Science.gov

Sample records for evolution macroevolutionary pattern

  1. Molecular evolution tracks macroevolutionary transitions in Cetacea.

    PubMed

    McGowen, Michael R; Gatesy, John; Wildman, Derek E

    2014-06-01

    Cetacea (whales, dolphins, and porpoises) is a model group for investigating the molecular signature of macroevolutionary transitions. Recent research has begun to reveal the molecular underpinnings of the remarkable anatomical and behavioral transformation in this clade. This shift from terrestrial to aquatic environments is arguably the best-understood major morphological transition in vertebrate evolution. The ancestral body plan and physiology were extensively modified and, in many cases, these crucial changes are recorded in cetacean genomes. Recent studies have highlighted cetaceans as central to understanding adaptive molecular convergence and pseudogene formation. Here, we review current research in cetacean molecular evolution and the potential of Cetacea as a model for the study of other macroevolutionary transitions from a genomic perspective. PMID:24794916

  2. Modelling macroevolutionary patterns: An ecological perspective

    NASA Astrophysics Data System (ADS)

    Solé, R. V.

    Complex ecosystems display well-defined macroscopic regularities suggesting that some generic dynamical rules operate at the ecosystem level where the relevance of the single-species features is rather weak. Most evolutionary theory deals with genes/species as the units of selection operating on populations. However, the role of ecological networks and external perturbations seems to be at least as important as microevolutionary events based on natural selection operating at the smalle st levels. Here we review some of the recent theoretical approximations to ecosystem evolution based on network dynamics. It is suggested that the evolutionary dynamics of ecological networks underlie fundamental laws of ecology-level dynamics which naturally decouple micro from macroevolutionary dynamics. Using simple models of macroevolution, most of the available statistical information obtained from the fossil record is remarkably well reproduced and explained within a new theoretical framework.

  3. Macroevolutionary patterns of salt tolerance in angiosperms

    PubMed Central

    Bromham, Lindell

    2015-01-01

    Background Halophytes are rare, with only 0·25 % of angiosperm species able to complete their life cycle in saline conditions. This could be interpreted as evidence that salt tolerance is difficult to evolve. However, consideration of the phylogenetic distribution of halophytes paints a different picture: salt tolerance has evolved independently in many different lineages, and halophytes are widely distributed across angiosperm families. In this Viewpoint, I will consider what phylogenetic analysis of halophytes can tell us about the macroevolution of salt tolerance. Hypothesis Phylogenetic analyses of salt tolerance have shown contrasting patterns in different families. In some families, such as chenopods, salt tolerance evolved early in the lineage and has been retained in many lineages. But in other families, including grasses, there have been a surprisingly large number of independent origins of salt tolerance, most of which are relatively recent and result in only one or a few salt-tolerant species. This pattern of many recent origins implies either a high transition rate (salt tolerance is gained and lost often) or a high extinction rate (salt-tolerant lineages do not tend to persist over macroevolutionary timescales). While salt tolerance can evolve in a wide range of genetic backgrounds, some lineages are more likely to produce halophytes than others. This may be due to enabling traits that act as stepping stones to developing salt tolerance. The ability to tolerate environmental salt may increase tolerance of other stresses or vice versa. Conclusions Phylogenetic analyses suggest that enabling traits and cross-tolerances may make some lineages more likely to adapt to increasing salinization, a finding that may prove useful in assessing the probable impact of rapid environmental change on vegetation communities, and in selecting taxa to develop for use in landscape rehabilitation and agriculture. PMID:25452251

  4. Toy models for macroevolutionary patterns and trends.

    PubMed

    Alicea, Bradly; Gordon, Richard

    2014-09-01

    Many models have been used to simplify and operationalize the subtle but complex mechanisms of biological evolution. Toy models are gross simplifications that nevertheless attempt to retain major essential features of evolution, bridging the gap between empirical reality and formal theoretical understanding. In this paper, we examine thirteen models which describe evolution that also qualify as such toy models, including the tree of life, branching processes, adaptive ratchets, fitness landscapes, and the role of nonlinear avalanches in evolutionary dynamics. Such toy models are intended to capture features such as evolutionary trends, coupled evolutionary dynamics of phenotype and genotype, adaptive change, branching, and evolutionary transience. The models discussed herein are applied to specific evolutionary contexts in various ways that simplify the complexity inherent in evolving populations. While toy models are overly simplistic, they also provide sufficient dynamics for capturing the fundamental mechanism(s) of evolution. Toy models might also be used to aid in high-throughput data analysis and the understanding of cultural evolutionary trends. This paper should serve as an introductory guide to the toy modeling of evolutionary complexity. PMID:25224014

  5. Macroevolutionary patterns of sexual size dimorphism in copepods.

    PubMed

    Hirst, Andrew G; Kiørboe, Thomas

    2014-09-22

    Major theories compete to explain the macroevolutionary trends observed in sexual size dimorphism (SSD) in animals. Quantitative genetic theory suggests that the sex under historically stronger directional selection will exhibit greater interspecific variance in size, with covariation between allometric slopes (male to female size) and the strength of SSD across clades. Rensch's rule (RR) also suggests a correlation, but one in which males are always the more size variant sex. Examining free-living pelagic and parasitic Copepoda, we test these competing predictions. Females are commonly the larger sex in copepod species. Comparing clades that vary by four orders of magnitude in their degree of dimorphism, we show that isometry is widespread. As such we find no support for either RR or for covariation between allometry and SSD. Our results suggest that selection on both sexes has been equally important. We next test the prediction that variation in the degree of SSD is related to the adult sex ratio. As males become relatively less abundant, it has been hypothesized that this will lead to a reduction in both inter-male competition and male size. However, the lack of such a correlation across diverse free-living pelagic families of copepods provides no support for this hypothesis. By comparison, in sea lice of the family Caligidae, there is some qualitative support of the hypothesis, males may suffer elevated mortality when they leave the host and rove for sedentary females, and their female-biased SSD is greater than in many free-living families. However, other parasitic copepods which do not appear to have obvious differences in sex-based mate searching risks also show similar or even more extreme SSD, therefore suggesting other factors can drive the observed extremes. PMID:25100692

  6. A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts.

    PubMed

    Paleo-López, Rocío; Quintero-Galvis, Julian F; Solano-Iguaran, Jaiber J; Sanchez-Salazar, Angela M; Gaitan-Espitia, Juan D; Nespolo, Roberto F

    2016-06-01

    When novel sources of ecological opportunity are available, physiological innovations can trigger adaptive radiations. This could be the case of yeasts (Saccharomycotina), in which an evolutionary novelty is represented by the capacity to exploit simple sugars from fruits (fermentation). During adaptive radiations, diversification and morphological evolution are predicted to slow-down after early bursts of diversification. Here, we performed the first comparative phylogenetic analysis in yeasts, testing the "early burst" prediction on species diversification and also on traits of putative ecological relevance (cell-size and fermentation versatility). We found that speciation rates are constant during the time-range we considered (ca., 150 millions of years). Phylogenetic signal of both traits was significant (but lower for cell-size), suggesting that lineages resemble each other in trait-values. Disparity analysis suggested accelerated evolution (diversification in trait values above Brownian Motion expectations) in cell-size. We also found a significant phylogenetic regression between cell-size and fermentation versatility (R (2) = 0.10), which suggests correlated evolution between both traits. Overall, our results do not support the early burst prediction both in species and traits, but suggest a number of interesting evolutionary patterns, that warrant further exploration. For instance, we show that the Whole Genomic Duplication that affected a whole clade of yeasts, does not seems to have a statistically detectable phenotypic effect at our level of analysis. In this regard, further studies of fermentation under common-garden conditions combined with comparative analyses are warranted. PMID:27516851

  7. Impacts of Niche Breadth and Dispersal Ability on Macroevolutionary Patterns.

    PubMed

    Qiao, Huijie; Saupe, Erin E; Soberón, Jorge; Peterson, A Townsend; Myers, Corinne E

    2016-08-01

    We describe a spatially explicit simulation experiment designed to assess relative impacts of macroecological traits on patterns of biological diversification under changing environmental conditions. Using a simulation framework, we assessed impacts of species' niche breadth (i.e., the range of their abiotic tolerances) and dispersal ability on resulting patterns of speciation and extinction and evaluated how these traits, in conjunction with environmental change, shape biological diversification. Simulation results supported both niche breadth and dispersal ability as important drivers of diversification in the face of environmental change, and suggested that the rate of environmental change influences how species interact with the extrinsic environment to generate diversity. Niche breadth had greater effects on speciation and extinction than dispersal ability when climate changed rapidly, whereas dispersal ability effects were elevated when climate changed slowly. Our simulations provide a bottom-up perspective on the generation and maintenance of diversity under climate change, offering a better understanding of potential interactions between species' intrinsic macroecological characteristics and a dynamic extrinsic environment in the process of biological diversification. PMID:27420781

  8. Macroevolutionary patterns of ultraviolet floral pigmentation explained by geography and associated bioclimatic factors.

    PubMed

    Koski, Matthew H; Ashman, Tia-Lynn

    2016-07-01

    Selection driven by biotic interactions can generate variation in floral traits. Abiotic selection, however, also contributes to floral diversity, especially with respect to patterns of pigmentation. Combining comparative studies of floral pigmentation and geography can reveal the bioclimatic factors that may drive macroevolutionary patterns of floral color. We create a molecular phylogeny and measure ultraviolet (UV) floral pattern for 177 species in the Potentilleae tribe (Rosaceae). Species are similar in flower shape and visible color but vary in UV floral pattern. We use comparative approaches to determine whether UV pigmentation variation is associated with geography and/or bioclimatic features (UV-B, precipitation, temperature). Floral UV pattern was present in half of the species, while others were uniformly UV-absorbing. Phylogenetic signal was detected for presence/absence of pattern, but among patterned species, quantitative variation in UV-absorbing area was evolutionarily labile. Uniformly UV-absorbing species tended to experience higher UV-B irradiance. Patterned species occurring at higher altitudes had larger UV-absorbing petal areas, corresponding with low temperature and high UV exposure. This analysis expands our understanding of the covariation of UV-B irradiance and UV floral pigmentation from within species to that among species, and supports the view that abiotic selection is associated with floral diversification among species. PMID:26987355

  9. Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution

    PubMed Central

    2013-01-01

    Abstract Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ. Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III), genetic revolution model of Mayr (class IV) or the frozen plasticity theory of Flegr (class V), suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation – while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III) or elastic (class IV and V) on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation. The punctuational theories have many evolutionary and ecological implications. Most of these predictions could be tested empirically, and should be analyzed in greater depth theoretically. The punctuational theories offer many new predictions that need to be tested, but also provide explanations for a much broader spectrum of known biological phenomena than classical gradualistic evolutionary theories. Reviewers This article was reviewed by Claus Wilke, Pierre Pantarotti and David Penny (nominated by Anthony Poole). PMID:23324625

  10. Is geographic variation within species related to macroevolutionary patterns between species?

    PubMed

    Fisher-Reid, M C; Wiens, J J

    2015-08-01

    The relationship between microevolution and macroevolution is a central topic in evolutionary biology. An aspect of this relationship that remains very poorly studied in modern evolutionary biology is the relationship between within-species geographic variation and among-species patterns of trait variation. Here, we tested the relationship between climate and morphology among and within species in the salamander genus Plethodon. We focus on a discrete colour polymorphism (presence and absence of a red dorsal stripe) that appears to be related to climatic distributions in a common, wide-ranging species (Plethodon cinereus). We find that this trait has been variable among (and possibly within) species for >40 million years. Furthermore, we find a strong relationship among species between climatic variation and within-species morph frequencies. These between-species patterns are similar (but not identical) to those in the broadly distributed Plethodon cinereus. Surprisingly, there are no significant climate-morphology relationships within most other polymorphic species, despite the strong between-species patterns. Overall, our study provides an initial exploration of how within-species geographic variation and large-scale macroevolutionary patterns of trait variation may be related. PMID:26079479

  11. Macroevolutionary patterns of glucosinolate defense and tests of defense-escalation and resource availability hypotheses.

    PubMed

    Cacho, N Ivalú; Kliebenstein, Daniel J; Strauss, Sharon Y

    2015-11-01

    We explored macroevolutionary patterns of plant chemical defense in Streptanthus (Brassicaceae), tested for evolutionary escalation of defense, as predicted by Ehrlich and Raven's plant-herbivore coevolutionary arms-race hypothesis, and tested whether species inhabiting low-resource or harsh environments invest more in defense, as predicted by the resource availability hypothesis (RAH). We conducted phylogenetically explicit analyses using glucosinolate profiles, soil nutrient analyses, and microhabitat bareness estimates across 30 species of Streptanthus inhabiting varied environments and soils. We found weak to moderate phylogenetic signal in glucosinolate classes and no signal in total glucosinolate production; a trend toward evolutionary de-escalation in the numbers and diversity of glucosinolates, accompanied by an evolutionary increase in the proportion of aliphatic glucosinolates; some support for the RAH relative to soil macronutrients, but not relative to serpentine soil use; and that the number of glucosinolates increases with microhabitat bareness, which is associated with increased herbivory and drought. Weak phylogenetic signal in chemical defense has been observed in other plant systems. A more holistic approach incorporating other forms of defense might be necessary to confidently reject escalation of defense. That defense increases with microhabitat bareness supports the hypothesis that habitat bareness is an underappreciated selective force on plants in harsh environments. PMID:26192213

  12. Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds.

    PubMed

    Rabosky, Daniel L; Matute, Daniel R

    2013-09-17

    The rate at which speciation occurs varies greatly among different kinds of organisms and is frequently assumed to result from species- or clade-specific factors that influence the rate at which populations acquire reproductive isolation. This premise leads to a fundamental prediction that has never been tested: Organisms that quickly evolve prezygotic or postzygotic reproductive isolation should have faster rates of speciation than organisms that slowly acquire reproductive isolation. We combined phylogenetic estimates of speciation rates from Drosophila and birds with a method for analyzing interspecific hybridization data to test whether the rate at which individual lineages evolve reproductive isolation predicts their macroevolutionary rate of species formation. We find that some lineages evolve reproductive isolation much more quickly than others, but this variation is decoupled from rates of speciation as measured on phylogenetic trees. For the clades examined here, reproductive isolation--especially intrinsic, postzygotic isolation--does not seem to be the rate-limiting control on macroevolutionary diversification dynamics. These results suggest that factors associated with intrinsic reproductive isolation may have less to do with the tremendous variation in species diversity across the evolutionary tree of life than is generally assumed. PMID:24003144

  13. Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds

    PubMed Central

    Rabosky, Daniel L.; Matute, Daniel R.

    2013-01-01

    The rate at which speciation occurs varies greatly among different kinds of organisms and is frequently assumed to result from species- or clade-specific factors that influence the rate at which populations acquire reproductive isolation. This premise leads to a fundamental prediction that has never been tested: Organisms that quickly evolve prezygotic or postzygotic reproductive isolation should have faster rates of speciation than organisms that slowly acquire reproductive isolation. We combined phylogenetic estimates of speciation rates from Drosophila and birds with a method for analyzing interspecific hybridization data to test whether the rate at which individual lineages evolve reproductive isolation predicts their macroevolutionary rate of species formation. We find that some lineages evolve reproductive isolation much more quickly than others, but this variation is decoupled from rates of speciation as measured on phylogenetic trees. For the clades examined here, reproductive isolation—especially intrinsic, postzygotic isolation—does not seem to be the rate-limiting control on macroevolutionary diversification dynamics. These results suggest that factors associated with intrinsic reproductive isolation may have less to do with the tremendous variation in species diversity across the evolutionary tree of life than is generally assumed. PMID:24003144

  14. Macroevolutionary Patterns in the Aphidini Aphids (Hemiptera: Aphididae): Diversification, Host Association, and Biogeographic Origins

    PubMed Central

    Kim, Hyojoong; Lee, Seunghwan; Jang, Yikweon

    2011-01-01

    Background Due to its biogeographic origins and rapid diversification, understanding the tribe Aphidini is key to understanding aphid evolution. Major questions about aphid evolution include origins of host alternation as well as age and patterns of diversification in relation to host plants. To address these questions, we reconstructed the phylogeny of the Aphidini which contains Aphis, the most diverse genus in the family. We used a combined dataset of one nuclear and four mitochondrial DNA regions. A molecular dating approach, calibrated with fossil records, was used to estimate divergence times of these taxa. Principal Findings Most generic divergences in Aphidini occurred in the Middle Tertiary, and species-level divergences occurred between the Middle and Late Tertiary. The ancestral state of host use for Aphidini was equivocal with respect to three states: monoecy on trees, heteroecy, and monoecy on grasses. The ancestral state of Rhopalosiphina likely included both heteroecy and monoecy, whereas that of Aphidina was most likely monoecy. The divergence times of aphid lineages at the generic or subgeneric levels are close to those of their primary hosts. The species-level divergences in aphids are consistent with the diversification of the secondary hosts, as a few examples suggest. The biogeographic origin of Aphidini as a whole was equivocal, but the major lineages within Aphidina likely separated into Nearctic, Western Palearctic, and Eastern Palearctic regions. Conclusions Most generic divergences in Aphidini occurred in the Middle Tertiary when primary hosts, mainly in the Rosaceae, were diverging, whereas species-level divergences were contemporaneous with diversification of the secondary hosts such as Poaceae in the Middle to Late Tertiary. Our results suggest that evolution of host alternation within Aphidini may have occurred during the Middle Tertiary (Oligocene) when the secondary hosts emerged. PMID:21935453

  15. Macroevolutionary patterns of bumblebee body size: detecting the interplay between natural and sexual selection

    PubMed Central

    del Castillo, Raúl Cueva; Fairbairn, Daphne J

    2012-01-01

    Bumblebees and other eusocial bees offer a unique opportunity to analyze the evolution of body size differences between sexes. The workers, being sterile females, are not subject to selection for reproductive function and thus provide a natural control for parsing the effects of selection on reproductive function (i.e., sexual and fecundity selection) from other natural selection. Using a phylogenetic comparative approach, we explored the allometric relationships among queens, males, and workers in 70 species of bumblebees (Bombus sp.). We found hyperallometry in thorax width for males relative to workers, indicating greater evolutionary divergence of body size in males than in sterile females. This is consistent with the hypothesis that selection for reproductive function, most probably sexual selection, has caused divergence in male size among species. The slope for males on workers was significantly steeper than that for queens on workers and the latter did not depart from isometry, providing further evidence of greater evolutionary divergence in male size than female size, and no evidence that reproductive selection has accelerated divergence of females. We did not detect significant hyperallometry when male size was regressed directly on queen size and our results thus add the genus Bombus to the increasing list of clades that have female-larger sexual size dimorphism and do not conform to Rensch's rule when analyzed according to standard methodology. Nevertheless, by using worker size as a common control, we were able to demonstrate that bumblee species do show the evolutionary pattern underlying Rensch's rule, that being correlated evolution of body size in males and females, but with greater evolutionary divergence in males. PMID:22408725

  16. Model for macroevolutionary dynamics

    PubMed Central

    Maruvka, Yosef E.; Shnerb, Nadav M.; Kessler, David A.; Ricklefs, Robert E.

    2013-01-01

    The highly skewed distribution of species among genera, although challenging to macroevolutionists, provides an opportunity to understand the dynamics of diversification, including species formation, extinction, and morphological evolution. Early models were based on either the work by Yule [Yule GU (1925) Philos Trans R Soc Lond B Biol Sci 213:21–87], which neglects extinction, or a simple birth–death (speciation–extinction) process. Here, we extend the more recent development of a generic, neutral speciation–extinction (of species)–origination (of genera; SEO) model for macroevolutionary dynamics of taxon diversification. Simulations show that deviations from the homogeneity assumptions in the model can be detected in species-per-genus distributions. The SEO model fits observed species-per-genus distributions well for class-to-kingdom–sized taxonomic groups. The model’s predictions for the appearance times (the time of the first existing species) of the taxonomic groups also approximately match estimates based on molecular inference and fossil records. Unlike estimates based on analyses of phylogenetic reconstruction, fitted extinction rates for large clades are close to speciation rates, consistent with high rates of species turnover and the relatively slow change in diversity observed in the fossil record. Finally, the SEO model generally supports the consistency of generic boundaries based on morphological differences between species and provides a comparator for rates of lineage splitting and morphological evolution. PMID:23781101

  17. Detecting Macroevolutionary Self-Destruction from Phylogenies.

    PubMed

    Bromham, Lindell; Hua, Xia; Cardillo, Marcel

    2016-01-01

    Phylogenetic analyses have lent support to the concept of lineage selection: that biological lineages can have heritable traits that influence their capacity to persist and diversify, and thereby affect their representation in biodiversity. While many discussions have focused on "positive" lineage selection, where stably heritable properties of lineages enhance their diversification rate, there are also intriguing examples that seem to represent "negative" lineage selection, where traits reduce the likelihood that a lineage will persist or speciate. In this article, we test whether a particular pattern of negative lineage selection is detectable from the distributions of the trait on a phylogeny. "Self-destructive" traits are those that arise often but then disappear again because they confer either a raised extinction rate or they are prone to a high rate of trait loss. For such a trait, the reconstructed origins will tend to be dispersed across the tips of the phylogeny, rather than defining large clades of related lineages that all share the trait. We examine the utility of four possible measures of "tippiness" as potential indicators of macroevolutionary self-destruction, applying them to phylogenies on which trait evolution has been simulated under different combinations of parameters for speciation, extinction, trait gain, and trait loss. We use an efficient simulation approach that starts with the required number of tips with and without the trait and uses a model to work "backwards" to construct different possible trees that result in that set of tips. We then apply these methods to a number of case studies: salt tolerance in grasses, color polymorphism in birds of prey, and selfing in nightshades. We find that the relative age of species, measured from tip length, can indicate a reduced speciation rate but does not identify traits that increase the extinction rate or the trait loss rate. We show that it is possible to detect cases of macroevolutionary self

  18. Omnivory in birds is a macroevolutionary sink.

    PubMed

    Burin, Gustavo; Kissling, W Daniel; Guimarães, Paulo R; Şekercioğlu, Çağan H; Quental, Tiago B

    2016-01-01

    Diet is commonly assumed to affect the evolution of species, but few studies have directly tested its effect at macroevolutionary scales. Here we use Bayesian models of trait-dependent diversification and a comprehensive dietary database of all birds worldwide to assess speciation and extinction dynamics of avian dietary guilds (carnivores, frugivores, granivores, herbivores, insectivores, nectarivores, omnivores and piscivores). Our results suggest that omnivory is associated with higher extinction rates and lower speciation rates than other guilds, and that overall net diversification is negative. Trait-dependent models, dietary similarity and network analyses show that transitions into omnivory occur at higher rates than into any other guild. We suggest that omnivory acts as macroevolutionary sink, where its ephemeral nature is retrieved through transitions from other guilds rather than from omnivore speciation. We propose that these dynamics result from competition within and among dietary guilds, influenced by the deep-time availability and predictability of food resources. PMID:27052750

  19. Omnivory in birds is a macroevolutionary sink

    PubMed Central

    Burin, Gustavo; Kissling, W. Daniel; Guimarães, Paulo R.; Şekercioğlu, Çağan H.; Quental, Tiago B.

