crown birds. Features of the foot indicate semizygodactyly (the ability to facultatively reverse the fourth pedal digit), and the arcuate arrangement of the pedal trochleae bears a striking resemblance to the conformation in owls (Strigiformes). Inclusion of fossil taxa and branch length estimates impacts ancestral state reconstructions, revealing support for the independent evolution of semizygodactyly in Coliiformes, Leptosomiformes, and Strigiformes, none of which is closely related to extant clades exhibiting full zygodactyly.

Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K-Pg mass extinction

NASA Astrophysics Data System (ADS)

Ksepka, Daniel T.; Stidham, Thomas A.; Williamson, Thomas E.

2017-07-01

Evidence is accumulating for a rapid diversification of birds following the K-Pg extinction. Recent molecular divergence dating studies suggest that birds radiated explosively during the first few million years of the Paleocene; however, fossils from this interval remain poorly represented, hindering our understanding of morphological and ecological specialization in early neoavian birds. Here we report a small fossil bird from the Nacimiento Formation of New Mexico, constrained to 62.221-62.517 Ma. This partial skeleton represents the oldest arboreal crown group bird known. Phylogenetic analyses recovered Tsidiiyazhi abini gen. et sp. nov. as a member of the Sandcoleidae, an extinct basal clade of stem mousebirds (Coliiformes). The discovery of Tsidiiyazhi pushes the minimum divergence ages of as many as nine additional major neoavian lineages into the earliest Paleocene, compressing the duration of the proposed explosive post-K-Pg radiation of modern birds into a very narrow temporal window parallel to that suggested for placental mammals. Simultaneously, Tsidiiyazhi provides evidence for the rapid morphological (and likely ecological) diversification of crown birds. Features of the foot indicate semizygodactyly (the ability to facultatively reverse the fourth pedal digit), and the arcuate arrangement of the pedal trochleae bears a striking resemblance to the conformation in owls (Strigiformes). Inclusion of fossil taxa and branch length estimates impacts ancestral state reconstructions, revealing support for the independent evolution of semizygodactyly in Coliiformes, Leptosomiformes, and Strigiformes, none of which is closely related to extant clades exhibiting full zygodactyly.

Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K–Pg mass extinction

PubMed Central

Ksepka, Daniel T.; Stidham, Thomas A.; Williamson, Thomas E.

2017-01-01

Evidence is accumulating for a rapid diversification of birds following the K–Pg extinction. Recent molecular divergence dating studies suggest that birds radiated explosively during the first few million years of the Paleocene; however, fossils from this interval remain poorly represented, hindering our understanding of morphological and ecological specialization in early neoavian birds. Here we report a small fossil bird from the Nacimiento Formation of New Mexico, constrained to 62.221–62.517 Ma. This partial skeleton represents the oldest arboreal crown group bird known. Phylogenetic analyses recovered Tsidiiyazhi abini gen. et sp. nov. as a member of the Sandcoleidae, an extinct basal clade of stem mousebirds (Coliiformes). The discovery of Tsidiiyazhi pushes the minimum divergence ages of as many as nine additional major neoavian lineages into the earliest Paleocene, compressing the duration of the proposed explosive post–K–Pg radiation of modern birds into a very narrow temporal window parallel to that suggested for placental mammals. Simultaneously, Tsidiiyazhi provides evidence for the rapid morphological (and likely ecological) diversification of crown birds. Features of the foot indicate semizygodactyly (the ability to facultatively reverse the fourth pedal digit), and the arcuate arrangement of the pedal trochleae bears a striking resemblance to the conformation in owls (Strigiformes). Inclusion of fossil taxa and branch length estimates impacts ancestral state reconstructions, revealing support for the independent evolution of semizygodactyly in Coliiformes, Leptosomiformes, and Strigiformes, none of which is closely related to extant clades exhibiting full zygodactyly. PMID:28696285

The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions.

PubMed

Brown, Jeremy M; Thomson, Robert C

2018-02-15

Bayesian phylogenetic inference involves sampling from posterior distributions of trees, which sometimes exhibit local optima, or peaks, separated by regions of low posterior density. Markov chain Monte Carlo (MCMC) algorithms are the most widely used numerical method for generating samples from these posterior distributions, but they are susceptible to entrapment on individual optima in rugged distributions when they are unable to easily cross through or jump across regions of low posterior density. Ruggedness of posterior distributions can result from a variety of factors, including unmodeled variation in evolutionary processes and unrecognized variation in the true topology across sites or genes. Ruggedness can also become exaggerated when constraints are placed on topologies that require the presence or absence of particular bipartitions (often referred to as positive or negative constraints, respectively). These types of constraints are frequently employed when conducting tests of topological hypotheses (Bergsten et al. 2013; Brown and Thomson 2017). Negative constraints can lead to particularly rugged distributions when the data strongly support a forbidden clade, because monophyly of the clade can be disrupted by inserting outgroup taxa in many different ways. However, topological moves between the alternative disruptions are very difficult, because they require swaps between the inserted outgroup taxa while the data constrain taxa from the forbidden clade to remain close together on the tree. While this precise form of ruggedness is particular to negative constraints, trees with high posterior density can be separated by similarly complicated topological rearrangements, even in the absence of constraints.

Can treefrog phylogeographical clades and species' phylogenetic topologies be recovered by bioacoustical analyses?

PubMed

Forti, Lucas Rodriguez; Lingnau, Rodrigo; Encarnação, Lais Carvalho; Bertoluci, Jaime; Toledo, Luís Felipe

2017-01-01

Phenotypic traits, such as the frog advertisement call, are generally correlated with interspecific genetic variation, and, as a consequence of strong sexual selection, these behaviors may carry a phylogenetic signal. However, variation in acoustic traits is not always correlated with genetic differences between populations (intraspecific variation); phenotypic plasticity and environmental variables may explain part of such variation. For example, local processes can affect acoustic properties in different lineages due to differences in physical structure, climatic conditions, and biotic interactions, particularly when populations are isolated. However, acoustic traits can be used to test phylogenetic hypotheses. We analyzed the advertisement calls of Dendropsophus elegans males from 18 sites and compared them with those of four closely related congeneric species, in order to test for differences between inter and intraspecific variation. We analyzed 451 calls of 45 males of these five species. Because males from distant sites were grouped together without population congruence, differences found in advertisement calls among individuals were not correlated with phylogeographical clades. Phylogenetic and cluster analyses of the D. elegans clades and those of closely related species grouped all five species into the same topology, as reported by previous molecular and morphological phylogenies. However, the topology of the D. elegans phylogeographical clades did not match the topology previously reported. Acoustic communication in D. elegans seems to be conserved among populations, and the phylogeographical history of the species does not explain the variation among lineages in call properties, despite some congruent phylogenetic signals evident at the species level. Based on molecular clocks retrieved from the literature, it seems that more than 6.5 million years of divergence (late Miocene) are necessary to allow significant changes to occur in the acoustic properties of these treefrog calls, making it possible to recover their phylogenetic history only based on acoustic evidence.