    2016-01-01

    Diet is commonly assumed to affect the evolution of species, but few studies have directly tested its effect at macroevolutionary scales. Here we use Bayesian models of trait-dependent diversification and a comprehensive dietary database of all birds worldwide to assess speciation and extinction dynamics of avian dietary guilds (carnivores, frugivores, granivores, herbivores, insectivores, nectarivores, omnivores and piscivores). Our results suggest that omnivory is associated with higher extinction rates and lower speciation rates than other guilds, and that overall net diversification is negative. Trait-dependent models, dietary similarity and network analyses show that transitions into omnivory occur at higher rates than into any other guild. We suggest that omnivory acts as macroevolutionary sink, where its ephemeral nature is retrieved through transitions from other guilds rather than from omnivore speciation. We propose that these dynamics result from competition within and among dietary guilds, influenced by the deep-time availability and predictability of food resources. PMID:27052750

  20. Multi-level human evolution: ecological patterns in hominin phylogeny.

    PubMed

    Parravicini, Andrea; Pievani, Telmo

    2016-06-20

    Evolution is a process that occurs at many different levels, from genes to ecosystems. Genetic variations and ecological pressures are hence two sides of the same coin; but due both to fragmentary evidence and to the influence of a gene-centered and gradualistic approach to evolutionary phenomena, the field of paleoanthropology has been slow to take the role of macro-evolutionary patterns (i.e. ecological and biogeographical at large scale) seriously. However, several very recent findings in paleoanthropology stress both climate instability and ecological disturbance as key factors affecting the highly branching hominin phylogeny, from the earliest hominins to the appearance of cognitively modern humans. Allopatric speciation due to geographic displacement, turnover-pulses of species, adaptive radiation, mosaic evolution of traits in several coeval species, bursts of behavioral innovation, serial dispersals out of Africa, are just some of the macro-evolutionary patterns emerging from the field. The multilevel approach to evolution proposed by paleontologist Niles Eldredge is adopted here as interpretative tool, and has yielded a larger picture of human evolution that integrates different levels of evolutionary change, from local adaptations in limited ecological niches to dispersal phenotypes able to colonize an unprecedented range of ecosystems. Changes in global climate and Earth's surface most greatly affected human evolution. Precisely because it is cognitively hard for us to appreciate the long-term common destiny we share with the whole biosphere, it is particularly valuable to highlight the accumulating evidence that human evolution has been deeply affected by global ecological changes that transformed our African continent of origin. PMID:26829575

  1. Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

    PubMed Central

    Stadler, Tanja; Degnan, James H.; Rosenberg, Noah A.

    2016-01-01

    Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth–death and multispecies coalescent model can explain the difference in empirical trees and birth–death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion. PMID:26968785

  2. Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

    PubMed

    Stadler, Tanja; Degnan, James H; Rosenberg, Noah A

    2016-07-01

    Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth-death and multispecies coalescent model can explain the difference in empirical trees and birth-death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion. PMID:26968785

  3. Tooth patterning and evolution.

    PubMed

    Salazar-Ciudad, Isaac

    2012-12-01

    Teeth are a good system for studying development and evolution. Tooth development is largely independent of the rest of the body and teeth can be grown in culture to attain almost normal morphology. Their development is not affected by the patterns of movement or sensorial perception in the embryo. Teeth are hard and easily preserved. Thus, there is plenty of easily accessible information about the patterns of morphological variation occurring between and within species. This review summarises recent work and describes how tooth development can be understood as the coupling between a reaction-diffusion system and differential growth produced by diffusible growth factors: which growth factors are involved, how they affect each other's expression and how they affect the spatial patterns of proliferation that lead to final morphology. There are some aspects of tooth development, however, that do not conform to some common assumptions in many reaction-diffusion models. Those are discussed here since they provide clues about how reaction-diffusion systems may work in actual developmental systems. Mathematical models implementing what we know about tooth development are discussed. PMID:23266218

  4. A Macroevolutionary Perspective on Multiple Sexual Traits in the Phasianidae (Galliformes)

    PubMed Central

    Kimball, Rebecca T.; Mary, Colette M. St.; Braun, Edward L.

    2011-01-01

    Traits involved in sexual signaling are ubiquitous among animals. Although a single trait appears sufficient to convey information, many sexually dimorphic species exhibit multiple sexual signals, which may be costly to signalers and receivers. Given that one signal may be enough, there are many microevolutionary hypotheses to explain the evolution of multiple signals. Here we extend these hypotheses to a macroevolutionary scale and compare those predictions to the patterns of gains and losses of sexual dimorphism in pheasants and partridges. Among nine dimorphic characters, including six intersexual signals and three indicators of competitive ability, all exhibited both gains and losses of dimorphism within the group. Although theories of intersexual selection emphasize gain and elaboration, those six characters exhibited greater rates of loss than gain; in contrast, the competitive traits showed a slight bias towards gains. The available models, when examined in a macroevolutionary framework, did not yield unique predictions, making it difficult to distinguish among them. Even with this limitation, when the predictions of these alternative models were compared with the heterogeneous patterns of evolution of dimorphism in phasianids, it is clear that many different selective processes have been involved in the evolution of sexual signals in this group. PMID:21716735

  5. Macroevolutionary History of the Planktic Foraminifera

    NASA Astrophysics Data System (ADS)

    Fraass, Andrew J.; Kelly, D. Clay; Peters, Shanan E.

    2015-05-01

    Planktic foraminifera are an abundant component of deep-sea sediment and are critical to geohistorical research, primarily because as a biological and geochemical system they are sensitive to coupled bio-hydro-lithosphere interactions. They are also well sampled and studied throughout their evolutionary history. Here, we combine a synoptic global compilation of planktic foraminifera with a stochastic null model of taxonomic turnover to identify statistically significant increases in macroevolutionary rates. There are three taxonomic diversifications and two distinct extinctions in the history of the group. The well-known Cretaceous-Paleogene extinction is of unprecedented magnitude and abruptness and is linked to rapid environmental perturbations associated with bolide impact. The Eocene-Oligocene boundary extinction occurs due to a combination of factors related to a major reorganization of the global climate system. Changes in ocean stratification, seawater chemistry, and global climate recur as primary determinants of both macroevolutionary turnover in planktic foraminifera and spatiotemporal patterns of deep-sea sedimentation over the past 130 Myr.

  6. Species coexistence: macroevolutionary relationships and the contingency of historical interactions.

    PubMed

    Germain, Rachel M; Weir, Jason T; Gilbert, Benjamin

    2016-03-30

    Evolutionary biologists since Darwin have hypothesized that closely related species compete more intensely and are therefore less likely to coexist. However, recent theory posits that species diverge in two ways: either through the evolution of 'stabilizing differences' that promote coexistence by causing individuals to compete more strongly with conspecifics than individuals of other species, or through the evolution of 'fitness differences' that cause species to differ in competitive ability and lead to exclusion of the weaker competitor. We tested macroevolutionary patterns of divergence by competing pairs of annual plant species that differ in their phylogenetic relationships, and in whether they have historically occurred in the same region or different regions (sympatric versus allopatric occurrence). For sympatrically occurring species pairs, stabilizing differences rapidly increased with phylogenetic distance. However, fitness differences also increased with phylogenetic distance, resulting in coexistence outcomes that were unpredictable based on phylogenetic relationships. For allopatric species, stabilizing differences showed no trend with phylogenetic distance, whereas fitness differences increased, causing coexistence to become less likely among distant relatives. Our results illustrate the role of species' historical interactions in shaping how phylogenetic relationships structure competitive dynamics, and offer an explanation for the evolution of invasion potential of non-native species. PMID:27009226

  7. Macroevolutionary perspectives to environmental change.

    PubMed

    Condamine, Fabien L; Rolland, Jonathan; Morlon, Hélène

    2013-05-01

    Predicting how biodiversity will be affected and will respond to human-induced environmental changes is one of the most critical challenges facing ecologists today. Here, we put current environmental changes and their effects on biodiversity in a macroevolutionary perspective. We build on research in palaeontology and recent developments in phylogenetic approaches to ask how macroevolution can help us understand how environmental changes have affected biodiversity in the past, and how they will affect biodiversity in the future. More and more paleontological and phylogenetic data are accumulated, and we argue that much of the potential these data have for understanding environmental changes remains to be explored. PMID:23331627

  8. Rapid diversification associated with a macroevolutionary pulse of developmental plasticity.

    PubMed

    Susoy, Vladislav; Ragsdale, Erik J; Kanzaki, Natsumi; Sommer, Ralf J

    2015-01-01

    Developmental plasticity has been proposed to facilitate phenotypic diversification in plants and animals, but the macroevolutionary potential of plastic traits remains to be objectively tested. We studied the evolution of feeding structures in a group of 90 nematodes, including Caenorhabditis elegans, some species of which have evolved a mouthpart polyphenism, moveable teeth, and predatory feeding. Comparative analyses of shape and form, using geometric morphometrics, and of structural complexity revealed a rapid process of diversification associated with developmental plasticity. First, dimorphism was associated with a sharp increase in complexity and elevated evolutionary rates, represented by a radiation of feeding-forms with structural novelties. Second, the subsequent assimilation of a single phenotype coincided with a decrease in mouthpart complexity but an even stronger increase in evolutionary rates. Our results suggest that a macroevolutionary 'pulse' of plasticity promotes novelties and, even after the secondary fixation of phenotypes, permits sustained rapid exploration of morphospace. PMID:25650739

  9. Geologic constraints on the macroevolutionary history of marine animals

    PubMed Central

    Peters, Shanan E.

    2005-01-01

    The causes of mass extinctions and the nature of taxonomic radiations are central questions in paleobiology. Several episodes of taxonomic turnover in the fossil record, particularly the major mass extinctions, are generally thought to transcend known biases in the geologic record and are widely interpreted as distinct macroevolutionary phenomena that require unique forcing mechanisms. Here, by using a previously undescribed compilation of the durations of sedimentary rock sequences, I compare the rates of expansion and truncation of preserved marine sedimentary basins to rates of origination and extinction among Phanerozoic marine animal genera. Many features of the highly variable record of taxonomic first and last occurrences in the marine animal fossil record, including the major mass extinctions, the frequency distribution of genus longevities, and short- and long-term patterns of genus diversity, can be predicted on the basis of the temporal continuity and quantity of preserved sedimentary rock. Although these results suggest that geologically mediated sampling biases have distorted macroevolutionary patterns in the fossil record, preservation biases alone cannot easily explain the extent to which the sedimentary record duplicates paleobiological patterns. Instead, these results suggest that the processes responsible for producing variability in the sedimentary rock record, such as plate tectonics and sea-level change, may have been dominant and consistent macroevolutionary forces throughout the Phanerozoic. PMID:16105949

  10. Prolegomenon to patterns in evolution.

    PubMed

    Kauffman, Stuart A

    2014-09-01

    Despite Darwin, we remain children of Newton and dream of a grand theory that is epistemologically complete and would allow prediction of the evolution of the biosphere. The main purpose of this article is to show that this dream is false, and bears on studying patterns of evolution. To do so, I must justify the use of the word "function" in biology, when physics has only happenings. The concept of "function" lifts biology irreducibly above physics, for as we shall see, we cannot prestate the ever new biological functions that arise and constitute the very phase space of evolution. Hence, we cannot mathematize the detailed becoming of the biosphere, nor write differential equations for functional variables we do not know ahead of time, nor integrate those equations, so no laws "entail" evolution. The dream of a grand theory fails. In place of entailing laws, I propose a post-entailing law explanatory framework in which Actuals arise in evolution that constitute new boundary conditions that are enabling constraints that create new, typically unprestatable, adjacent possible opportunities for further evolution, in which new Actuals arise, in a persistent becoming. Evolution flows into a typically unprestatable succession of adjacent possibles. Given the concept of function, the concept of functional closure of an organism making a living in its world becomes central. Implications for patterns in evolution include historical reconstruction, and statistical laws such as the distribution of extinction events, or species per genus, and the use of formal cause, not efficient cause, laws. PMID:24704211

  11. Fossils and living taxa agree on patterns of body mass evolution: a case study with Afrotheria.

    PubMed

    Puttick, Mark N; Thomas, Gavin H

    2015-12-22

    Most of life is extinct, so incorporating some fossil evidence into analyses of macroevolution is typically seen as necessary to understand the diversification of life and patterns of morphological evolution. Here we test the effects of inclusion of fossils in a study of the body size evolution of afrotherian mammals, a clade that includes the elephants, sea cows and elephant shrews. We find that the inclusion of fossil tips has little impact on analyses of body mass evolution; from a small ancestral size (approx. 100 g), there is a shift in rate and an increase in mass leading to the larger-bodied Paenungulata and Tubulidentata, regardless of whether fossils are included or excluded from analyses. For Afrotheria, the inclusion of fossils and morphological character data affect phylogenetic topology, but these differences have little impact upon patterns of body mass evolution and these body mass evolutionary patterns are consistent with the fossil record. The largest differences between our analyses result from the evolutionary model, not the addition of fossils. For some clades, extant-only analyses may be reliable to reconstruct body mass evolution, but the addition of fossils and careful model selection is likely to increase confidence and accuracy of reconstructed macroevolutionary patterns. PMID:26674947

  12. Fossils and living taxa agree on patterns of body mass evolution: a case study with Afrotheria

    PubMed Central

    Puttick, Mark N.; Thomas, Gavin H.

    2015-01-01

    Most of life is extinct, so incorporating some fossil evidence into analyses of macroevolution is typically seen as necessary to understand the diversification of life and patterns of morphological evolution. Here we test the effects of inclusion of fossils in a study of the body size evolution of afrotherian mammals, a clade that includes the elephants, sea cows and elephant shrews. We find that the inclusion of fossil tips has little impact on analyses of body mass evolution; from a small ancestral size (approx. 100 g), there is a shift in rate and an increase in mass leading to the larger-bodied Paenungulata and Tubulidentata, regardless of whether fossils are included or excluded from analyses. For Afrotheria, the inclusion of fossils and morphological character data affect phylogenetic topology, but these differences have little impact upon patterns of body mass evolution and these body mass evolutionary patterns are consistent with the fossil record. The largest differences between our analyses result from the evolutionary model, not the addition of fossils. For some clades, extant-only analyses may be reliable to reconstruct body mass evolution, but the addition of fossils and careful model selection is likely to increase confidence and accuracy of reconstructed macroevolutionary patterns. PMID:26674947

  13. 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. PMID:26250386

  14. Patterns of maximum body size evolution in Cenozoic land mammals: eco-evolutionary processes and abiotic forcing

    PubMed Central

    Saarinen, Juha J.; Boyer, Alison G.; Brown, James H.; Costa, Daniel P.; Ernest, S. K. Morgan; Evans, Alistair R.; Fortelius, Mikael; Gittleman, John L.; Hamilton, Marcus J.; Harding, Larisa E.; Lintulaakso, Kari; Lyons, S. Kathleen; Okie, Jordan G.; Sibly, Richard M.; Stephens, Patrick R.; Theodor, Jessica; Uhen, Mark D.; Smith, Felisa A.

    2014-01-01

    There is accumulating evidence that macroevolutionary patterns of mammal evolution during the Cenozoic follow similar trajectories on different continents. This would suggest that such patterns are strongly determined by global abiotic factors, such as climate, or by basic eco-evolutionary processes such as filling of niches by specialization. The similarity of pattern would be expected to extend to the history of individual clades. Here, we investigate the temporal distribution of maximum size observed within individual orders globally and on separate continents. While the maximum size of individual orders of large land mammals show differences and comprise several families, the times at which orders reach their maximum size over time show strong congruence, peaking in the Middle Eocene, the Oligocene and the Plio-Pleistocene. The Eocene peak occurs when global temperature and land mammal diversity are high and is best explained as a result of niche expansion rather than abiotic forcing. Since the Eocene, there is a significant correlation between maximum size frequency and global temperature proxy. The Oligocene peak is not statistically significant and may in part be due to sampling issues. The peak in the Plio-Pleistocene occurs when global temperature and land mammal diversity are low, it is statistically the most robust one and it is best explained by global cooling. We conclude that the macroevolutionary patterns observed are a result of the interplay between eco-evolutionary processes and abiotic forcing. PMID:24741007

  15. Mosaic evolution and the pattern of transitions in the hominin lineage.

    PubMed

    Foley, Robert A

    2016-07-01

    Humans are uniquely unique, in terms of the extreme differences between them and other living organisms, and the impact they are having on the biosphere. The evolution of humans can be seen, as has been proposed, as one of the major transitions in evolution, on a par with the origins of multicellular organisms or the eukaryotic cell (Maynard Smith & Szathmáry 1997 Major transitions in evolution). Major transitions require the evolution of greater complexity and the emergence of new evolutionary levels or processes. Does human evolution meet these conditions? I explore the diversity of evidence on the nature of transitions in human evolution. Four levels of transition are proposed-baseline, novel taxa, novel adaptive zones and major transitions-and the pattern of human evolution considered in the light of these. The primary conclusions are that changes in human evolution occur continuously and cumulatively; that novel taxa and the appearance of new adaptations are not clustered very tightly in particular periods, although there are three broad transitional phases (Pliocene, Plio-Pleistocene and later Quaternary). Each phase is distinctive, with the first based on ranging and energetics, the second on technology and niche expansion, and the third on cognition and cultural processes. I discuss whether this constitutes a 'major transition' in the context of the evolutionary processes more broadly; the role of behaviour in evolution; and the opportunity provided by the rich genetic, phenotypic (fossil morphology) and behavioural (archaeological) record to examine in detail major transitions and the microevolutionary patterns underlying macroevolutionary change. It is suggested that the evolution of the hominin lineage is consistent with a mosaic pattern of change.This article is part of the themed issue 'Major transitions in human evolution'. PMID:27298474

  16. Tempo and mode in the macroevolutionary reconstruction of Darwinism.

    PubMed Central

    Gould, S J

    1994-01-01

    Among the several central meanings of Darwinism, his version of Lyellian uniformitarianism--the extrapolationist commitment to viewing causes of small-scale, observable change in modern populations as the complete source, by smooth extension through geological time, of all magnitudes and sequences in evolution--has most contributed to the causal hegemony of microevolution and the assumption that paleontology can document the contingent history of life but cannot act as a domain of novel evolutionary theory. G. G. Simpson tried to combat this view of paleontology as theoretically inert in his classic work, Tempo and Mode in Evolution (1944), with a brilliant argument that the two subjects of his title fall into a unique paleontological domain and that modes (processes and causes) can be inferred from the quantitative study of tempos (pattern). Nonetheless, Simpson did not cash out his insight to paleontology's theoretical benefit because he followed the strict doctrine of the Modern Synthesis. He studied his domain of potential theory and concluded that no actual theory could be found--and that a full account of causes could therefore be located in the microevolutionary realm after all. I argue that Simpson was unduly pessimistic and that modernism's belief in reductionistic unification (the conventional view of Western intellectuals from the 1920s to the 1950s) needs to be supplanted by a postmodernist commitment to pluralism and multiple levels of causation. Macro- and microevolution should not be viewed as opposed, but as truly complementary. I describe the two major domains where a helpful macroevolutionary theory may be sought--unsmooth causal boundaries between levels (as illustrated by punctuated equilibrium and mass extinction) and hierarchical expansion of the theory of natural selection to levels both below (gene and cell-line) and above organisms (demes, species, and clades). Problems remain in operationally defining selection at non-organismic levels

  17. Tempo and mode in the macroevolutionary reconstruction of Darwinism.

    PubMed

    Gould, S J

    1994-07-19

    Among the several central meanings of Darwinism, his version of Lyellian uniformitarianism--the extrapolationist commitment to viewing causes of small-scale, observable change in modern populations as the complete source, by smooth extension through geological time, of all magnitudes and sequences in evolution--has most contributed to the causal hegemony of microevolution and the assumption that paleontology can document the contingent history of life but cannot act as a domain of novel evolutionary theory. G. G. Simpson tried to combat this view of paleontology as theoretically inert in his classic work, Tempo and Mode in Evolution (1944), with a brilliant argument that the two subjects of his title fall into a unique paleontological domain and that modes (processes and causes) can be inferred from the quantitative study of tempos (pattern). Nonetheless, Simpson did not cash out his insight to paleontology's theoretical benefit because he followed the strict doctrine of the Modern Synthesis. He studied his domain of potential theory and concluded that no actual theory could be found--and that a full account of causes could therefore be located in the microevolutionary realm after all. I argue that Simpson was unduly pessimistic and that modernism's belief in reductionistic unification (the conventional view of Western intellectuals from the 1920s to the 1950s) needs to be supplanted by a postmodernist commitment to pluralism and multiple levels of causation. Macro- and microevolution should not be viewed as opposed, but as truly complementary. I describe the two major domains where a helpful macroevolutionary theory may be sought--unsmooth causal boundaries between levels (as illustrated by punctuated equilibrium and mass extinction) and hierarchical expansion of the theory of natural selection to levels both below (gene and cell-line) and above organisms (demes, species, and clades). Problems remain in operationally defining selection at non-organismic levels

  18. A universal driver of macroevolutionary change in the size of marine phytoplankton over the Cenozoic.

    PubMed

    Finkel, Z V; Sebbo, J; Feist-Burkhardt, S; Irwin, A J; Katz, M E; Schofield, O M E; Young, J R; Falkowski, P G

    2007-12-18

    The size structure of phytoplankton assemblages strongly influences energy transfer through the food web and carbon cycling in the ocean. We determined the macroevolutionary trajectory in the median size of dinoflagellate cysts to compare with the macroevolutionary size change in other plankton groups. We found the median size of the dinoflagellate cysts generally decreases through the Cenozoic. Diatoms exhibit an extremely similar pattern in their median size over time, even though species diversity of the two groups has opposing trends, indicating that the macroevolutionary size change is an active response to selection pressure rather than a passive response to changes in diversity. The changes in the median size of dinoflagellate cysts are highly correlated with both deep ocean temperatures and the thermal gradient between the surface and deep waters, indicating the magnitude and frequency of nutrient availability may have acted as a selective factor in the macroevolution of cell size in the plankton. Our results suggest that climate, because it affects stratification in the ocean, is a universal abiotic driver that has been responsible for macroevolutionary changes in the size structure of marine planktonic communities over the past 65 million years of Earth's history. PMID:18077334

  19. Patterns of Conceptual Change in Evolution.

    ERIC Educational Resources Information Center

    Demastes, Sherry S.; And Others

    1996-01-01

    Investigates the patterns of students' conceptual restructuring within the theoretical framework of biologic evolution. Results indicate that many conceptions in this content are closely interwoven, so that a change in one conception requires a change in many others. Reports four patterns of conceptual change: cascade, wholesale, incremental, and…

  20. Convergence and Divergence in the Evolution of Cat Skulls: Temporal and Spatial Patterns of Morphological Diversity

    PubMed Central

    Sakamoto, Manabu; Ruta, Marcello

    2012-01-01

    Background Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. Methodology/Principal Findings A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. Conclusions/Significance Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in

  1. Macroevolutionary Immunology: A Role for Immunity in the Diversification of Animal life.

    PubMed

    Loker, Eric S

    2012-01-01

    An emerging picture of the nature of immune systems across animal phyla reveals both conservatism of some features and the appearance among and within phyla of novel, lineage-specific defense solutions. The latter collectively represent a major and underappreciated form of animal diversity. Factors influencing this macroevolutionary (above the species level) pattern of novelty are considered and include adoption of different life styles, life histories, and body plans; a general advantage of being distinctive with respect to immune defenses; and the responses required to cope with parasites, many of which afflict hosts in a lineage-specific manner. This large-scale pattern of novelty implies that immunological phenomena can affect microevolutionary processes (at the population level within species) that can eventually lead to macroevolutionary events such as speciation, radiations, or extinctions. Immunologically based phenomena play a role in favoring intraspecific diversification, specialization and host specificity of parasites, and mechanisms are discussed whereby this could lead to parasite speciation. Host switching - the acquisition of new host species by parasites - is a major mechanism that drives parasite diversity and is frequently involved in disease emergence. It is also one that can be favored by reductions in immune competence of new hosts. Mechanisms involving immune phenomena favoring intraspecific diversification and speciation of host species are also discussed. A macroevolutionary perspective on immunology is invaluable in today's world, including the need to study a broader range of species with distinctive immune systems. Many of these species are faced with extinction, another macroevolutionary process influenced by immune phenomena. PMID:22566909

  2. Macroevolutionary Immunology: A Role for Immunity in the Diversification of Animal life

    PubMed Central

    Loker, Eric S.

    2012-01-01

    An emerging picture of the nature of immune systems across animal phyla reveals both conservatism of some features and the appearance among and within phyla of novel, lineage-specific defense solutions. The latter collectively represent a major and underappreciated form of animal diversity. Factors influencing this macroevolutionary (above the species level) pattern of novelty are considered and include adoption of different life styles, life histories, and body plans; a general advantage of being distinctive with respect to immune defenses; and the responses required to cope with parasites, many of which afflict hosts in a lineage-specific manner. This large-scale pattern of novelty implies that immunological phenomena can affect microevolutionary processes (at the population level within species) that can eventually lead to macroevolutionary events such as speciation, radiations, or extinctions. Immunologically based phenomena play a role in favoring intraspecific diversification, specialization and host specificity of parasites, and mechanisms are discussed whereby this could lead to parasite speciation. Host switching – the acquisition of new host species by parasites – is a major mechanism that drives parasite diversity and is frequently involved in disease emergence. It is also one that can be favored by reductions in immune competence of new hosts. Mechanisms involving immune phenomena favoring intraspecific diversification and speciation of host species are also discussed. A macroevolutionary perspective on immunology is invaluable in today’s world, including the need to study a broader range of species with distinctive immune systems. Many of these species are faced with extinction, another macroevolutionary process influenced by immune phenomena. PMID:22566909

  3. Patterns and Processes of Vertebrate Evolution

    NASA Astrophysics Data System (ADS)

    Carroll, Robert Lynn

    1997-04-01

    This new text provides an integrated view of the forces that influence the patterns and rates of vertebrate evolution from the level of living populations and species to those that resulted in the origin of the major vertebrate groups. The evolutionary roles of behavior, development, continental drift, and mass extinctions are compared with the importance of variation and natural selection that were emphasized by Darwin. It is extensively illustrated, showing major transitions between fish and amphibians, dinosaurs and birds, and land mammals to whales. No book since Simpson's Major Features of Evolution has attempted such a broad study of the patterns and forces of evolutionary change. Undergraduate students taking a general or advanced course on evolution, and graduate students and professionals in evolutionary biology and paleontology will find the book of great interest.

  4. Predator-induced macroevolutionary trends in Mesozoic crinoids

    PubMed Central

    Gorzelak, Przemysław; Salamon, Mariusz A.; Baumiller, Tomasz K.

    2012-01-01

    Sea urchins are a major component of recent marine communities where they exert a key role as grazers and benthic predators. However, their impact on past marine organisms, such as crinoids, is hard to infer in the fossil record. Analysis of bite mark frequencies on crinoid columnals and comprehensive genus-level diversity data provide unique insights into the importance of sea urchin predation through geologic time. These data show that over the Mesozoic, predation intensity on crinoids, as measured by bite mark frequencies on columnals, changed in step with diversity of sea urchins. Moreover, Mesozoic diversity changes in the predatory sea urchins show a positive correlation with diversity of motile crinoids and a negative correlation with diversity of sessile crinoids, consistent with a crinoid motility representing an effective escape strategy. We contend that the Mesozoic diversity history of crinoids likely represents a macroevolutionary response to changes in sea urchin predation pressure and that it may have set the stage for the recent pattern of crinoid diversity in which motile forms greatly predominate and sessile forms are restricted to deep-water refugia. PMID:22509040

  5. Predator-induced macroevolutionary trends in Mesozoic crinoids

    NASA Astrophysics Data System (ADS)

    Gorzelak, Przemysław; Salamon, Mariusz A.; Baumiller, Tomasz K.

    2012-05-01

    Sea urchins are a major component of recent marine communities where they exert a key role as grazers and benthic predators. However, their impact on past marine organisms, such as crinoids, is hard to infer in the fossil record. Analysis of bite mark frequencies on crinoid columnals and comprehensive genus-level diversity data provide unique insights into the importance of sea urchin predation through geologic time. These data show that over the Mesozoic, predation intensity on crinoids, as measured by bite mark frequencies on columnals, changed in step with diversity of sea urchins. Moreover, Mesozoic diversity changes in the predatory sea urchins show a positive correlation with diversity of motile crinoids and a negative correlation with diversity of sessile crinoids, consistent with a crinoid motility representing an effective escape strategy. We contend that the Mesozoic diversity history of crinoids likely represents a macroevolutionary response to changes in sea urchin predation pressure and that it may have set the stage for the recent pattern of crinoid diversity in which motile forms greatly predominate and sessile forms are restricted to deep-water refugia.

  6. Evolution of bioconvective patterns in variable gravity

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1991-01-01

    Measurements are reported of the evolution of bioconvective patterns in shallow, dense cultures of microorganisms subjected to varying gravity. Various statistical properties of this random, quasi-two-dimensional structure have been found: Aboav's law is obeyed, the average vertex angles follow predictions for regular polygons, and the area of a pattern varies linearly with its number of sides. As gravity varies between 1 g and 1.8 g, these statistical properties continue to hold despite a tripling of the number of polygons and a reduced average polygon dimension by a third. This work compares with experiments on soap foams, Langmuir monolayer foams, metal grains, and simulations.

  7. The Evolution of Trilobite Body Patterning

    NASA Astrophysics Data System (ADS)

    Hughes, Nigel C.

    2007-05-01

    The good fossil record of trilobite exoskeletal anatomy and ontogeny, coupled with information on their nonbiomineralized tissues, permits analysis of how the trilobite body was organized and developed, and the various evolutionary modifications of such patterning within the group. In several respects trilobite development and form appears comparable with that which may have characterized the ancestor of most or all euarthropods, giving studies of trilobite body organization special relevance in the light of recent advances in the understanding of arthropod evolution and development. The Cambrian diversification of trilobites displayed modifications in the patterning of the trunk region comparable with those seen among the closest relatives of Trilobita. In contrast, the Ordovician diversification of trilobites, although contributing greatly to the overall diversity within the clade, did so within a narrower range of trunk conditions. Trilobite evolution is consistent with an increased premium on effective enrollment and protective strategies, and with an evolutionary trade-off between the flexibility to vary the number of trunk segments and the ability to regionalize portions of the trunk.

  8. Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria).

    PubMed

    Bapst, D W; Wright, A M; Matzke, N J; Lloyd, G T

    2016-07-01

    Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian 'tip-dating' methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences. PMID:27405380

  9. Chromosome differentiation patterns during cichlid fish evolution

    PubMed Central

    2010-01-01

    Background Cichlid fishes have been the subject of increasing scientific interest because of their rapid adaptive radiation which has led to an extensive ecological diversity and their enormous importance to tropical and subtropical aquaculture. To increase our understanding of chromosome evolution among cichlid species, karyotypes of one Asian, 22 African, and 30 South American cichlid species were investigated, and chromosomal data of the family was reviewed. Results Although there is extensive variation in the karyotypes of cichlid fishes (from 2n = 32 to 2n = 60 chromosomes), the modal chromosome number for South American species was 2n = 48 and the modal number for the African ones was 2n = 44. The only Asian species analyzed, Etroplus maculatus, was observed to have 46 chromosomes. The presence of one or two macro B chromosomes was detected in two African species. The cytogenetic mapping of 18S ribosomal RNA (18S rRNA) gene revealed a variable number of clusters among species varying from two to six. Conclusions The karyotype diversification of cichlids seems to have occurred through several chromosomal rearrangements involving fissions, fusions and inversions. It was possible to identify karyotype markers for the subfamilies Pseudocrenilabrinae (African) and Cichlinae (American). The karyotype analyses did not clarify the phylogenetic relationship among the Cichlinae tribes. On the other hand, the two major groups of Pseudocrenilabrinae (tilapiine and haplochromine) were clearly discriminated based on the characteristics of their karyotypes. The cytogenetic mapping of 18S ribosomal RNA (18S rRNA) gene did not follow the chromosome diversification in the family. The dynamic evolution of the repeated units of rRNA genes generates patterns of chromosomal distribution that do not help follows the phylogenetic relationships among taxa. The presence of B chromosomes in cichlids is of particular interest because they may not be represented in the reference genome

  10. Heterochronical patterns of evolution in the transitional stages of vertebrate classes.

    PubMed

    Schad, W

    1993-12-01

    Transitional forms of the recent classes of vertebrates are only known in paleontology. The well described examples are: Eusthenopteron foordi (Crossopterygii), Ichthyostega and Acanthostega (Labyrinthodontia) between Osteichthyes and Amphibia, Seymouria baylorensis (Amphibiosaria) between Amphibia and Reptilia, Archaeopteryx lithographica (Archaeornithes) between Reptilia and Aves, and the mammal-like reptiles Pelycosauria, Therapsida and Cynodontia between Reptilia and Aves, and the description of their phylogenetical heterochronies in terms of peramorphosis and paedomorphosis shows the progressive role of the motorial, especially the locomotorial organ systems and their functions in comparison with the retarded evolution of the axial system, especially the skull and central nervous system. The evolution of the Hominidae shows the same rule. The evaluation of these transitional forms in their fossil context reveals them as inhabitants of biotopes situated in the border areas of coastal and shore landscapes of marine, brackish or fresh water. These biotopes have obviously favoured the innovations on the high taxonimic level of macro-evolutionary characteristics. PMID:8191805

  11. PSEMA: An Algorithm for Pattern Stimulated Evolution of Music

    NASA Astrophysics Data System (ADS)

    Mavrogianni, A. N.; Vlachos, D. S.; Harvalias, G.

    2008-11-01

    An algorithm for pattern stimulating evolution of music is presented in this work (PSEMA). The system combines a pattern with a genetic algorithm for automatic music composition in order to create a musical phrase uniquely characterizing the pattern. As an example a musical portrait is presented. The initialization of the musical phrases is done with a Markov Chain process. The evolution is dominated by an arbitrary correspondence between the pattern (feature extraction of the pattern may be used in this step) and the esthetic result of the musical phrase.

  12. Effects of allometry, productivity and lifestyle on rates and limits of body size evolution

    PubMed Central

    Okie, Jordan G.; Boyer, Alison G.; Brown, James H.; Costa, Daniel P.; Ernest, S. K. Morgan; Evans, Alistair R.; Fortelius, Mikael; Gittleman, John L.; Hamilton, Marcus J.; Harding, Larisa E.; Lintulaakso, Kari; Lyons, S. Kathleen; Saarinen, Juha J.; Smith, Felisa A.; Stephens, Patrick R.; Theodor, Jessica; Uhen, Mark D.; Sibly, Richard M.

    2013-01-01

    Body size affects nearly all aspects of organismal biology, so it is important to understand the constraints and dynamics of body size evolution. Despite empirical work on the macroevolution and macroecology of minimum and maximum size, there is little general quantitative theory on rates and limits of body size evolution. We present a general theory that integrates individual productivity, the lifestyle component of the slow–fast life-history continuum, and the allometric scaling of generation time to predict a clade's evolutionary rate and asymptotic maximum body size, and the shape of macroevolutionary trajectories during diversifying phases of size evolution. We evaluate this theory using data on the evolution of clade maximum body sizes in mammals during the Cenozoic. As predicted, clade evolutionary rates and asymptotic maximum sizes are larger in more productive clades (e.g. baleen whales), which represent the fast end of the slow–fast lifestyle continuum, and smaller in less productive clades (e.g. primates). The allometric scaling exponent for generation time fundamentally alters the shape of evolutionary trajectories, so allometric effects should be accounted for in models of phenotypic evolution and interpretations of macroevolutionary body size patterns. This work highlights the intimate interplay between the macroecological and macroevolutionary dynamics underlying the generation and maintenance of morphological diversity. PMID:23760865

  13. Crack patterning effects in evolution of damage

    SciTech Connect

    Lacy, T.E.; McDowell, D.L.; Taireja, R.

    1995-12-31

    Recent micromechanically inspired phenomenological theories using internal state variable representations of damage have been used to predict the thermomechanical behavior of microcracking solids. These models do not, in an explicit manner, account for distributions of microcracks in a Representative Volume Element (RVE) and have been successfully used only to determine the effective moduli of damaged solids. It has been demonstrated that while the distribution. and interaction of damage entities within a RVE have a minor effect on the effective moduli, they have a significant effect on the evolution of damage and failure at the macroscale. Damage evolution rates cannot, in general, be adequately described by such theories because of their inability to account for interactions between damage entities in an arbitrary distribution. In the present work, finite element solutions to two-dimensional problems with growing microcracks are obtained for both uniform and non-uniform crack arrays. Effective moduli and RVE-averaged driving forces for non-uniformly distributed interacting crack systems are calculated across a range of microcrack distribution parameters. Results are compared to existing solutions. Damage evolution is studied by allowing incremental advance under specified growth criteria of different crack systems within a RVE. Concepts for the inclusion of discrete sub-RVE length scales in the specific Helmholtz free energy and dissipation potentials are outlined. Use of multivariate distribution functions to characterize damage is discussed.

  14. Extreme Postnatal Scaling in Bat Feeding Performance: A View of Ecomorphology from Ontogenetic and Macroevolutionary Perspectives.

    PubMed

    Santana, Sharlene E; Miller, Kimberly E

    2016-09-01

    Ecomorphology studies focus on understanding how anatomical and behavioral diversity result in differences in performance, ecology, and fitness. In mammals, the determinate growth of the skeleton entails that bite performance should change throughout ontogeny until the feeding apparatus attains its adult size and morphology. Then, interspecific differences in adult phenotypes are expected to drive food resource partitioning and patterns of lineage diversification. However, Formal tests of these predictions are lacking for the majority of mammal groups, and thus our understanding of mammalian ecomorphology remains incomplete. By focusing on a fundamental measure of feeding performance, bite force, and capitalizing on the extraordinary morphological and dietary diversity of bats, we discuss how the intersection of ontogenetic and macroevolutionary changes in feeding performance may impact ecological diversity in these mammals. We integrate data on cranial morphology and bite force gathered through longitudinal studies of captive animals and comparative studies of free-ranging individuals. We demonstrate that ontogenetic trajectories and evolutionary changes in bite force are highly dependent on changes in body and head size, and that bats exhibit dramatic, allometric increases in bite force during ontogeny. Interspecific variation in bite force is highly dependent on differences in cranial morphology and function, highlighting selection for ecological specialization. While more research is needed to determine how ontogenetic changes in size and bite force specifically impact food resource use and fitness in bats, interspecific diversity in cranial morphology and bite performance seem to closely match functional differences in diet. Altogether, these results suggest direct ecomorphological relationships at ontogenetic and macroevolutionary scales in bats. PMID:27371380

  15. Shared rules of development predict patterns of evolution in vertebrate segmentation.

    PubMed

    Young, Nathan M; Winslow, Benjamin; Takkellapati, Sowmya; Kavanagh, Kathryn

    2015-01-01

    Phenotypic diversity is not uniformly distributed, but how biased patterns of evolutionary variation are generated and whether common developmental mechanisms are responsible remains debatable. High-level 'rules' of self-organization and assembly are increasingly used to model organismal development, even when the underlying cellular or molecular players are unknown. One such rule, the inhibitory cascade, predicts that proportions of segmental series derive from the relative strengths of activating and inhibitory interactions acting on both local and global scales. Here we show that this developmental design rule explains population-level variation in segment proportions, their response to artificial selection and experimental blockade of putative signals and macroevolutionary diversity in limbs, digits and somites. Together with evidence from teeth, these results indicate that segmentation across independent developmental modules shares a common regulatory 'logic', which has a predictable impact on both their short and long-term evolvability. PMID:25827599

  16. Patterns of iron use in societal evolution.

    PubMed

    Müller, Daniel B; Wang, Tao; Duval, Benjamin

    2011-01-01

    A dynamic material flow model was used to analyze the patterns of iron stocks in use for six industrialized countries. The contemporary iron stock in the remaining countries was estimated assuming that they follow a similar pattern of iron stock per economic activity. Iron stocks have reached a plateau of about 8-12 tons per capita in the United States, France, and the United Kingdom, but not yet in Japan, Canada, and Australia. The global average iron stock was determined to be 2.7 tons per capita. An increase to a level of 10 tons over the next decades would deplete about the currently identified reserves. A subsequent saturation would open a long-term potential to dramatically shift resource use from primary to secondary sources. The observed saturation pattern implies that developing countries with rapidly growing stocks have a lower potential for recycling domestic scrap and hence for greenhouse gas emissions saving than industrialized countries, a fact that has not been addressed sufficiently in the climate change debate. PMID:21121663

  17. Pattern evolution during ion beam sputtering; reductionistic view

    NASA Astrophysics Data System (ADS)

    Kim, J.-H.; Kim, J.-S.

    2016-09-01

    The development of the ripple pattern during the ion beam sputtering (IBS) is expounded via the evolution of its constituent ripples. For that purpose, we perform numerical simulation of the ripple evolution that is based on Bradley-Harper model and its non-linear extension. The ripples are found to evolve via various well-defined processes such as ripening, averaging, bifurcation and their combinations, depending on their neighboring ripples. Those information on the growth kinetics of each ripple allow the detailed description of the pattern development in real space that the instability argument and the diffraction study both made in k-space cannot provide.

  18. Analysis and visualization of complex macroevolutionary dynamics: an example from Australian scincid lizards.

    PubMed

    Rabosky, Daniel L; Donnellan, Stephen C; Grundler, Michael; Lovette, Irby J

    2014-07-01

    The correlation between species diversification and morphological evolution has long been of interest in evolutionary biology. We investigated the relationship between these processes during the radiation of 250+scincid lizards that constitute Australia's most species-rich clade of terrestrial vertebrates. We generated a time-calibrated phylogenetic tree for the group that was more than 85% complete at the species level and collected multivariate morphometric data for 183 species. We reconstructed the dynamics of species diversification and trait evolution using a Bayesian statistical framework (BAMM) that simultaneously accounts for variation in evolutionary rates through time and among lineages. We extended the BAMM model to accommodate time-dependent phenotypic evolution, and we describe several new methods for summarizing and visualizing macroevolutionary rate heterogeneity on phylogenetic trees. Two major clades (Lerista, Ctenotus; >90 spp. each) are associated with high rates of species diversification relative to the background rate across Australian sphenomorphine skinks. The Lerista clade is characterized by relatively high lability of body form and has undergone repeated instances of limb reduction, but Ctenotus is characterized by an extreme deceleration in the rate of body shape evolution. We estimate that rates of phenotypic evolution decreased by more than an order of magnitude in the common ancestor of the Ctenotus clade. These results provide evidence for a modal shift in phenotypic evolutionary dynamics and demonstrate that major axes of morphological variation can be decoupled from species diversification. More generally, the Bayesian framework described here can be used to identify and characterize complex mixtures of dynamic processes on phylogenetic trees. [Bayesian; diversification; evolvability; lizard; macroevolution, punctuated equilibrium, speciation.]. PMID:24682412

  19. Transcriptome-wide patterns of divergence during allopatric evolution.

    PubMed

    Pereira, Ricardo J; Barreto, Felipe S; Pierce, N Tessa; Carneiro, Miguel; Burton, Ronald S

    2016-04-01

    Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among populations within the same species may shed light on the underlying evolutionary processes. Here, we examine transcriptome-wide divergence and polymorphism in the marine copepod Tigriopus californicus, a species where allopatric evolution has led to replicate sets of populations with varying degrees of divergence and hybrid incompatibility. Our analyses suggest that relatively small effective population sizes have resulted in an exponential decline of shared polymorphisms during population divergence and also facilitated the fixation of slightly deleterious mutations within allopatric populations. Five interpopulation comparisons at three different stages of divergence show that nonsynonymous mutations tend to accumulate in a specific set of proteins. These include proteins with central roles in cellular metabolism, such as those encoded in mtDNA, but also include an additional set of proteins that repeatedly show signatures of positive selection during allopatric divergence. Although our results are consistent with a contribution of nonadaptive processes, such as genetic drift and gene expression levels, generating repeatable patterns of genomic divergence in closely related taxa, they also indicate that adaptive evolution targeting a specific set of genes contributes to this pattern. Our results yield insights into the predictability of evolution at the gene level. PMID:26859844

  20. Tempo and Mode of the Evolution of Venom and Poison in Tetrapods.

    PubMed

    Harris, Richard J; Arbuckle, Kevin

    2016-01-01

    Toxic weaponry in the form of venom and poison has evolved in most groups of animals, including all four major lineages of tetrapods. Moreover, the evolution of such traits has been linked to several key aspects of the biology of toxic animals including life-history and diversification. Despite this, attempts to investigate the macroevolutionary patterns underlying such weaponry are lacking. In this study we analyse patterns of venom and poison evolution across reptiles, amphibians, mammals, and birds using a suite of phylogenetic comparative methods. We find that each major lineage has a characteristic pattern of trait evolution, but mammals and reptiles evolve under a surprisingly similar regime, whilst that of amphibians appears to be particularly distinct and highly contrasting compared to other groups. Our results also suggest that the mechanism of toxin acquisition may be an important distinction in such evolutionary patterns; the evolution of biosynthesis is far less dynamic than that of sequestration of toxins from the diet. Finally, contrary to the situation in amphibians, other tetrapod groups show an association between the evolution of toxic weaponry and higher diversification rates. Taken together, our study provides the first broad-scale analysis of macroevolutionary patterns of venom and poison throughout tetrapods. PMID:27348001

  1. Tempo and Mode of the Evolution of Venom and Poison in Tetrapods

    PubMed Central

    Harris, Richard J.; Arbuckle, Kevin

    2016-01-01

    Toxic weaponry in the form of venom and poison has evolved in most groups of animals, including all four major lineages of tetrapods. Moreover, the evolution of such traits has been linked to several key aspects of the biology of toxic animals including life-history and diversification. Despite this, attempts to investigate the macroevolutionary patterns underlying such weaponry are lacking. In this study we analyse patterns of venom and poison evolution across reptiles, amphibians, mammals, and birds using a suite of phylogenetic comparative methods. We find that each major lineage has a characteristic pattern of trait evolution, but mammals and reptiles evolve under a surprisingly similar regime, whilst that of amphibians appears to be particularly distinct and highly contrasting compared to other groups. Our results also suggest that the mechanism of toxin acquisition may be an important distinction in such evolutionary patterns; the evolution of biosynthesis is far less dynamic than that of sequestration of toxins from the diet. Finally, contrary to the situation in amphibians, other tetrapod groups show an association between the evolution of toxic weaponry and higher diversification rates. Taken together, our study provides the first broad-scale analysis of macroevolutionary patterns of venom and poison throughout tetrapods. PMID:27348001

  2. Evolution of central pattern generators and rhythmic behaviours.

    PubMed

    Katz, Paul S

    2016-01-01

    Comparisons of rhythmic movements and the central pattern generators (CPGs) that control them uncover principles about the evolution of behaviour and neural circuits. Over the course of evolutionary history, gradual evolution of behaviours and their neural circuitry within any lineage of animals has been a predominant occurrence. Small changes in gene regulation can lead to divergence of circuit organization and corresponding changes in behaviour. However, some behavioural divergence has resulted from large-scale rewiring of the neural network. Divergence of CPG circuits has also occurred without a corresponding change in behaviour. When analogous rhythmic behaviours have evolved independently, it has generally been with different neural mechanisms. Repeated evolution of particular rhythmic behaviours has occurred within some lineages due to parallel evolution or latent CPGs. Particular motor pattern generating mechanisms have also evolved independently in separate lineages. The evolution of CPGs and rhythmic behaviours shows that although most behaviours and neural circuits are highly conserved, the nature of the behaviour does not dictate the neural mechanism and that the presence of homologous neural components does not determine the behaviour. This suggests that although behaviour is generated by neural circuits, natural selection can act separately on these two levels of biological organization. PMID:26598733

  3. Instabilities and pattern evolution in a vertically heated annulus

    NASA Astrophysics Data System (ADS)

    Wang, BoFu; Guo, ZhiWei; Ma, DongJun; Sun, DeJun

    2013-02-01

    The convection in an annular container with heated bottom, cooled top and insulated side walls are studied by both linear instability analysis and direct numerical simulation. The onset of convection is investigated by linear stability analysis and corresponding pattern selection mechanisms are discussed. The nonlinear evolution of different flow patterns and the convective heat transfer are simulated. The transition to oscillatory flow is also given by stability analysis where the base flow is a steady three dimensional flow. The stability predictions are in good agreement with the numerical simulations, including both the growth rate and the dimensionless frequency.

  4. The fossil record and macroevolutionary history of the beetles.

    PubMed

    Smith, Dena M; Marcot, Jonathan D

    2015-04-22

    Coleoptera (beetles) is the most species-rich metazoan order, with approximately 380 000 species. To understand how they came to be such a diverse group, we compile a database of global fossil beetle occurrences to study their macroevolutionary history. Our database includes 5553 beetle occurrences from 221 fossil localities. Amber and lacustrine deposits preserve most of the beetle diversity and abundance. All four extant suborders are found in the fossil record, with 69% of all beetle families and 63% of extant beetle families preserved. Considerable focus has been placed on beetle diversification overall, however, for much of their evolutionary history it is the clade Polyphaga that is most responsible for their taxonomic richness. Polyphaga had an increase in diversification rate in the Early Cretaceous, but instead of being due to the radiation of the angiosperms, this was probably due to the first occurrences of beetle-bearing amber deposits in the record. Perhaps, most significant is that polyphagan beetles had a family-level extinction rate of zero for most of their evolutionary history, including across the Cretaceous-Palaeogene boundary. Therefore, focusing on the factors that have inhibited beetle extinction, as opposed to solely studying mechanisms that may promote speciation, should be examined as important determinants of their great diversity today. PMID:25788597

  5. The fossil record and macroevolutionary history of the beetles

    PubMed Central

    Smith, Dena M.; Marcot, Jonathan D.

    2015-01-01

    Coleoptera (beetles) is the most species-rich metazoan order, with approximately 380 000 species. To understand how they came to be such a diverse group, we compile a database of global fossil beetle occurrences to study their macroevolutionary history. Our database includes 5553 beetle occurrences from 221 fossil localities. Amber and lacustrine deposits preserve most of the beetle diversity and abundance. All four extant suborders are found in the fossil record, with 69% of all beetle families and 63% of extant beetle families preserved. Considerable focus has been placed on beetle diversification overall, however, for much of their evolutionary history it is the clade Polyphaga that is most responsible for their taxonomic richness. Polyphaga had an increase in diversification rate in the Early Cretaceous, but instead of being due to the radiation of the angiosperms, this was probably due to the first occurrences of beetle-bearing amber deposits in the record. Perhaps, most significant is that polyphagan beetles had a family-level extinction rate of zero for most of their evolutionary history, including across the Cretaceous–Palaeogene boundary. Therefore, focusing on the factors that have inhibited beetle extinction, as opposed to solely studying mechanisms that may promote speciation, should be examined as important determinants of their great diversity today. PMID:25788597

  6. Movement Patterns, Social Dynamics, and the Evolution of Cooperation

    PubMed Central

    Smaldino, Paul E.; Schank, Jeffrey C.

    2012-01-01

    The structure of social interactions influences many aspects of social life, including the spread of information and behavior, and the evolution of social phenotypes. After dispersal, organisms move around throughout their lives, and the patterns of their movement influence their social encounters over the course of their lifespan. Though both space and mobility are known to influence social evolution, there is little analysis of the influence of specific movement patterns on evolutionary dynamics. We explored the effects of random movement strategies on the evolution of cooperation using an agent-based prisoner’s dilemma model with mobile agents. This is the first systematic analysis of a model in which cooperators and defectors can use different random movement strategies, which we chose to fall on a spectrum between highly exploratory and highly restricted in their search tendencies. Because limited dispersal and restrictions to local neighborhood size are known to influence the ability of cooperators to effectively assort, we also assessed the robustness of our findings with respect to dispersal and local capacity constraints. We show that differences in patterns of movement can dramatically influence the likelihood of cooperator success, and that the effects of different movement patterns are sensitive to environmental assumptions about offspring dispersal and local space constraints. Since local interactions implicitly generate dynamic social interaction networks, we also measured the average number of unique and total interactions over a lifetime and considered how these emergent network dynamics helped explain the results. This work extends what is known about mobility and the evolution of cooperation, and also has general implications for social models with randomly moving agents. PMID:22838026

  7. Evolution and convergence of the patterns of international scientific collaboration

    PubMed Central

    Wang, Lili

    2016-01-01

    International research collaboration plays an important role in the social construction and evolution of science. Studies of science increasingly analyze international collaboration across multiple organizations for its impetus in improving research quality, advancing efficiency of the scientific production, and fostering breakthroughs in a shorter time. However, long-run patterns of international research collaboration across scientific fields and their structural changes over time are hardly known. Here we show the convergence of international scientific collaboration across research fields over time. Our study uses a dataset by the National Science Foundation and computes the fraction of papers that have international institutional coauthorships for various fields of science. We compare our results with pioneering studies carried out in the 1970s and 1990s by applying a standardization method that transforms all fractions of internationally coauthored papers into a comparable framework. We find, over 1973–2012, that the evolution of collaboration patterns across scientific disciplines seems to generate a convergence between applied and basic sciences. We also show that the general architecture of international scientific collaboration, based on the ranking of fractions of international coauthorships for different scientific fields per year, has tended to be unchanged over time, at least until now. Overall, this study shows, to our knowledge for the first time, the evolution of the patterns of international scientific collaboration starting from initial results described by literature in the 1970s and 1990s. We find a convergence of these long-run collaboration patterns between the applied and basic sciences. This convergence might be one of contributing factors that supports the evolution of modern scientific fields. PMID:26831098

  8. Evolution and convergence of the patterns of international scientific collaboration.

    PubMed

    Coccia, Mario; Wang, Lili

    2016-02-23

    International research collaboration plays an important role in the social construction and evolution of science. Studies of science increasingly analyze international collaboration across multiple organizations for its impetus in improving research quality, advancing efficiency of the scientific production, and fostering breakthroughs in a shorter time. However, long-run patterns of international research collaboration across scientific fields and their structural changes over time are hardly known. Here we show the convergence of international scientific collaboration across research fields over time. Our study uses a dataset by the National Science Foundation and computes the fraction of papers that have international institutional coauthorships for various fields of science. We compare our results with pioneering studies carried out in the 1970s and 1990s by applying a standardization method that transforms all fractions of internationally coauthored papers into a comparable framework. We find, over 1973-2012, that the evolution of collaboration patterns across scientific disciplines seems to generate a convergence between applied and basic sciences. We also show that the general architecture of international scientific collaboration, based on the ranking of fractions of international coauthorships for different scientific fields per year, has tended to be unchanged over time, at least until now. Overall, this study shows, to our knowledge for the first time, the evolution of the patterns of international scientific collaboration starting from initial results described by literature in the 1970s and 1990s. We find a convergence of these long-run collaboration patterns between the applied and basic sciences. This convergence might be one of contributing factors that supports the evolution of modern scientific fields. PMID:26831098

  9. Ecological interactions on macroevolutionary time scales: clams and brachiopods are more than ships that pass in the night.

    PubMed

    Liow, Lee Hsiang; Reitan, Trond; Harnik, Paul G

    2015-10-01

    Competition among organisms has ecological and evolutionary consequences. However, whether the consequences of competition are manifested and measureable on macroevolutionary time scales is equivocal. Marine bivalves and brachiopods have overlapping niches such that competition for food and space may occur. Moreover, there is a long-standing debate over whether bivalves outcompeted brachiopods evolutionarily, because brachiopod diversity declined through time while bivalve diversity increased. To answer this question, we estimate the origination and extinction dynamics of fossil marine bivalve and brachiopod genera from the Ordovician through to the Recent while simultaneously accounting for incomplete sampling. Then, using stochastic differential equations, we assess statistical relationships among diversification and sampling dynamics of brachiopods and bivalves and five paleoenvironmental proxies. None of these potential environmental drivers had any detectable influence on brachiopod or bivalve diversification. In contrast, elevated bivalve extinction rates causally increased brachiopod origination rates, suggesting that bivalves have suppressed brachiopod evolution. PMID:26293753

  10. Building the backbone: the development and evolution of vertebral patterning.

    PubMed

    Fleming, Angeleen; Kishida, Marcia G; Kimmel, Charles B; Keynes, Roger J

    2015-05-15

    The segmented vertebral column comprises a repeat series of vertebrae, each consisting of two key components: the vertebral body (or centrum) and the vertebral arches. Despite being a defining feature of the vertebrates, much remains to be understood about vertebral development and evolution. Particular controversy surrounds whether vertebral component structures are homologous across vertebrates, how somite and vertebral patterning are connected, and the developmental origin of vertebral bone-mineralizing cells. Here, we assemble evidence from ichthyologists, palaeontologists and developmental biologists to consider these issues. Vertebral arch elements were present in early stem vertebrates, whereas centra arose later. We argue that centra are homologous among jawed vertebrates, and review evidence in teleosts that the notochord plays an instructive role in segmental patterning, alongside the somites, and contributes to mineralization. By clarifying the evolutionary relationship between centra and arches, and their varying modes of skeletal mineralization, we can better appreciate the detailed mechanisms that regulate and diversify vertebral patterning. PMID:25968309

  11. Flow-pattern evolution of the last British Ice Sheet

    NASA Astrophysics Data System (ADS)

    Hughes, Anna L. C.; Clark, Chris D.; Jordan, Colm J.

    2014-04-01

    We present a 10-stage reconstruction of the evolution in ice-flow patterns of the last British Ice Sheet from build-up to demise derived from geomorphological evidence. 100 flowsets identified in the subglacial bedform record (drumlins, mega-scale glacial lineations, and ribbed moraine) are combined with ancillary evidence (erratic-transport paths, absolute dates and a semi-independently reconstructed retreat pattern) to define flow patterns, ice divides and ice-sheet margins during build-up, maximum glaciation and retreat. Overprinting and cross-cutting of landform assemblages are used to define the relative chronology of flow patterns and a tentative absolute chronology is presented based on a collation of available dates for ice advance and retreat. The ice-flow configuration of the last British Ice Sheet was not static. Some ice divides were remarkably stable, persisting through multiple stages of the ice-sheet evolution, whereas others were transient features existing for a short time and/or shifting in position 10s km. The 10 reconstructed stages of ice-sheet geometry capture two main modes of operation; first as an integrated ice sheet with a broadly N-S orientated ice divide, and second as a multi-domed ice sheet orientated parallel with the shelf edge. A thick integrated ice sheet developed as ice expanded out of source areas in Scotland to envelop southerly ice caps in northern England and Wales, and connect with the Irish Ice Sheet to the west and the Scandinavian Ice Sheet across the North Sea. Following break-up of ice over the North Sea, ice streaming probably drove mass loss and ice-sheet thinning to create a more complex divide structure, where ice-flow patterns were largely controlled by the form of the underlying topography. Ice surface lowering occurred before separation of, and retreat to, multiple ice centres centred over high ground. We consider this 10-stage reconstruction of the evolution in ice-sheet configuration to be the simplest palaeo

  12. Adaptive evolution of facial colour patterns in Neotropical primates

    PubMed Central

    Santana, Sharlene E.; Lynch Alfaro, Jessica; Alfaro, Michael E.

    2012-01-01

    The rich diversity of primate faces has interested naturalists for over a century. Researchers have long proposed that social behaviours have shaped the evolution of primate facial diversity. However, the primate face constitutes a unique structure where the diverse and potentially competing functions of communication, ecology and physiology intersect, and the major determinants of facial diversity remain poorly understood. Here, we provide the first evidence for an adaptive role of facial colour patterns and pigmentation within Neotropical primates. Consistent with the hypothesis that facial patterns function in communication and species recognition, we find that species living in smaller groups and in sympatry with a higher number of congener species have evolved more complex patterns of facial colour. The evolution of facial pigmentation and hair length is linked to ecological factors, and ecogeographical rules related to UV radiation and thermoregulation are met by some facial regions. Our results demonstrate the interaction of behavioural and ecological factors in shaping one of the most outstanding facial diversities of any mammalian lineage. PMID:22237906

  13. Evolution: Bioluminescent Courtship as an Engine of Diversity.

    PubMed

    Alfaro, Michael E

    2016-07-25

    A new study finds that the evolution of bioluminescent sexual displays drives high species richness across animal lineages, providing a crucial link between microevolutionary and macroevolutionary explanations of biodiversity. PMID:27458910

  14. Environmental changes define ecological limits to species richness and reveal the mode of macroevolutionary competition.

    PubMed

    Ezard, Thomas H G; Purvis, Andy

    2016-08-01

    Co-dependent geological and climatic changes obscure how species interact in deep time. The interplay between these environmental factors makes it hard to discern whether ecological competition exerts an upper limit on species richness. Here, using the exceptional fossil record of Cenozoic Era macroperforate planktonic foraminifera, we assess the evidence for alternative modes of macroevolutionary competition. Our models support an environmentally dependent macroevolutionary form of contest competition that yields finite upper bounds on species richness. Models of biotic competition assuming unchanging environmental conditions were overwhelmingly rejected. In the best-supported model, temperature affects the per-lineage diversification rate, while both temperature and an environmental driver of sediment accumulation defines the upper limit. The support for contest competition implies that incumbency constrains species richness by restricting niche availability, and that the number of macroevolutionary niches varies as a function of environmental changes. PMID:27278857

  15. Evolution of Patterning Systems and Circuit Elements for Locomotion

    PubMed Central

    Jung, Heekyung; Dasen, Jeremy S.

    2015-01-01

    Summary Evolutionary modifications in nervous systems enabled organisms to adapt to their specific environments and underlie the remarkable diversity of behaviors expressed by animals. Resolving the pathways that shaped and modified neural circuits during evolution remains a significant challenge. Comparative studies have revealed a surprising conservation in the intrinsic signaling systems involved in early patterning of bilaterian nervous systems, but also raise the question of how neural circuit compositions and architectures evolved within specific animal lineages. In this Review we discuss the mechanisms that contributed to the emergence and diversity of animal nervous systems, focusing on the circuits governing vertebrate locomotion. PMID:25710528

  16. Macroevolutionary persistence of heritable endosymbionts: acquisition, retention and expression of adaptive phenotypes in Spiroplasma.

    PubMed

    Haselkorn, Tamara S; Jaenike, John

    2015-07-01

    The phylogenetic incongruence between insects and their facultative maternally transmitted endosymbionts indicates that these infections are generally short-lived evolutionarily. Therefore, long-term persistence of many endosymbionts must depend on their ability to colonize and spread within new host species. At least 17 species of Drosophila are infected with endosymbiotic Spiroplasma that have various phenotypic effects. We transinfected five strains of Spiroplasma from three divergent clades into Drosophila neotestacea to test their capacity to spread in a novel host. A strain that causes male killing in Drosophila melanogaster (its native host) also does so in D. neotestacea, even though these host species diverged 40-60 mya. A strain native to D. neotestacea (designated sNeo) and the two other strains of the poulsonii clade of Spiroplasma confer resistance to wasp parasitism, suggesting that this trait may be ancestral within this clade of Spiroplasma. Conversely, no strain other than sNeo conferred resistance to the sterilizing effects of nematode parasitism, suggesting that nematode resistance is a recently derived condition. The apparent addition of nematode resistance to a Spiroplasma lineage that already confers resistance to wasp parasitism suggests endosymbionts can increase the repertoire of traits conducive to their spread. The capacity of an endosymbiont to undergo maternal transmission and express adaptive phenotypes in novel hosts, without requiring a period of host-symbiont co-evolution, enables the spread of such symbionts immediately after the colonization of a new host. This could be critical for the macroevolutionary persistence of facultative endosymbionts whose sojourn times within individual host species are relatively brief. PMID:26053523

  17. Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

    PubMed Central

    Springer, Mark S.; Meredith, Robert W.; Gatesy, John; Emerling, Christopher A.; Park, Jong; Rabosky, Daniel L.; Stadler, Tanja; Steiner, Cynthia; Ryder, Oliver A.; Janečka, Jan E.; Fisher, Colleen A.; Murphy, William J.

    2012-01-01

    Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts. PMID:23166696

  18. Is evolution finished?

    PubMed

    Davison, John A

    2004-01-01

    Since speciation seems to be no longer in progress, one is compelled to conclude that sexual reproduction is incompetent as a macroevolutionary device. I propose that the reason some might insist that evolution is still in progress stems primarily from the influence of two authorities, the geologist Charles Lyell, with his doctrine of uniformitarianism and Gregor Mendel, the discoverer of sexually mediated transmission genetics. William Bateson, the father of modern genetics, clearly foresaw the failure of Mendelism to explain macroevolutionary change, a perspective with which I am in full agreement. PMID:15648214

  19. The evolution of isochore patterns in vertebrate genomes

    PubMed Central

    Costantini, Maria; Cammarano, Rosalia; Bernardi, Giorgio

    2009-01-01

    Background Previous work from our laboratory showed that (i) vertebrate genomes are mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous in base composition; (ii) isochores belong to a small number of families (five in the human genome) characterized by different GC levels; (iii) isochore family patterns are different in fishes/amphibians and mammals/birds, the latter showing GC-rich isochore families that are absent or very scarce in the former; (iv) there are two modes of genome evolution, a conservative one in which isochore patterns basically do not change (e.g., among mammalian orders), and a transitional one, in which they do change (e.g., between amphibians and mammals); and (v) isochores are tightly linked to a number of basic biological properties, such as gene density, gene expression, replication timing and recombination. Results The present availability of a number of fully sequenced genomes ranging from fishes to mammals allowed us to carry out investigations that (i) more precisely quantified our previous conclusions; (ii) showed that the different isochore families of vertebrate genomes are largely conserved in GC levels and dinucleotide frequencies, as well as in isochore size; and (iii) isochore family patterns can be either conserved or change within both warm- and cold-blooded vertebrates. Conclusion On the basis of the results presented, we propose that (i) the large conservation of GC levels and dinucleotide frequencies may reflect the conservation of chromatin structures; (ii) the conservation of isochore size may be linked to the role played by isochores in chromosome structure and replication; (iii) the formation, the maintainance and the changes of isochore patterns are due to natural selection. PMID:19344507

  20. Segment formation in Annelids: patterns, processes and evolution.

    PubMed

    Balavoine, Guillaume

    2014-01-01

    The debate on the origin of segmentation is a central question in the study of body plan evolution in metazoans. Annelids are the most conspicuously metameric animals as most of the trunk is formed of identical anatomical units. In this paper, I summarize the various patterns of evolution of the metameric body plan in annelids, showing the remarkable evolvability of this trait, similar to what is also found in arthropods. I then review the different modes of segment formation in the annelid tree, taking into account the various processes taking place in the life histories of these animals, including embryogenesis, post-embryonic development, regeneration and asexual reproduction. As an example of the variations that occur at the cellular and genetic level in annelid segment formation, I discuss the processes of teloblastic growth or posterior addition in key groups in the annelid tree. I propose a comprehensive definition for the teloblasts, stem cells that are responsible for sequential segment addition. There are a diversity of different mechanisms used in annelids to produce segments depending on the species, the developmental time and also the life history processes of the worm. A major goal for the future will be to reconstitute an ancestral process (or several ancestral processes) in the ancestor of the whole clade. This in turn will provide key insights in the current debate on ancestral bilaterian segmentation. PMID:25690963

  1. Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution.

    PubMed

    Zanno, Lindsay E; Makovicky, Peter J

    2011-01-01

    Interpreting key ecological parameters, such as diet, of extinct organisms without the benefit of direct observation or explicit fossil evidence poses a formidable challenge for paleobiological studies. To date, dietary categorizations of extinct taxa are largely generated by means of modern analogs; however, for many species the method is subject to considerable ambiguity. Here we present a refined approach for assessing trophic habits in fossil taxa and apply the method to coelurosaurian dinosaurs--a clade for which diet is particularly controversial. Our findings detect 21 morphological features that exhibit statistically significant correlations with extrinsic fossil evidence of coelurosaurian herbivory, such as stomach contents and a gastric mill. These traits represent quantitative, extrinsically founded proxies for identifying herbivorous ecomorphology in fossils and are robust despite uncertainty in phylogenetic relationships among major coelurosaurian subclades. The distribution of these features suggests that herbivory was widespread among coelurosaurians, with six major subclades displaying morphological evidence of the diet, and that contrary to previous thought, hypercarnivory was relatively rare and potentially secondarily derived. Given the potential for repeated, independent evolution of herbivory in Coelurosauria, we also test for repetitive patterns in the appearance of herbivorous traits within sublineages using rank concordance analysis. We find evidence for a common succession of increasing specialization to herbivory in the subclades Ornithomimosauria and Oviraptorosauria, perhaps underlain by intrinsic functional and/or developmental constraints, as well as evidence indicating that the early evolution of a beak in coelurosaurians correlates with an herbivorous diet. PMID:21173263

  2. A simple model for research interest evolution patterns

    NASA Astrophysics Data System (ADS)

    Jia, Tao; Wang, Dashun; Szymanski, Boleslaw

    Sir Isaac Newton supposedly remarked that in his scientific career he was like ``...a boy playing on the sea-shore ...finding a smoother pebble or a prettier shell than ordinary''. His remarkable modesty and famous understatement motivate us to seek regularities in how scientists shift their research focus as the career develops. Indeed, despite intensive investigations on how microscopic factors, such as incentives and risks, would influence a scientist's choice of research agenda, little is known on the macroscopic patterns in the research interest change undertaken by individual scientists throughout their careers. Here we make use of over 14,000 authors' publication records in physics. By quantifying statistical characteristics in the interest evolution, we model scientific research as a random walk, which reproduces patterns in individuals' careers observed empirically. Despite myriad of factors that shape and influence individual choices of research subjects, we identified regularities in this dynamical process that are well captured by a simple statistical model. The results advance our understanding of scientists' behaviors during their careers and open up avenues for future studies in the science of science.

  3. 2D pattern evolution constrained by complex network dynamics

    NASA Astrophysics Data System (ADS)

    da Rocha, L. E. C.; Costa, L. da F.

    2007-03-01

    Complex networks have established themselves in recent years as being particularly suitable and flexible for representing and modelling several complex natural and artificial systems. In the same time in which the structural intricacies of such networks are being revealed and understood, efforts have also been directed at investigating how such connectivity properties define and constrain the dynamics of systems unfolding on such structures. However, less attention has been focused on hybrid systems, i.e. involving more than one type of network and/or dynamics. Several real systems present such an organization, e.g. the dynamics of a disease coexisting with the dynamics of the immune system. The current paper investigates a specific system involving diffusive (linear and nonlinear) dynamics taking place in a regular network while interacting with a complex network of defensive agents following Erdös Rényi (ER) and Barabási Albert (BA) graph models with moveable nodes. More specifically, the complex network is expected to control, and if possible, to extinguish the diffusion of some given unwanted process (e.g. fire, oil spilling, pest dissemination, and virus or bacteria reproduction during an infection). Two types of pattern evolution are considered: Fick and Gray Scott. The nodes of the defensive network then interact with the diffusing patterns and communicate between themselves in order to control the diffusion. The main findings include the identification of higher efficiency for the BA control networks and the presence of relapses in the case of the ER model.

  4. Histone modification pattern evolution after yeast gene duplication

    PubMed Central

    2012-01-01

    Background Gene duplication and subsequent functional divergence especially expression divergence have been widely considered as main sources for evolutionary innovations. Many studies evidenced that genetic regulatory network evolved rapidly shortly after gene duplication, thus leading to accelerated expression divergence and diversification. However, little is known whether epigenetic factors have mediated the evolution of expression regulation since gene duplication. In this study, we conducted detailed analyses on yeast histone modification (HM), the major epigenetics type in this organism, as well as other available functional genomics data to address this issue. Results Duplicate genes, on average, share more common HM-code patterns than random singleton pairs in their promoters and open reading frames (ORF). Though HM-code divergence between duplicates in both promoter and ORF regions increase with their sequence divergence, the HM-code in ORF region evolves slower than that in promoter region, probably owing to the functional constraints imposed on protein sequences. After excluding the confounding effect of sequence divergence (or evolutionary time), we found the evidence supporting the notion that in yeast, the HM-code may co-evolve with cis- and trans-regulatory factors. Moreover, we observed that deletion of some yeast HM-related enzymes increases the expression divergence between duplicate genes, yet the effect is lower than the case of transcription factor (TF) deletion or environmental stresses. Conclusions Our analyses demonstrate that after gene duplication, yeast histone modification profile between duplicates diverged with evolutionary time, similar to genetic regulatory elements. Moreover, we found the evidence of the co-evolution between genetic and epigenetic elements since gene duplication, together contributing to the expression divergence between duplicate genes. PMID:22776110

  5. The evolution of egg colour and patterning in birds.

    PubMed

    Kilner, R M

    2006-08-01

    Avian eggs differ so much in their colour and patterning from species to species that any attempt to account for this diversity might initially seem doomed to failure. Here I present a critical review of the literature which, when combined with the results of some comparative analyses, suggests that just a few selective agents can explain much of the variation in egg appearance. Ancestrally, bird eggs were probably white and immaculate. Ancient diversification in nest location, and hence in the clutch's vulnerability to attack by predators, can explain basic differences between bird families in egg appearance. The ancestral white egg has been retained by species whose nests are safe from attack by predators, while those that have moved to a more vulnerable nest site are now more likely to lay brown eggs, covered in speckles, just as Wallace hypothesized more than a century ago. Even blue eggs might be cryptic in a subset of nests built in vegetation. It is possible that some species have subsequently turned these ancient adaptations to new functions, for example to signal female quality, to protect eggs from damaging solar radiation, or to add structural strength to shells when calcium is in short supply. The threat of predation, together with the use of varying nest sites, appears to have increased the diversity of egg colouring seen among species within families, and among clutches within species. Brood parasites and their hosts have probably secondarily influenced the diversity of egg appearance. Each drives the evolution of the other's egg colour and patterning, as hosts attempt to avoid exploitation by rejecting odd-looking eggs from their nests, and parasites attempt to outwit their hosts by laying eggs that will escape detection. This co-evolutionary arms race has increased variation in egg appearance both within and between species, in parasites and in hosts, sometimes resulting in the evolution of egg colour polymorphisms. It has also reduced variation in

  6. Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

    PubMed Central

    Moyers, Bryan A.; Zhang, Jianzhi

    2015-01-01

    Phylostratigraphy is a method for dating the evolutionary emergence of a gene or gene family by identifying its homologs across the tree of life, typically by using BLAST searches. Applying this method to all genes in a species, or genomic phylostratigraphy, allows investigation of genome-wide patterns in new gene origination at different evolutionary times and thus has been extensively used. However, gene age estimation depends on the challenging task of detecting distant homologs via sequence similarity, which is expected to have differential accuracies for different genes. Here, we evaluate the accuracy of phylostratigraphy by realistic computer simulation with parameters estimated from genomic data, and investigate the impact of its error on findings of genome evolution. We show that 1) phylostratigraphy substantially underestimates gene age for a considerable fraction of genes, 2) the error is especially serious when the protein evolves rapidly, is short, and/or its most conserved block of sites is small, and 3) these errors create spurious nonuniform distributions of various gene properties among age groups, many of which cannot be predicted a priori. Given the high likelihood that conclusions about gene age are faulty, we advocate the use of realistic simulation to determine if observations from phylostratigraphy are explainable, at least qualitatively, by a null model of biased measurement, and in all cases, critical evaluation of results. PMID:25312911

  7. Macroevolutionary assembly of ant/plant symbioses: Pseudomyrmex ants and their ant-housing plants in the Neotropics.

    PubMed

    Chomicki, Guillaume; Ward, Philip S; Renner, Susanne S

    2015-11-22

    Symbioses include some of the clearest cases of coevolution, but their origin, loss or reassembly with different partners can rarely be inferred. Here we use ant/plant symbioses involving three plant clades to investigate the evolution of symbioses. We generated phylogenies for the big-eyed arboreal ants (Pseudomyrmecinae), including 72% of their 286 species, as well as for five of their plant host groups, in each case sampling more than 61% of the species. We show that the ant-housing Vachellia (Mimosoideae) clade and its ants co-diversified for the past 5 Ma, with some species additionally colonized by younger plant-nesting ant species, some parasitic. An apparent co-radiation of ants and Tachigali (Caesalpinioideae) was followed by waves of colonization by the same ant clade, and subsequent occupation by a younger ant group. Wide crown and stem age differences between the ant-housing genus Triplaris (Polygonaceae) and its obligate ant inhabitants, and stochastic trait mapping, indicate that its domatium evolved earlier than the ants now occupying it, suggesting previous symbioses that dissolved. Parasitic ant species evolved from generalists, not from mutualists, and are younger than the mutualistic systems they parasitize. Our study illuminates the macroevolutionary assembly of ant/plant symbioses, which has been highly dynamic, even in very specialized systems. PMID:26582029

  8. A systems-analytical approach to macro-evolutionary phenomena.

    PubMed

    Riedl, R

    1977-12-01

    Two sets of evolutionary phenomena find no explanation through current theory. For the static phenomena (such as homology, homonomy, systematic weight, and "Type") there is no causal base, although these principles are responsible for all phenomena of predictable order in the living world. The dynamic phenomena (such as homodynamy, coadaptation, parallel evolution, orthogenesis, Cartesian transformation, typostrophy, hetermorphosis, systemic mutation, and spontaneous atavism) have no causal explanation, although they are responsible for all directed phenomena in macroevolution. These phenomena share one unifying principle which can be explained by a system theory of evolution based on, but extending, the current synthetic theory. This system theory envisages feedback conditions between genotype and phenotype by which the chances of successful adaptation increase if the genetic units, by insertion of superimposed genes, copy the functional dependencies of those phene structures for which they code. This positive feedback of the adaptive speed (or probability) within a single adaptive direction is compensated by negative feedback in most of the alternative directions. The negative feedback operates as selection not be environmental but by systemic conditions developed by the organization of the organism. The consequences are an imitatively organized system of gene interractions, the rehabilitation of classical systematics, the reality of the "natural system," and, in general, the resolution of the contradiction between neodarwinists and their critics, between reductionists and holists, between "a priori" and "a posteriori" views, between idealism and materialism, and between the notions of freedom and of purpose in evolution. PMID:343152

  9. Influence of continental history on the ecological specialization and macroevolutionary processes in the mammalian assemblage of South America: Differences between small and large mammals

    PubMed Central

    2008-01-01

    mammalian evolution. Nevertheless, deviations from the expectations indicate the importance of differences in reproductive traits and paleobiogeographic history for the macroevolutionary processes involved. In the case of South American mammals, the Pliocene Great American Biotic Interchange strongly influences the ecological characteristics of this assemblage. Furthermore, the Andes have acted as a fertile ground for speciation in environments prone to vicariance. Finally, the micromammals appear as more prone to biomic specialization than larger species. These factors are responsible for some of the differences found between South America and Africa in the studied pattern. For example, the extensive South American mountain ranges favour a higher number of combinations of inhabited biomes in comparison with Africa. PMID:18366786

  10. The evolution of pattern camouflage strategies in waterfowl and game birds.

    PubMed

    Marshall, Kate L A; Gluckman, Thanh-Lan

    2015-05-01

    Visual patterns are common in animals. A broad survey of the literature has revealed that different patterns have distinct functions. Irregular patterns (e.g., stipples) typically function in static camouflage, whereas regular patterns (e.g., stripes) have a dual function in both motion camouflage and communication. Moreover, irregular and regular patterns located on different body regions ("bimodal" patterning) can provide an effective compromise between camouflage and communication and/or enhanced concealment via both static and motion camouflage. Here, we compared the frequency of these three pattern types and traced their evolutionary history using Bayesian comparative modeling in aquatic waterfowl (Anseriformes: 118 spp.), which typically escape predators by flight, and terrestrial game birds (Galliformes: 170 spp.), which mainly use a "sit and hide" strategy to avoid predation. Given these life histories, we predicted that selection would favor regular patterning in Anseriformes and irregular or bimodal patterning in Galliformes and that pattern function complexity should increase over the course of evolution. Regular patterns were predominant in Anseriformes whereas regular and bimodal patterns were most frequent in Galliformes, suggesting that patterns with multiple functions are broadly favored by selection over patterns with a single function in static camouflage. We found that the first patterns to evolve were either regular or bimodal in Anseriformes and either irregular or regular in Galliformes. In both orders, irregular patterns could evolve into regular patterns but not the reverse. Our hypothesis of increasing complexity in pattern camouflage function was supported in Galliformes but not in Anseriformes. These results reveal a trajectory of pattern evolution linked to increasing function complexity in Galliformes although not in Anseriformes, suggesting that both ecology and function complexity can have a profound influence on pattern evolution

  11. The evolution of pattern camouflage strategies in waterfowl and game birds

    PubMed Central

    Marshall, Kate L A; Gluckman, Thanh-Lan

    2015-01-01

    Visual patterns are common in animals. A broad survey of the literature has revealed that different patterns have distinct functions. Irregular patterns (e.g., stipples) typically function in static camouflage, whereas regular patterns (e.g., stripes) have a dual function in both motion camouflage and communication. Moreover, irregular and regular patterns located on different body regions (“bimodal” patterning) can provide an effective compromise between camouflage and communication and/or enhanced concealment via both static and motion camouflage. Here, we compared the frequency of these three pattern types and traced their evolutionary history using Bayesian comparative modeling in aquatic waterfowl (Anseriformes: 118 spp.), which typically escape predators by flight, and terrestrial game birds (Galliformes: 170 spp.), which mainly use a “sit and hide” strategy to avoid predation. Given these life histories, we predicted that selection would favor regular patterning in Anseriformes and irregular or bimodal patterning in Galliformes and that pattern function complexity should increase over the course of evolution. Regular patterns were predominant in Anseriformes whereas regular and bimodal patterns were most frequent in Galliformes, suggesting that patterns with multiple functions are broadly favored by selection over patterns with a single function in static camouflage. We found that the first patterns to evolve were either regular or bimodal in Anseriformes and either irregular or regular in Galliformes. In both orders, irregular patterns could evolve into regular patterns but not the reverse. Our hypothesis of increasing complexity in pattern camouflage function was supported in Galliformes but not in Anseriformes. These results reveal a trajectory of pattern evolution linked to increasing function complexity in Galliformes although not in Anseriformes, suggesting that both ecology and function complexity can have a profound influence on pattern

  12. Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution

    PubMed Central

    Patterson, Larissa B.; Bain, Emily J.; Parichy, David M.

    2014-01-01

    Fishes have diverse pigment patterns, yet mechanisms of pattern evolution remain poorly understood. In zebrafish, Danio rerio, pigment-cell autonomous interactions generate dark stripes of melanophores that alternate with light interstripes of xanthophores and iridophores. Here, we identify mechanisms underlying the evolution of a uniform pattern in D. albolineatus in which all three pigment cell classes are intermingled. We show that in this species xanthophores differentiate precociously over a wider area, and that cis regulatory evolution has increased expression of xanthogenic Colony Stimulating Factor-1 (Csf1). Expressing Csf1 similarly in D. rerio has cascading effects, driving the intermingling of all three pigment cell classes and resulting in the loss of stripes, as in D. albolineatus. Our results identify novel mechanisms of pattern development and illustrate how pattern diversity can be generated when a core network of pigment-cell autonomous interactions is coupled with changes in pigment cell differentiation. PMID:25374113

  13. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

    PubMed

    Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

    2014-12-12

    To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

  14. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

    PubMed Central

    Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

    2015-01-01

    To provide context for the diversifications of archosaurs, the group that includes crocodilians, dinosaurs and birds, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the relatively rapid evolution of bird genomes represents an autapomorphy within that clade. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

  15. Evolution of Fractal Patterns during a Classical-Quantum Transition

    SciTech Connect

    Micolich, A. P.; Taylor, R. P.; Davies, A. G.; Bird, J. P.; Newbury, R.; Fromhold, T. M.; Ehlert, A.; Linke, H.; Macks, L. D.; Tribe, W. R.

    2001-07-16

    We investigate how fractals evolve into nonfractal behavior as the generation process is gradually suppressed. Fractals observed in the conductance of semiconductor billiards are of particular interest because the generation process is semiclassical and can be suppressed by transitions towards either fully classical or fully quantum-mechanical conduction. Investigating a range of billiards, we identify a ''universal'' behavior in the changeover from fractal to nonfractal conductance, which is described by a smooth evolution rather than deterioration in the fractal scaling properties.

  16. Phenotypic Evolution in Fossil Species: Pattern and Process

    NASA Astrophysics Data System (ADS)

    Hunt, Gene; Rabosky, Daniel L.

    2014-05-01

    Since Darwin, scientists have looked to the fossil record with the hope of using it to document how the phenotypes of species change over substantial periods of time. How best to interpret this record has been controversial, but empirical and methodological advances have resolved at least two issues about pattern: (a) directional transformations are seldom sustained over geological timescales, and (b) net rates of morphological change in fossil species are usually quite slow. Considerable uncertainty remains, however, about the processes responsible for these patterns, but most fruitful explanations use the framework of adaptive landscapes to consider the role of natural selection and other processes. An additional, unresolved issue is the claim that most phenotypic change is associated with speciation. A variety of methods, using data from both fossil and extant species, have supported such a link, at least in some clades and traits, but its prevalence and underlying mechanism remain unresolved.

  17. Convergent evolution in locomotory patterns of flying and swimming animals.

    PubMed

    Gleiss, Adrian C; Jorgensen, Salvador J; Liebsch, Nikolai; Sala, Juan E; Norman, Brad; Hays, Graeme C; Quintana, Flavio; Grundy, Edward; Campagna, Claudio; Trites, Andrew W; Block, Barbara A; Wilson, Rory P

    2011-01-01

    Locomotion is one of the major energetic costs faced by animals and various strategies have evolved to reduce its cost. Birds use interspersed periods of flapping and gliding to reduce the mechanical requirements of level flight while undergoing cyclical changes in flight altitude, known as undulating flight. Here we equipped free-ranging marine vertebrates with accelerometers and demonstrate that gait patterns resembling undulating flight occur in four marine vertebrate species comprising sharks and pinnipeds. Both sharks and pinnipeds display intermittent gliding interspersed with powered locomotion. We suggest, that the convergent use of similar gait patterns by distinct groups of animals points to universal physical and physiological principles that operate beyond taxonomic limits and shape common solutions to increase energetic efficiency. Energetically expensive large-scale migrations performed by many vertebrates provide common selection pressure for efficient locomotion, with potential for the convergence of locomotory strategies by a wide variety of species. PMID:21673673

  18. The evolution of embryonic patterning mechanisms in animals

    NASA Technical Reports Server (NTRS)

    Wray, G. A.

    2000-01-01

    Animals exhibit an enormous diversity of life cycles and larval morphologies. The developmental basis for this diversity is not well understood. It is clear, however, that mechanisms of pattern formation in early embryos differ significantly among and within groups of animals. These differences show surprisingly little correlation with phylogenetic relationships; instead, many are correlated with ecological factors, such as changes in life histories. Copyright 2000 Academic Press.

  19. Quantitative patterns of stylistic influence in the evolution of literature

    PubMed Central

    Hughes, James M.; Foti, Nicholas J.; Krakauer, David C.; Rockmore, Daniel N.

    2012-01-01

    Literature is a form of expression whose temporal structure, both in content and style, provides a historical record of the evolution of culture. In this work we take on a quantitative analysis of literary style and conduct the first large-scale temporal stylometric study of literature by using the vast holdings in the Project Gutenberg Digital Library corpus. We find temporal stylistic localization among authors through the analysis of the similarity structure in feature vectors derived from content-free word usage, nonhomogeneous decay rates of stylistic influence, and an accelerating rate of decay of influence among modern authors. Within a given time period we also find evidence for stylistic coherence with a given literary topic, such that writers in different fields adopt different literary styles. This study gives quantitative support to the notion of a literary “style of a time” with a strong trend toward increasingly contemporaneous stylistic influence. PMID:22547796

  20. Quantitative patterns of stylistic influence in the evolution of literature.

    PubMed

    Hughes, James M; Foti, Nicholas J; Krakauer, David C; Rockmore, Daniel N

    2012-05-15

    Literature is a form of expression whose temporal structure, both in content and style, provides a historical record of the evolution of culture. In this work we take on a quantitative analysis of literary style and conduct the first large-scale temporal stylometric study of literature by using the vast holdings in the Project Gutenberg Digital Library corpus. We find temporal stylistic localization among authors through the analysis of the similarity structure in feature vectors derived from content-free word usage, nonhomogeneous decay rates of stylistic influence, and an accelerating rate of decay of influence among modern authors. Within a given time period we also find evidence for stylistic coherence with a given literary topic, such that writers in different fields adopt different literary styles. This study gives quantitative support to the notion of a literary "style of a time" with a strong trend toward increasingly contemporaneous stylistic influence. PMID:22547796

  1. Neotectonics, flooding patterns and landscape evolution in southern Amazonia

    NASA Astrophysics Data System (ADS)

    Lombardo, U.

    2014-12-01

    The paper examines the role of neotectonic activity in the evolution of the landscape in southern Amazonia during the Holocene. It uses both new and published data based on the analysis of remote sensing imagery and extensive field work in the Llanos de Moxos, Bolivian Amazon. The study of the region's modern and palaeorivers, ria lakes, palaeosols and topography provides a strong case in favour of the thesis that the northern part of the Llanos de Moxos constitutes the southern margin of the Fitzcarrald Arch and that it has experienced uplift during the Holocene. The paper assesses the extent and timing of the neotectonic activity in light of the new data and reconstructs the evolution of the landscape since the late Pleistocene. The evidence suggests that at least two uplift events took place: a first uplift in the late Pleistocene, which caused the formation of Lake Oceano, and a second uplift during the mid-Holocene, which formed Lake Rogaguado. These two uplifts appear to be linked to the knickpoints observed close to the towns of Guayaramerín and Puerto Siles respectively. The backwater effect due to these uplifts transformed the region's major rivers in seasonal ria lakes, causing the deposition of thick organic clay layers along the Beni, Mamoré and Madre de Dios river banks. I argue that neotectonic episodes could have dramatically changed the drainage of the Llanos de Moxos, determining its flooding regime, soil properties and forest-savannah ecotone. These results stress the need for geomorphologists, palaeo-ecologists and archaeologists to take into account neotectonics when reconstructing the region's past.

  2. Neotectonics, flooding patterns and landscape evolution in southern Amazonia

    NASA Astrophysics Data System (ADS)

    Lombardo, U.

    2014-07-01

    The paper examines the role of neotectonic activity in the evolution of the landscape in southern Amazonia during the Holocene. It uses both new and published data based on the analysis of remote sensing imagery and extensive field work in the Llanos de Moxos, Bolivian Amazon. The study of the region's modern and paleo rivers, ria lakes, paleosols and topography provides a strong case in favour of the thesis that the northern part of the Llanos de Moxos constitutes the southern margin of the Fitzcarrald arch and that it has experienced uplift during the Holocene. The paper assesses the extent and timing of the neotectonic activity in light of the new data and reconstructs the evolution of the landscape since the late Pleistocene. The evidence suggests that at least two uplift events took place: a first uplift in the late Pleistocene, which caused the formation of Lake Oceano, and a second uplift during the mid-Holocene, which formed Lake Rogaguado. These two uplifts appear to be linked to the knickpoints observed close to the towns of Guayaramerín and Puerto Siles respectively. The backwater effect due to these uplifts transformed the region's major rivers in seasonal ria lakes, causing the deposition of thick organic clay layers along the Beni, Mamoré and Madre de Dios river banks. I argue that neotectonic episodes could have dramatically changed the drainage of the Llanos, determining its flooding regime, soil properties and forest-savannah ecotone. These results stress the need for geomorphologists, paleoecologists and archaeologists to take into account neotectonics when reconstructing the region's past.

  3. Dental patterning in the earliest sharks: Implications for tooth evolution.

    PubMed

    Maisey, John G; Turner, Susan; Naylor, Gavin J P; Miller, Randall F

    2014-05-01

    Doliodus problematicus is the oldest known fossil shark-like fish with an almost intact dentition (Emsian, Lower Devonian, c. 397Ma). We provide a detailed description of the teeth and dentition in D. problematicus, based on tomographic analysis of NBMG 10127 (New Brunswick Museum, Canada). Comparisons with modern shark dentitions suggest that Doliodus was a ram-feeding predator with a dentition adapted to seizing and disabling prey. Doliodus provides several clues about the early evolution of the "shark-like" dentition in chondrichthyans and also raises new questions about the evolution of oral teeth in jawed vertebrates. As in modern sharks, teeth in Doliodus were replaced in a linguo-labial sequence within tooth families at fixed positions along the jaws (12-14 tooth families per jaw quadrant in NBMG 10127). Doliodus teeth were replaced much more slowly than in modern sharks. Nevertheless, its tooth formation was apparently as highly organized as in modern elasmobranchs, in which future tooth positions are indicated by synchronized expression of shh at fixed loci within the dental epithelium. Comparable dental arrays are absent in osteichthyans, placoderms, and many "acanthodians"; a "shark-like" dentition, therefore, may be a synapomorphy of chondrichthyans and gnathostomes such as Ptomacanthus. The upper anterior teeth in Doliodus were not attached to the palatoquadrates, but were instead supported by the ethmoid region of the prechordal basicranium, as in some other Paleozoic taxa (e.g., Triodus, Ptomacanthus). This suggests that the chondrichthyan dental lamina was originally associated with prechordal basicranial cartilage as well as jaw cartilage, and that the modern elasmobranch condition (in which the oral dentition is confined to the jaws) is phylogenetically advanced. Thus, oral tooth development in modern elasmobranchs does not provide a complete developmental model for chondrichthyans or gnathostomes. PMID:24347366

  4. Similar patterns of cortical expansion during human development and evolution

    PubMed Central

    Hill, Jason; Inder, Terrie; Neil, Jeffrey; Dierker, Donna; Harwell, John; Van Essen, David

    2010-01-01

    The cerebral cortex of the human infant at term is complexly folded in a similar fashion to adult cortex but has only one third the total surface area. By comparing 12 healthy infants born at term with 12 healthy young adults, we demonstrate that postnatal cortical expansion is strikingly nonuniform: regions of lateral temporal, parietal, and frontal cortex expand nearly twice as much as other regions in the insular and medial occipital cortex. This differential postnatal expansion may reflect regional differences in the maturity of dendritic and synaptic architecture at birth and/or in the complexity of dendritic and synaptic architecture in adults. This expression may also be associated with differential sensitivity of cortical circuits to childhood experience and insults. By comparing human and macaque monkey cerebral cortex, we infer that the pattern of human evolutionary expansion is remarkably similar to the pattern of human postnatal expansion. To account for this correspondence, we hypothesize that it is beneficial for regions of recent evolutionary expansion to remain less mature at birth, perhaps to increase the influence of postnatal experience on the development of these regions or to focus prenatal resources on regions most important for early survival. PMID:20624964

  5. Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?

    PubMed

    Rivas-Ubach, Albert; Hódar, José A; Sardans, Jordi; Kyle, Jennifer E; Kim, Young-Mo; Oravec, Michal; Urban, Otmar; Guenther, Alex; Peñuelas, Josep

    2016-07-01

    The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but also the entire metabolome. Metabolomes are the final products of genotypes and are constrained by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from three closely related Pinus species with distant coevolutionary histories with the caterpillar of the processionary moth respond similarly to its attack. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of terpenes were in the attacked trees supporting the hypothesis that herbivores avoid plant individuals with higher concentrations. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant-insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade-offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant-insect coevolution. PMID:27386082

  6. Not just black and white: pigment pattern development and evolution in vertebrates

    PubMed Central

    Mills, Margaret G.; Patterson, Larissa B.

    2009-01-01

    Animals display diverse colors and patterns that vary within and between species. Similar phenotypes appear in both closely related and widely divergent taxa. Pigment patterns thus provide an opportunity to explore how development is altered to produce differences in form and whether similar phenotypes share a common genetic basis. Understanding the development and evolution of pigment patterns requires knowledge of the cellular interactions and signaling pathways that produce those patterns. These complex traits provide unparalleled opportunities for integrating studies from ecology and behavior to molecular biology and biophysics. PMID:19073271

  7. Temporal evolution of the chemical structure during the pattern transfer by ion-beam sputtering

    NASA Astrophysics Data System (ADS)

    Ha, N.-B.; Jeong, S.; Yu, S.; Ihm, H.-I.; Kim, J.-S.

    2015-01-01

    Ru films patterned by ion-beam sputtering (IBS) serve as sacrificial masks for the transfer of the patterns to Si(1 0 0) and metallic glass substrates by continued IBS. Under the same sputter condition, however, both bare substrates remain featureless. Chemical analyses of the individual nano structures simultaneously with the investigation of their morphological evolution reveal that the pattern transfer, despite its apparent success, suffers from premature degradation before the mask is fully removed by IBS. Moreover, the residue of the mask or Ru atoms stubbornly remains near the surface, resulting in unintended doping or alloying of both patterned substrates.

  8. Dorsoventral Patterning in Hemichordates: Insights into Early Chordate Evolution

    PubMed Central

    Lowe, Christopher J; Terasaki, Mark; Wu, Michael; Freeman, Robert M; Runft, Linda; Kwan, Kristen; Haigo, Saori; Aronowicz, Jochanan; Lander, Eric; Gruber, Chris; Smith, Mark; Kirschner, Marc; Gerhart, John

    2006-01-01

    We have compared the dorsoventral development of hemichordates and chordates to deduce the organization of their common ancestor, and hence to identify the evolutionary modifications of the chordate body axis after the lineages split. In the hemichordate embryo, genes encoding bone morphogenetic proteins (Bmp) 2/4 and 5/8, as well as several genes for modulators of Bmp activity, are expressed in a thin stripe of ectoderm on one midline, historically called “dorsal.” On the opposite midline, the genes encoding Chordin and Anti-dorsalizing morphogenetic protein (Admp) are expressed. Thus, we find a Bmp-Chordin developmental axis preceding and underlying the anatomical dorsoventral axis of hemichordates, adding to the evidence from Drosophila and chordates that this axis may be at least as ancient as the first bilateral animals. Numerous genes encoding transcription factors and signaling ligands are expressed in the three germ layers of hemichordate embryos in distinct dorsoventral domains, such as pox neuro, pituitary homeobox, distalless, and tbx2/3 on the Bmp side and netrin, mnx, mox, and single-minded on the Chordin-Admp side. When we expose the embryo to excess Bmp protein, or when we deplete endogenous Bmp by small interfering RNA injections, these expression domains expand or contract, reflecting their activation or repression by Bmp, and the embryos develop as dorsalized or ventralized limit forms. Dorsoventral patterning is independent of anterior/posterior patterning, as in Drosophila but not chordates. Unlike both chordates and Drosophila, neural gene expression in hemichordates is not repressed by high Bmp levels, consistent with their development of a diffuse rather than centralized nervous system. We suggest that the common ancestor of hemichordates and chordates did not use its Bmp-Chordin axis to segregate epidermal and neural ectoderm but to pattern many other dorsoventral aspects of the germ layers, including neural cell fates within a diffuse

  9. Patterning and evolution of floral structures - marking time.

    PubMed

    McKim, Sarah; Hay, Angela

    2010-08-01

    The diversity of flowering structures dazzles the eye, dominates the landscape, and invites evolutionary questions regarding the development of such variety. Comparative work in a number of genetically tractable plant species has addressed how diverse floral architectures develop, and started to reveal the balance between conservation and divergence of the patterning mechanisms responsible for when and where flowers form on a plant. We highlight findings from Petunia where conserved LFY/UFO function is under species-specific regulation, and a novel mechanism involving WOX homeodomain proteins for modulating cyme development in diverse nightshades. We also draw attention to recent findings in Arabidopsis of miRNA and chromatin-based timing mechanisms controlling floral development, and illustrate how genetic studies in Arabidopsis relatives can reveal how evolutionary changes in such mechanisms generate diversity in form. PMID:20452201

  10. Dynamic pattern evolution on scale-free networks

    PubMed Central

    Zhou, Haijun; Lipowsky, Reinhard

    2005-01-01

    A general class of dynamic models on scale-free networks is studied by analytical methods and computer simulations. Each network consists of N vertices and is characterized by its degree distribution, P(k), which represents the probability that a randomly chosen vertex is connected to k nearest neighbors. Each vertex can attain two internal states described by binary variables or Ising-like spins that evolve in time according to local majority rules. Scale-free networks, for which the degree distribution has a power law tail P(k) ∼ k-γ, are shown to exhibit qualitatively different dynamic behavior for γ < 5/2 and γ > 5/2, shedding light on the empirical observation that many real-world networks are scale-free with 2 < γ < 5/2. For 2 < γ < 5/2, strongly disordered patterns decay within a finite decay time even in the limit of infinite networks. For γ > 5/2, on the other hand, this decay time diverges as ln(N) with the network size N. An analogous distinction is found for a variety of more complex models including Hopfield models for associative memory networks. In the latter case, the storage capacity is found, within mean field theory, to be independent of N in the limit of large N for γ > 5/2 but to grow as Nα with α = (5 - 2γ)/(γ - 1) for 2 < γ < 5/2. PMID:16006533

  11. The pattern of phylogenomic evolution of the Canidae.

    PubMed

    Nash, W G; Menninger, J C; Wienberg, J; Padilla-Nash, H M; O'Brien, S J

    2001-01-01

    Canidae species fall into two categories with respect to their chromosome composition: those with high numbered largely acrocentric karyotypes and others with a low numbered principally metacentric karyotype. Those species with low numbered metacentric karyotypes are derived from multiple independent fusions of chromosome segments found as acrocentric chromosomes in the high numbered species. Extensive chromosome homology is apparent among acrocentric chromosome arms within Canidae species; however, little chromosome arm homology exists between Canidae species and those from other Carnivore families. Here we use Zoo-FISH (fluorescent in situ hybridization, also called chromosomal painting) probes from flow-sorted chromosomes of the Japanese raccoon dog (Nyctereutes procyonoides) to examine two phylogenetically divergent canids, the arctic fox (Alopex lagopus) and the crab-eating fox (Cerdocyon thous). The results affirm intra-canid chromosome homologies, also implicated by G-banding. In addition, painting probes from domestic cat (Felis catus), representative of the ancestral carnivore karyotype (ACK), and giant panda (Ailuropoda melanoleuca) were used to define primitive homologous segments apparent between canids and other carnivore families. Canid chromosomes seem unique among carnivores in that many canid chromosome arms are mosaics of two to four homology segments of the ACK chromosome arms. The mosaic pattern apparently preceded the divergence of modern canid species since conserved homology segments among different canid species are common, even though those segments are rearranged relative to the ancestral carnivore genome arrangement. The results indicate an ancestral episode of extensive centric fission leading to an ancestral canid genome organization that was subsequently reorganized by multiple chromosome fusion events in some but not all Canidae lineages. PMID:12063402

  12. Evolution patterns and parameter regimes in edge localized modes on the National Spherical Torus Experiment

    NASA Astrophysics Data System (ADS)

    Smith, D. R.; Fonck, R. J.; McKee, G. R.; Diallo, A.; Kaye, S. M.; LeBlanc, B. P.; Sabbagh, S. A.

    2016-04-01

    We implement unsupervised machine learning techniques to identify characteristic evolution patterns and associated parameter regimes in edge localized mode (ELM) events observed on the National Spherical Torus Experiment. Multi-channel, localized measurements spanning the pedestal region capture the complex evolution patterns of ELM events on Alfvén timescales. Some ELM events are active for less than 100 μs, but others persist for up to 1 ms. Also, some ELM events exhibit a single dominant perturbation, but others are oscillatory. Clustering calculations with time-series similarity metrics indicate the ELM database contains at least two and possibly three groups of ELMs with similar evolution patterns. The identified ELM groups trigger similar stored energy loss, but the groups occupy distinct parameter regimes for ELM-relevant quantities like plasma current, triangularity, and pedestal height. Notably, the pedestal electron pressure gradient is not an effective parameter for distinguishing the ELM groups, but the ELM groups segregate in terms of electron density gradient and electron temperature gradient. The ELM evolution patterns and corresponding parameter regimes can shape the formulation or validation of nonlinear ELM models. Finally, the techniques and results demonstrate an application of unsupervised machine learning at a data-rich fusion facility.

  13. Evolution patterns and parameter regimes in edge localized modes on the National Spherical Torus Experiment

    NASA Astrophysics Data System (ADS)

    Smith, David R.; Fonck, R. J.; McKee, G. R.; Diallo, A.; Kaye, S. M.; Leblanc, B. P.

    2015-11-01

    We implement unsupervised machine learning techniques to identify characteristic evolution patterns and associated parameter regimes in edge localized mode (ELM) events observed on the National Spherical Torus Experiment. Multi-channel, localized measurements spanning the pedestal region capture the complex evolution patterns of ELM events on Alfven timescales. Some ELM events are active for less than 100 micro-s, but others persist for up to 1 ms. Also, some ELM events exhibit a single dominant perturbation, but others are oscillatory. Clustering calculations with time-series similarity metrics indicate the ELM database contains at least two and possibly three groups of ELMs with similar evolution patterns. The identified ELM groups trigger similar stored energy loss, but the groups occupy distinct parameter regimes for ELM-relevant quantities like plasma current, triangularity, and pedestal height. Notably, the pedestal electron pressure gradient is not an effective parameter for distinguishing the ELM groups, but the ELM groups segregate in terms of electron density gradient and electron temperature gradient. The ELM evolution patterns and corresponding parameter regimes can shape the formulation or validation of nonlinear ELM models. Finally, the techniques and results demonstrate an application of unsupervised machine learning at a data-rich fusion facility. Supported by the US Dept. of Energy.

  14. Host resistance influences patterns of experimental viral adaptation and virulence evolution

    PubMed Central

    Kubinak, Jason L; Potts, Wayne K

    2013-01-01

    Infectious diseases are major threats to all living systems, so understanding the forces of selection that limit the evolution of more virulent pathogens is of fundamental importance; this includes the practical application of identifying possible mitigation strategies for at-risk host populations. The evolution of more virulent pathogens has been classically understood to be limited by the tradeoff between within-host growth rate and transmissibility. Importantly, heterogeneity among hosts can influence both of these factors. However, despite our substantial understanding of how the immune system operates to control pathogen replication during infection, we have only a limited appreciation of how variability in intrinsic (i.e., genetically determined) levels of host resistance influences patterns of pathogen adaptation and virulence evolution. Here, we describe results from experimental evolution studies using a model host–pathogen (virus–mammal) system; we demonstrate that variability in intrinsic levels of resistance among host genotypes can have significant effects on patterns of pathogen adaptation and virulence evolution during serial passage. Both the magnitude of adaptive response as well as the degree of pathogen specialization was positively correlated with host resistance, while mean overall virulence of post-passage virus was negatively correlated with host resistance. These results are consistent with a model whereby resistant host genotypes impose stronger selection on adapting pathogen populations, which in turn leads to the evolution of more specialized pathogen variants whose overall (i.e., mean) virulence across host genotypes is reduced. PMID:23645287

  15. a Quantitative Study of Pattern Evolution and Time Dependence in Rayleigh Benard Convection

    NASA Astrophysics Data System (ADS)

    Heutmaker, Michael Steven

    In a thin fluid layer, Rayleigh-Benard convection patterns typi- cally adapt to the geometry of the sidewalls through the formation of bent rolls and defects. Instead of a single wavenumber q, the two-dimensional wavevector field (')q((')r) must be used in order to quantitatively specify the structure of these textured patterns. Changes in the Rayleigh number R influence the form and stability of the flow. Quantitative measurements of the flow structure are needed to characterize stable and time-dependent regimes of pattern evolu- tion. In this investigation, digital image analysis was utilized to measure the wavevector field (')q((')r) from shadowgraph images. The local magnitude and direction of (')q were found from the spacing and orientation of roll boundaries. We found three regimes of pattern evolution. The stability of patterns in these regimes can be roughly predicted from a com- parison between the distribution of wavenumbers P(q) within the patterns and the band of stable wavenumbers predicted by non- linear stability theory. (1) Surprisingly, for R sufficiently close to the onset of convection (in the approximate range (epsilon) < 0.2, where (epsilon) = (R-R(,c))/R(,c)), flows are persistently and non-periodically time-dependent. (2) In an intermediate range 0.2 < (epsilon) < 3.5, textured patterns are stable. (3) Sufficiently far from onset, for (epsilon) > 3.5, patterns are non-periodically time-dependent. In the time-dependent regimes (1) and (3), P(q) exceeds the threshold of secondary instabilities that limit the stable wavenumber band. The presence of unstable wavenumbers provides a possible explanation for persistent time dependence close to onset, but stability theory alone cannot explain the variations of P(q) with (epsilon). We also compare transient evolution (regime (2) above) to the predictions of the Swift-Hohenberg model. In this model, pattern evolution minimizes a Lyapunov functional F, analogous to the mini- mization of the free energy

  16. Patterns of evolution of research strands in the hydrologic sciences

    NASA Astrophysics Data System (ADS)

    Schwartz, F. W.; Fang, Y. C.; Parthasarathy, S.

    2005-03-01

    This paper examines issues of impact and innovation in groundwater research by using bibliometric data and citation analysis.The analysis is based on 3120 papers from the journal Water Resources Research with full contents and their citation data from the ISI Web of Science. The research is designed to develop a better understanding of the way citation numbers can be interpreted by scientists. Not surprisingly, the most highly cited papers appear to be pioneers in the field with papers departing significantly from what has come before and to be effective in creating similar, follow-on papers. Papers that are early contributions to a new research strand that is highly influential will be on average highly cited. However, the importance of a research strand as measured by citations seems to fall with time. The citation patterns of some classic papers show that the activity in the topical area and impact of follow-on papers gradually decline with time, which has similarities with Kuhn's ideas of revolutionary and normal science. The results of this study reinforce the importance of being a pioneer in a research strand, strategically shifting research strands, adopting strategies that can facilitate really major research breakthroughs. L'article examine les problèmes d'impact et d'innovation dans la recherche des eaux souterraines en utilisant les données bibliométriques et l'analyse des citations. L'analyse a été faite sur 3120 articles parus dans Water Resources Research en tenant compte de leur texte complet et de toutes citations parues dans l' ISI Web de la Science. Le but de la recherche a été de mieux comprendre comment le nombre des citations peut être interprété par les scientifiques. Ce n'est pas une surprise que les plus cités articles soient les articles-pionniers dans leurs domaines, qui s'écartent d'une manière significative de ce qui a été écrit auparavant et qui ont été suivi par des nouveaux articles. Les articles qui présentent une

  17. Patterns of evolution of research strands in the hydrologic sciences

    NASA Astrophysics Data System (ADS)

    Schwartz, F. W.; Fang, Y. C.; Parthasarathy, S.

    2005-03-01

    This paper examines issues of impact and innovation in groundwater research by using bibliometric data and citation analysis.The analysis is based on 3120 papers from the journal Water Resources Research with full contents and their citation data from the ISI Web of Science. The research is designed to develop a better understanding of the way citation numbers can be interpreted by scientists. Not surprisingly, the most highly cited papers appear to be pioneers in the field with papers departing significantly from what has come before and to be effective in creating similar, follow-on papers. Papers that are early contributions to a new research strand that is highly influential will be on average highly cited. However, the importance of a research strand as measured by citations seems to fall with time. The citation patterns of some classic papers show that the activity in the topical area and impact of follow-on papers gradually decline with time, which has similarities with Kuhn's ideas of revolutionary and normal science. The results of this study reinforce the importance of being a pioneer in a research strand, strategically shifting research strands, adopting strategies that can facilitate really major research breakthroughs. L'article examine les problèmes d'impact et d'innovation dans la recherche des eaux souterraines en utilisant les données bibliométriques et l'analyse des citations. L'analyse a été faite sur 3120 articles parus dans Water Resources Research en tenant compte de leur texte complet et de toutes citations parues dans l' ISI Web de la Science. Le but de la recherche a été de mieux comprendre comment le nombre des citations peut être interprété par les scientifiques. Ce n'est pas une surprise que les plus cités articles soient les articles-pionniers dans leurs domaines, qui s'écartent d'une manière significative de ce qui a été écrit auparavant et qui ont été suivi par des nouveaux articles. Les articles qui présentent une

  18. Why colour in subterranean vertebrates? Exploring the evolution of colour patterns in caecilian amphibians.

    PubMed

    Wollenberg, K C; Measey, C John

    2009-05-01

    The proximate functions of animal skin colour are difficult to assign as they can result from natural selection, sexual selection or neutral evolution under genetic drift. Most often colour patterns are thought to signal visual stimuli; so,their presence in subterranean taxa is perplexing. We evaluate the adaptive nature of colour patterns in nearly a third of all known species of caecilians, an order of amphibians most of which live in tropical soils and leaf litter. We found that certain colour pattern elements in caecilians can be explained based on characteristics concerning above-ground movement. Our study implies that certain caecilian colour patterns have convergently evolved under selection and we hypothesize their function most likely to be a synergy of aposematism and crypsis, related to periods when individuals move overground. In a wider context, our results suggest that very little exposure to daylight is required to evolve and maintain a varied array of colour patterns in animal skin. PMID:21462404

  19. Cellular pattern evolution in gaseous detonation diffraction in a 90-degree-branched channel

    SciTech Connect

    Guo, Changming; Wang, Changjian; Xu, Shengli; Zhang, Hanhong

    2007-02-15

    This paper presents recent results of an experimental investigation on gaseous detonation diffraction in a 90-degree-branched channel. The entire process of diffraction is demonstrated by cellular patterns and the analysis is mainly based on their evolution. Detonation pressure history and velocity are measured and the corresponding cellular patterns are recorded on soot foils around the branched segment. Results show that detonation propagation is notably disturbed by the branched wall geometry and that a complex wave configuration appears in both channels. Cellular patterns show that an expansion fan appears at the T-junction area with a Mach reflection taking place in the horizontal channel, while regular reflection takes place in the vertical channel. Subsequently, it appears that there is a transition from a regular reflection to a Mach reflection in the vertical channel. Details of the cellular pattern indicate that from the early stage to the end of diffraction, the detonation wave sequentially experiences attenuation, front decoupling, and degradation into deflagration, reinitiation, and recuperation. According to cellular pattern evolution and velocity measurement, a recuperated detonation with nearly the same velocity as the undisturbed incoming wave finally develops downstream in both channels, at a distance of about four times the channel height (160 mm). The mechanism of diffraction is explored based on the ZND (Zel'dovich-von Neumann-Doering) model, and the soot foils in both channels show a pattern consistent with air shock-wave diffraction in a 90-degree-branched channel. (author)

  20. What explains patterns of species richness? The relative importance of climatic-niche evolution, morphological evolution, and ecological limits in salamanders.

    PubMed

    Kozak, Kenneth H; Wiens, John J

    2016-08-01

    A major goal of evolutionary biology and ecology is to understand why species richness varies among clades. Previous studies have suggested that variation in richness among clades might be related to variation in rates of morphological evolution among clades (e.g., body size and shape). Other studies have suggested that richness patterns might be related to variation in rates of climatic-niche evolution. However, few studies, if any, have tested the relative importance of these variables in explaining patterns of richness among clades. Here, we test their relative importance among major clades of Plethodontidae, the most species-rich family of salamanders. Earlier studies have suggested that climatic-niche evolution explains patterns of diversification among plethodontid clades, whereas rates of morphological evolution do not. A subsequent study stated that rates of morphological evolution instead explained patterns of species richness among plethodontid clades (along with "ecological limits" on richness of clades, leading to saturation of clades with species, given limited resources). However, they did not consider climatic-niche evolution. Using phylogenetic multiple regression, we show that rates of climatic-niche evolution explain most variation in richness among plethodontid clades, whereas rates of morphological evolution do not. We find little evidence that ecological limits explain patterns of richness among plethodontid clades. We also test whether rates of morphological and climatic-niche evolution are correlated, and find that they are not. Overall, our results help explain richness patterns in a major amphibian group and provide possibly the first test of the relative importance of climatic niches and morphological evolution in explaining diversity patterns. PMID:27547367

  1. Derivation of a Differential Equation Exhibiting Replicative Time-Evolution Patterns by Inverse Ultra-Discretization

    NASA Astrophysics Data System (ADS)

    Tanaka, Hiroshi; Nakajima, Asumi; Nishiyama, Akinobu; Tokihiro, Tetsuji

    2009-03-01

    A differential equation exhibiting replicative time-evolution patterns is derived by inverse ultradiscretizatrion of Fredkin’s game, which is one of the simplest replicative cellular automaton (CA) in two dimensions. This is achieved by employing a certain filter and a clock function in the equation. These techniques are applicable to the inverse ultra-discretization (IUD) of other CA and stabilize the time-evolution of the obtained differential equation. Application to the game of life, another CA in two dimensions, is also presented.

  2. Characteristics of pattern formation and evolution in approximations of Physarum transport networks.

    PubMed

    Jones, Jeff

    2010-01-01

    Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation. PMID:20067403

  3. The macroevolutionary consequences of phenotypic integration: from development to deep time

    PubMed Central

    Goswami, A.; Smaers, J. B.; Soligo, C.; Polly, P. D.

    2014-01-01

    Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. Phenotypic integration and modularity have been hypothesized to shape morphological evolution, and we extended simulations to confirm that trait integration can influence both the trajectory and magnitude of response to selection. We further demonstrate that phenotypic integration can produce both more and less disparate organisms than would be expected under random walk models by repartitioning variance in preferred directions. This effect can also be expected to favour homoplasy and convergent evolution. New empirical analyses of the carnivoran cranium show that rates of evolution, in contrast, are not strongly influenced by phenotypic integration and show little relationship to morphological disparity, suggesting that phenotypic integration may shape the direction of evolutionary change, but not necessarily the speed of it. Nonetheless, phenotypic integration is problematic for morphological clocks and should be incorporated more widely into models that seek to accurately reconstruct both trait and organismal evolution. PMID:25002699

  4. Time Curves: Folding Time to Visualize Patterns of Temporal Evolution in Data.

    PubMed

    Bach, Benjamin; Shi, Conglei; Heulot, Nicolas; Madhyastha, Tara; Grabowski, Tom; Dragicevic, Pierre

    2016-01-01

    We introduce time curves as a general approach for visualizing patterns of evolution in temporal data. Examples of such patterns include slow and regular progressions, large sudden changes, and reversals to previous states. These patterns can be of interest in a range of domains, such as collaborative document editing, dynamic network analysis, and video analysis. Time curves employ the metaphor of folding a timeline visualization into itself so as to bring similar time points close to each other. This metaphor can be applied to any dataset where a similarity metric between temporal snapshots can be defined, thus it is largely datatype-agnostic. We illustrate how time curves can visually reveal informative patterns in a range of different datasets. PMID:26529718

  5. Decoupled temporal patterns of evolution and ecology in two post-Paleozoic clades

    NASA Technical Reports Server (NTRS)

    McKinney, F. K.; Lidgard, S.; Sepkoski, J. J. Jr; Taylor, P. D.

    1998-01-01

    Counts of taxonomic diversity are the prevailing standards for documenting large-scale patterns of evolution in the fossil record. However, the secular pattern of relative ecological importance between the bryozoan clades Cyclostomata and Cheilostomata is not reflected fully in compilations of generic diversity or within-fauna species richness, and the delayed ecological recovery of the Cheilostomata after the mass extinction at the Cretaceous-Tertiary boundary is missed entirely. These observations demonstrate that evolutionary success and ecological dominance can be decoupled and profoundly different, even over tens of millions of years.

  6. Phylomemetic patterns in science evolution--the rise and fall of scientific fields.

    PubMed

    Chavalarias, David; Cointet, Jean-Philippe

    2013-01-01

    We introduce an automated method for the bottom-up reconstruction of the cognitive evolution of science, based on big-data issued from digital libraries, and modeled as lineage relationships between scientific fields. We refer to these dynamic structures as phylomemetic networks or phylomemies, by analogy with biological evolution; and we show that they exhibit strong regularities, with clearly identifiable phylomemetic patterns. Some structural properties of the scientific fields - in particular their density -, which are defined independently of the phylomemy reconstruction, are clearly correlated with their status and their fate in the phylomemy (like their age or their short term survival). Within the framework of a quantitative epistemology, this approach raises the question of predictibility for science evolution, and sketches a prototypical life cycle of the scientific fields: an increase of their cohesion after their emergence, the renewal of their conceptual background through branching or merging events, before decaying when their density is getting too low. PMID:23408947

  7. Antigenic Patterns and Evolution of the Human Influenza A (H1N1) Virus

    PubMed Central

    Liu, Mi; Zhao, Xiang; Hua, Sha; Du, Xiangjun; Peng, Yousong; Li, Xiyan; Lan, Yu; Wang, Dayan; Wu, Aiping; Shu, Yuelong; Jiang, Taijiao

    2015-01-01

    The influenza A (H1N1) virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A deep understanding of the antigenic patterns and evolution of human influenza A (H1N1) virus is extremely important for its effective surveillance and prevention. Through development of antigenicity inference method for human influenza A (H1N1), named PREDAC-H1, we systematically mapped the antigenic patterns and evolution of the human influenza A (H1N1) virus. Eight dominant antigenic clusters have been inferred for seasonal H1N1 viruses since 1977, which demonstrated sequential replacements over time with a similar pattern in Asia, Europe and North America. Among them, six clusters emerged first in Asia. As for China, three of the eight antigenic clusters were detected in South China earlier than in North China, indicating the leading role of South China in H1N1 transmission. The comprehensive view of the antigenic evolution of human influenza A (H1N1) virus can help formulate better strategy for its prevention and control. PMID:26412348

  8. Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures

    PubMed Central

    Moore, Brian R.; Höhna, Sebastian; May, Michael R.; Rannala, Bruce; Huelsenbeck, John P.

    2016-01-01

    Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of BAMM reveals two major theoretical errors: (i) the likelihood function (which estimates the model parameters from the data) is incorrect, and (ii) the compound Poisson process prior model (which describes the prior distribution of diversification-rate shifts across branches) is incoherent. Using simulation, we demonstrate that these theoretical issues cause statistical pathologies; posterior estimates of the number of diversification-rate shifts are strongly influenced by the assumed prior, and estimates of diversification-rate parameters are unreliable. Moreover, the inability to correctly compute the likelihood or to correctly specify the prior for rate-variable trees precludes the use of Bayesian approaches for testing hypotheses regarding the number and location of diversification-rate shifts using BAMM. PMID:27512038

  9. Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures.

    PubMed

    Moore, Brian R; Höhna, Sebastian; May, Michael R; Rannala, Bruce; Huelsenbeck, John P

    2016-08-23

    Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of BAMM reveals two major theoretical errors: (i) the likelihood function (which estimates the model parameters from the data) is incorrect, and (ii) the compound Poisson process prior model (which describes the prior distribution of diversification-rate shifts across branches) is incoherent. Using simulation, we demonstrate that these theoretical issues cause statistical pathologies; posterior estimates of the number of diversification-rate shifts are strongly influenced by the assumed prior, and estimates of diversification-rate parameters are unreliable. Moreover, the inability to correctly compute the likelihood or to correctly specify the prior for rate-variable trees precludes the use of Bayesian approaches for testing hypotheses regarding the number and location of diversification-rate shifts using BAMM. PMID:27512038

  10. Complex and changing patterns of natural selection explain the evolution of the human hip.

    PubMed

    Grabowski, Mark; Roseman, Charles C

    2015-08-01

    Causal explanations for the dramatic changes that occurred during the evolution of the human hip focus largely on selection for bipedal function and locomotor efficiency. These hypotheses rest on two critical assumptions. The first-that these anatomical changes served functional roles in bipedalism-has been supported in numerous analyses showing how postcranial changes likely affected locomotion. The second-that morphological changes that did play functional roles in bipedalism were the result of selection for that behavior-has not been previously explored and represents a major gap in our understanding of hominin hip evolution. Here we use evolutionary quantitative genetic models to test the hypothesis that strong directional selection on many individual aspects of morphology was responsible for the large differences observed across a sample of fossil hominin hips spanning the Plio-Pleistocene. Our approach uses covariance among traits and the differences between relatively complete fossils to estimate the net selection pressures that drove the major transitions in hominin hip evolution. Our findings show a complex and changing pattern of natural selection drove hominin hip evolution, and that many, but not all, traits hypothesized to play functional roles in bipedalism evolved as a direct result of natural selection. While the rate of evolutionary change for all transitions explored here does not exceed the amount expected if evolution was occurring solely through neutral processes, it was far above rates of evolution for morphological traits in other mammalian groups. Given that stasis is the norm in the mammalian fossil record, our results suggest that large shifts in the adaptive landscape drove hominin evolution. PMID:26164108

  11. An Ecological Drill: Biogeomorphic Pattern Evolution in a Low-Relief Carbonate Landscape

    NASA Astrophysics Data System (ADS)

    Cohen, M. J.; Quintero, C.; Ward, N. D.; Raines, E.; Brown, A.; Martin, J. B.; Bianchi, T. S.; Mclaughlin, D. L.; Osborne, T.; Heffernan, J. B.; Watts, A.

    2015-12-01

    Feedbacks between hydrology, ecosystem metabolism, and mineral weathering are proposed to explain the striking geometric patterning of wetland basins in the low-relief carbonate landscape of Big Cypress (BICY) National Preserve in southwest Florida. In contrast to critical zone evolution in systems dominated by siliciclastic rocks, our conceptual model for this and other carbonate landscapes highlights the importance of congruent mineral weathering, which alters both the depth and geometry of the critical zone, and invokes metabolism as a core control on landscape morphology via impacts to CO2 acidity. In the case of BICY, our motivation is to understand the origins of visually compelling, and geostatistically regular, landscape patterning. Using preliminary evidence from archival data synthesis, lidar-derived elevations, field surveys of sediment thickness and vegetation biomass, characterization of deep sediment cores, and high temporal resolution measurements of water levels, solute concentrations, and gas fluxes we offer support for a conceptual model that invokes critical zone processes as the basis for Holocene pattern emergence. Of particular interest is our invocation of episodic landscape hydrologic connectivity as integral to pattern emergence. While our findings are specific to the unique features of this extremely flat eogenetic karst landscape where a clay confining unit precludes deep drainage feature evolution, we posit that the feedbacks between hydrology, ecosystem metabolism and carbonate weathering are general to critical zone processes in karst areas globally.

  12. Electrodeposition modeling and optimization to improve thin film patterning with orchestrated structure evolution

    NASA Astrophysics Data System (ADS)

    Abbasi, Shaghayegh; Kitayaporn, Sathana; Siedlik, Michael J.; Schwartz, Daniel T.; Böhringer, Karl F.

    2012-08-01

    Orchestrated structure evolution is an alternative nanomanufacturing approach that combines the advantages of top-down patterning and bottom-up self-organizing growth. It relies upon tool-directed patterning to create ‘seed’ locations on a surface from which a subsequent deposition process produces the final, merged film. Despite its demonstrated ability to reduce patterning time by orders of magnitude, our prior reliance on mass transfer limited deposition and square seed arrays resulted in extraneous film growth along pattern edges, thereby limiting the pattern quality of the final film. Here, quality improvements are demonstrated by modeling and tuning the growth mechanism of the deposition step to include charge transfer effects. In addition, a seed positioning optimization technique derived from simulated annealing is introduced as a method for relocating the seeds to minimize film overgrowth at the pattern edges. These improvements enable OSE to maintain geometric quality while substantially reducing the time and cost compared to traditional direct-write manufacturing methods.

  13. Patterns of philopatry and longevity contribute to the evolution of post-reproductive lifespan in mammals

    PubMed Central

    Zecherle, L.; Arbuckle, K.

    2016-01-01

    While menopause has long been known as a characteristic trait of human reproduction, evidence for post-reproductive lifespan (PRLS) has recently been found in other mammals. Adaptive and non-adaptive hypotheses have been proposed to explain the evolution of PRLS, but formal tests of these are rare. We use a phylogenetic approach to evaluate hypotheses for the evolution of PRLS among mammals. In contrast to theoretical models predicting that PRLS may be promoted by male philopatry (which increases relatedness between a female and her group in old age), we find little evidence that male philopatry led to the evolution of a post-reproductive period. However, the proportion of life spent post-reproductive was related to lifespan and patterns of philopatry, suggesting that the duration of PRLS may be impacted by both non-adaptive and adaptive processes. Finally, the proportion of females experiencing PRLS was higher in species with male philopaty and larger groups, in accordance with adaptive models of PRLS. We suggest that the origin of PRLS primarily follows the non-adaptive ‘mismatch’ scenario, but that patterns of philopatry may subsequently confer adaptive benefits of late-life helping. PMID:26888915

  14. Evolution of the insect terminal patterning system--insights from the milkweed bug, Oncopeltus fasciatus.

    PubMed

    Weisbrod, Anat; Cohen, Mira; Chipman, Ariel D

    2013-08-01

    The anterior and posterior ends of the insect embryo are patterned through the terminal patterning system, which is best known from the fruitfly Drosophila melanogaster. In Drosophila, the RTK receptor Torso and its presumed co-activator Torso-like initiate a signaling cascade, which activates two terminal gap genes, tailless and huckebein. These in turn interact with various patterning genes to define terminal structures. Work on other insect species has shown that this system is poorly conserved, and not all of its components have been found in all cases studied. We place the variability of the system within a broader phylogenetic framework. We describe the expression and knock-down phenotypes of the homologues of terminal patterning genes in the hemimetabolous Oncopeltus fasciatus. We have examined the interactions among these genes and between them and other patterning genes. We demonstrate that all of these genes have different roles in Oncopeltus relative to Drosophila; torso-like is expressed in follicle cells during oogenesis and is involved in the invagination of the blastoderm to form the germ band, and possibly also in defining the growth zone; tailless is regulated by orthodenticle and has a role only in anterior determination; huckebein is expressed only in the middle of the blastoderm; finally, torso was not found in Oncopeltus and its role in terminal patterning seems novel within holometabolous insects. We then use our data, together with published data on other insects, to reconstruct the evolution of the terminal patterning gene network in insects. We suggest that the Drosophila terminal patterning network evolved recently in the lineage leading to the Diptera, and represents an example of evolutionary "tinkering", where pre-existing pathways are co-opted for a new function. PMID:23665175

  15. Distinctive Patterns of Evolution of the δ-Globin Gene (HBD) in Primates

    PubMed Central

    Moleirinho, Ana; Lopes, Alexandra M.; Seixas, Susana; Morales-Hojas, Ramiro; Prata, Maria J.; Amorim, António

    2015-01-01

    In most vertebrates, hemoglobin (Hb) is a heterotetramer composed of two dissimilar globin chains, which change during development according to the patterns of expression of α- and β-globin family members. In placental mammals, the β-globin cluster includes three early-expressed genes, ε(HBE)-γ(HBG)-ψβ(HBBP1), and the late expressed genes, δ (HBD) and β (HBB). While HBB encodes the major adult β-globin chain, HBD is weakly expressed or totally silent. Paradoxically, in human populations HBD shows high levels of conservation typical of genes under strong evolutionary constraints, possibly due to a regulatory role in the fetal-to-adult switch unique of Anthropoid primates. In this study, we have performed a comprehensive phylogenetic and comparative analysis of the two adult β-like globin genes in a set of diverse mammalian taxa, focusing on the evolution and functional divergence of HBD in primates. Our analysis revealed that anthropoids are an exception to a general pattern of concerted evolution in placental mammals, showing a high level of sequence conservation at HBD, less frequent and shorter gene conversion events. Moreover, this lineage is unique in the retention of a functional GATA-1 motif, known to be involved in the control of the developmental expression of the β-like globin genes. We further show that not only the mode but also the rate of evolution of the δ-globin gene in higher primates are strictly associated with the fetal/adult β-cluster developmental switch. To gain further insight into the possible functional constraints that have been shaping the evolutionary history of HBD in primates, we calculated dN/dS (ω) ratios under alternative models of gene evolution. Although our results indicate that HBD might have experienced different selective pressures throughout primate evolution, as shown by different ω values between apes and Old World Monkeys + New World Monkeys (0.06 versus 0.43, respectively), these estimates corroborated a

  16. Evolution of oropharyngeal patterning mechanisms involving Dlx and endothelins in vertebrates.

    PubMed

    Kuraku, Shigehiro; Takio, Yoko; Sugahara, Fumiaki; Takechi, Masaki; Kuratani, Shigeru

    2010-05-01

    In jawed vertebrates, the Dlx code, or nested expression patterns of Dlx genes, specify the dorsoventral polarity of pharyngeal arches, downstream of endothelin-1 (Edn-1) and its effectors, Bapx1 (Nkx3.2) and dHand (Hand2). To elucidate the evolution of the specification mechanism of the oropharyngeal skeletal system, lamprey homologs of Dlx, Edn, endothelin receptor (Ednr), Bapx1, and dHand were identified. Our analysis suggested that the Edn gene family emerged at the advent of vertebrates, and that gene duplications leading to the different Edn gnathostome subtypes (Edn1-3) occurred before the cyclostome-gnathostome split. This timing of gene duplications, giving rise to multiple subtypes, was also implied for Dlx, Ednr, Hand, and Bapx. In lamprey embryos, nested expressions of Dlx genes were not observed in pharyngeal arches, nor was any focal expression of Bapx1, known in gnathostomes to specify the jaw joint. The dHand homolog, however, was expressed more intensively ventrally, as in gnathostomes. Lamprey homologs of Edn-1 and EdnrA were also shown to be expressed as described in mice, indicating involvement of this signaling pathway in the craniofacial patterning early in vertebrate evolution. These results suggest that the last common ancestor of all the extant vertebrates would have possessed basic gene repertoires involved in oropharyngeal patterning in gnathostomes, but the elaborate genetic program leading to the Dlx code is likely to have been acquired uniquely in gnathostomes. PMID:20171204

  17. Genome evolution and speciation: toward quantitative descriptions of pattern and process.

    PubMed

    Nosil, Patrik; Feder, Jeffrey L

    2013-09-01

    Studies of patterns of differentiation across genomes are accumulating, yet integrative work that combines approaches and fully capitalizes on new technologies to test explicit hypotheses is still rare. Thus, debates persist about the rate, magnitude, and causes of genomic change. This special section is devoted to helping resolve these debates. The eight studies contained within demonstrate how we can begin to move away from vague metaphors toward quantitative and more precise descriptors of patterns of genetic architecture and divergence. However, a particular genomic pattern can often arise via different combinations of various processes such as selection, gene flow, recombination, mutation, genetic drift, and demographic variability. Thus, substantial challenges remain in elucidating which evolutionary processes generated observed genomic patterns. Nonetheless, the studies in this section demonstrate ways forward toward bridging pattern and process, including experimental work, genetic mapping, increased knowledge of natural history and demography, and comparative studies spanning taxa at different points in the speciation continuum. Such collective work will lead to more powerful hypothesis testing. Future work can also help better integrate the contributions of ecology, genome structure (e.g., inversions and translocations), and genetic conflict to genome evolution. PMID:24033160

  18. Evolution-development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures.

    PubMed

    Kohsokabe, Takahiro; Kaneko, Kunihiko

    2016-01-01

    Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical-systems theory, which lead to the evolution-development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. PMID:26678220

  19. Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata.

    PubMed

    Maurer-Alcalá, Xyrus X; Katz, Laura A

    2016-01-01

    The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a "heteromeric" macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into "gene-sized" chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a "gene bank" that facilitates rapid changes in expression of genes required only in specific life history stages. By using "nonmodel" organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features. PMID:27189988

  20. Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata

    PubMed Central

    Maurer-Alcalá, Xyrus X.; Katz, Laura A.

    2016-01-01

    The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a “heteromeric” macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into “gene-sized” chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a “gene bank” that facilitates rapid changes in expression of genes required only in specific life history stages. By using “nonmodel” organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features. PMID:27189988

  1. The Repeat Pattern Toolkit (RPT): Analyzing the structure and evolution of the C. elegans genome

    SciTech Connect

    Agarwal, P.; States, D.J.

    1994-12-31

    Over 3.6 million bases of DNA sequence from chromosome III of the C. elegans have been determined. The availability of this extended region of contiguous sequence has allowed us to analyze the nature and prevalence of repetitive sequences in the genome of a eukaryotic organism with a high gene density. We have assembled a Repeat Pattern Toolkit (RPT) to analyze the patterns of repeats occurring in DNA. The tools include identifying significant local alignments (utilizing both two-way and three-way alignments), dividing the set of alignments into connected components (signifying repeat families), computing evolutionary distance between repeat family members, constructing minimum spanning trees from the connected components, and visualizing the evolution of the repeat families. Over 7000 families of repetitive sequences were identified. The size of the families ranged from isolated pairs to over 1600 segments of similar sequence. Approximately 12.3% of the analyzed sequence participates in a repeat element.

  2. Exploring the patterns and evolution of self-organized urban street networks through modeling

    NASA Astrophysics Data System (ADS)

    Rui, Yikang; Ban, Yifang; Wang, Jiechen; Haas, Jan

    2013-03-01

    As one of the most important subsystems in cities, urban street networks have recently been well studied by using the approach of complex networks. This paper proposes a growing model for self-organized urban street networks. The model involves a competition among new centers with different values of attraction radius and a local optimal principle of both geometrical and topological factors. We find that with the model growth, the local optimization in the connection process and appropriate probability for the loop construction well reflect the evolution strategy in real-world cities. Moreover, different values of attraction radius in centers competition process lead to morphological change in patterns including urban network, polycentric and monocentric structures. The model succeeds in reproducing a large diversity of road network patterns by varying parameters. The similarity between the properties of our model and empirical results implies that a simple universal growth mechanism exists in self-organized cities.

  3. Phylogeographic patterns and evolution of the mitochondrial DNA control region in two neotropical cats (Mammalia, felidae).

    PubMed

    Eizirik, E; Bonatto, S L; Johnson, W E; Crawshaw, P G; Vié, J C; Brousset, D M; O'Brien, S J; Salzano, F M

    1998-11-01

    The ocelot (Leopardus pardalis) and margay (L. wiedii) are sister-species of Neotropical cats which evolved from a lineage that migrated into South America during the formation of the Panamanian land bridge 3-5 million years ago. Patterns of population genetic divergence of each species were studied by phylogenetic analyses of mitochondrial DNA (mtDNA) control region sequences in individuals sampled across the distribution of these taxa. Abundant genetic diversity and remarkably concordant phylogeographic partitions for both species were observed, identifying parallel geographic regions which likely reflect historical faunal barriers. Inferred aspects of phylogeography, population genetic structure, and demographic history were used to formulate conservation recommendations for these species. In addition, observed patterns of sequence variation provided insight into the molecular evolution of the mtDNA control region in closely related felids. PMID:9797412

  4. The maximum rate of mammal evolution.

    PubMed

    Evans, Alistair R; Jones, David; Boyer, Alison G; Brown, James H; Costa, Daniel P; Ernest, S K Morgan; Fitzgerald, Erich M G; Fortelius, Mikael; Gittleman, John L; Hamilton, Marcus J; Harding, Larisa E; Lintulaakso, Kari; Lyons, S Kathleen; Okie, Jordan G; Saarinen, Juha J; Sibly, Richard M; Smith, Felisa A; Stephens, Patrick R; Theodor, Jessica M; Uhen, Mark D

    2012-03-13

    How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous-Paleogene (K-Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes. PMID:22308461

  5. The maximum rate of mammal evolution

    NASA Astrophysics Data System (ADS)

    Evans, Alistair R.; Jones, David; Boyer, Alison G.; Brown, James H.; Costa, Daniel P.; Ernest, S. K. Morgan; Fitzgerald, Erich M. G.; Fortelius, Mikael; Gittleman, John L.; Hamilton, Marcus J.; Harding, Larisa E.; Lintulaakso, Kari; Lyons, S. Kathleen; Okie, Jordan G.; Saarinen, Juha J.; Sibly, Richard M.; Smith, Felisa A.; Stephens, Patrick R.; Theodor, Jessica M.; Uhen, Mark D.

    2012-03-01

    How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous-Paleogene (K-Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes.

  6. The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster.

    PubMed

    Campos, José L; Halligan, Daniel L; Haddrill, Penelope R; Charlesworth, Brian

    2014-04-01

    Genetic recombination associated with sexual reproduction increases the efficiency of natural selection by reducing the strength of Hill-Robertson interference. Such interference can be caused either by selective sweeps of positively selected alleles or by background selection (BGS) against deleterious mutations. Its consequences can be studied by comparing patterns of molecular evolution and variation in genomic regions with different rates of crossing over. We carried out a comprehensive study of the benefits of recombination in Drosophila melanogaster, both by contrasting five independent genomic regions that lack crossing over with the rest of the genome and by comparing regions with different rates of crossing over, using data on DNA sequence polymorphisms from an African population that is geographically close to the putatively ancestral population for the species, and on sequence divergence from a related species. We observed reductions in sequence diversity in noncrossover (NC) regions that are inconsistent with the effects of hard selective sweeps in the absence of recombination. Overall, the observed patterns suggest that the recombination rate experienced by a gene is positively related to an increase in the efficiency of both positive and purifying selection. The results are consistent with a BGS model with interference among selected sites in NC regions, and joint effects of BGS, selective sweeps, and a past population expansion on variability in regions of the genome that experience crossing over. In such crossover regions, the X chromosome exhibits a higher rate of adaptive protein sequence evolution than the autosomes, implying a Faster-X effect. PMID:24489114

  7. Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host.

    PubMed

    Kattoor, Jobin Jose; Malik, Yashpal Singh; Sasidharan, Aravind; Rajan, Vishnuraj Mangalathu; Dhama, Kuldeep; Ghosh, Souvik; Bányai, Krisztián; Kobayashi, Nobumichi; Singh, Raj Kumar

    2015-08-01

    Rotavirus infection is a worldwide problem, with occurrence of highly divergent viruses classified in 8 species (A-H). We report here the evolution assessment of codon usage patterns in virus-host system in avian rotavirus (AvRV) of species RVA, RVD, RVF and RVG (preferentially affecting birds). The nucleotide contents, codon usage bias (CUB), relative synonymous codon usage (RSCU), and effective number of codons (ENCs) values were investigated targeting overexpressing major inner capsid viral protein (VP6) of these AvRV species. The results confirm that the evolutionary characteristics influences the rotavirus (RV) genetic diversity and impact of host's natural selection on the AvRVs codons. Synonymous codon usage patterns were evaluated following multivariate statistical procedures on all available AvRV coding gene sequences. RSCU trees accommodated all AvRV species and preferred host sequences in one topology confirming greater imminence of AvRVs with the host chicken cell genes. Similarly, the codon adaptation index (CAI) results also displayed a higher adaptation of AvRVs to its chicken host. The codon preference analysis of RVs revealed that VP6 gene express more proficiently in the yeast system, whereas, codon optimization might be required for the effectual expression in Escherichia coli and Homo sapiens. The findings provide basic evidence on the dynamics of AvRV evolution and its host adaptation, which could be exploited for additional research on avian species in future. PMID:26086995

  8. Unique expression patterns of multiple key genes associated with the evolution of mammalian flight

    PubMed Central

    Wang, Zhe; Dai, Mengyao; Wang, Yao; Cooper, Kimberly L.; Zhu, Tengteng; Dong, Dong; Zhang, Junpeng; Zhang, Shuyi

    2014-01-01

    Bats are the only mammals capable of true flight. Critical adaptations for flight include a pair of dramatically elongated hands with broad wing membranes. To study the molecular mechanisms of bat wing evolution, we perform genomewide mRNA sequencing and in situ hybridization for embryonic bat limbs. We identify seven key genes that display unique expression patterns in embryonic bat wings and feet, compared with mouse fore- and hindlimbs. The expression of all 5′HoxD genes (Hoxd9–13) and Tbx3, six known crucial transcription factors for limb and digit development, is extremely high and prolonged in the elongating wing area. The expression of Fam5c, a tumour suppressor, in bat limbs is bat-specific and significantly high in all short digit regions (the thumb and foot digits). These results suggest multiple genetic changes occurred independently during the evolution of bat wings to elongate the hand digits, promote membrane growth and keep other digits short. Our findings also indicate that the evolution of limb morphology depends on the complex integration of multiple gene regulatory networks and biological processes that control digit formation and identity, chondrogenesis, and interdigital regression or retention. PMID:24695426

  9. Holocene denudation pattern across the South-Eastern Australian Escarpment and implications for its evolution

    NASA Astrophysics Data System (ADS)

    Godard, Vincent; Dosseto, Anthony; Bellier, Olivier; Bourlès, Didier; Fleury, Jules; Aster Team

    2016-04-01

    Developing a process based understanding of continental relief evolution requires to quantify rates of denudation and to compare their distribution with the evolution of geomorphic parameters. The analysis of denudation and exhumation spatial patterns based from cosmogenic nuclides and low temperature thermochronology are routinely used to document the processes associated with the geomorphic evolution of continental relief over various timescales. Passive margin escarpments are among some of the most salient continental geomorphic features outside of orogenic areas. Their evolution have been studied intensively over the long-term (several Ma to tens of Ma), using for example low-temperature thermochronology. However, datasets documenting their shorter-term (1-10 ka) dynamics are scarcer, and only a limited number of case studies have used quantitative techniques such as cosmogenic nuclides to document the denudation pattern across such escarpments. The South Eastern Australian Escarpment is such a place where cosmogenic nuclides have been intensively used over the last two decades to constrain processes of landscape evolution over short wavelength, with, for example the calibration of the soil production function. Such existing data and constraints provide an ideal setting to carry on further long-wavelength exploration of the dynamics of the whole escarpment. We have sampled 17 catchments across the South Eastern Australian Escarpment, starting from the coastal plain and moving westward up to the low relief plateau surface. The observed landscape denudation rates are 10-20 mm/ka in the coastal area and progressively increases up to ~60 mm/ka toward the edge of the escarpment. In the low-relief areas located west of the continental drainage divide denudation rates fall back to 10-20 mm/ka. This nearly four-fold contrast in denudation across the divide is characteristic of a major disequilibrium in the dynamics of the river network associated with a progressive

  10. Evolution of Muscle Activity Patterns Driving Motions of the Jaw and Hyoid during Chewing in Gnathostomes

    PubMed Central

    Konow, Nicolai; Herrel, Anthony; Ross, Callum F.; Williams, Susan H.; German, Rebecca Z.; Sanford, Christopher P. J.; Gintof, Chris

    2011-01-01

    Although chewing has been suggested to be a basal gnathostome trait retained in most major vertebrate lineages, it has not been studied broadly and comparatively across vertebrates. To redress this imbalance, we recorded EMG from muscles powering anteroposterior movement of the hyoid, and dorsoventral movement of the mandibular jaw during chewing. We compared muscle activity patterns (MAP) during chewing in jawed vertebrate taxa belonging to unrelated groups of basal bony fishes and artiodactyl mammals. Our aim was to outline the evolution of coordination in MAP. Comparisons of activity in muscles of the jaw and hyoid that power chewing in closely related artiodactyls using cross-correlation analyses identified reorganizations of jaw and hyoid MAP between herbivores and omnivores. EMG data from basal bony fishes revealed a tighter coordination of jaw and hyoid MAP during chewing than seen in artiodactyls. Across this broad phylogenetic range, there have been major structural reorganizations, including a reduction of the bony hyoid suspension, which is robust in fishes, to the acquisition in a mammalian ancestor of a muscle sling suspending the hyoid. These changes appear to be reflected in a shift in chewing MAP that occurred in an unidentified anamniote stem-lineage. This shift matches observations that, when compared with fishes, the pattern of hyoid motion in tetrapods is reversed and also time-shifted relative to the pattern of jaw movement. PMID:21705368

  11. Evolution of large amplitude 3D fold patterns: A FEM study

    NASA Astrophysics Data System (ADS)

    Schmid, D. W.; Dabrowski, M.; Krotkiewski, M.

    2008-12-01

    The numerical study of three-dimensional (3D) fold patterns formation in randomly perturbed layers requires large numbers of degrees of freedom (≥100,000,000). We have developed BILAMIN, an unstructured (geometry fitted) mesh implementation of the finite element method for incompressible Stokes flow that is capable of solving such systems. All repetitive and computationally intensive steps are fully parallelized. One of the main components is the iterative solver. We chose the minimum residual method (MINRES) because it allows operating directly on the indefinite systems resulting from the incompressibility condition. We use BILAMIN in a case study of fold pattern evolution. Folds are ubiquitous in nature, and contain both mechanical and kinematic information that can be deciphered with appropriate tools. Our results show that there is a relationship between fold aspect ratio and in-plane loading conditions. We propose that this finding can be used to determine the complete parameter set potentially contained in the geometry of three-dimensional folds: mechanical properties of natural rocks, maximum strain, and relative strength of the in-plane far-field load components. Furthermore, we show how folds in 3D amplify and that there is a second deformation mode, besides continuous amplification, where compression leads to a lateral rearrangement of blocks of folds. Finally, we demonstrate that the textbook prediction of egg carton-shaped dome and basin structures resulting from folding instabilities in constriction is largely oversimplified. The fold patterns resulting in this setting are curved, elongated folds with random orientation.

  12. Climate change, body size evolution, and Cope's Rule in deep-sea ostracodes.

    PubMed

    Hunt, Gene; Roy, Kaustuv

    2006-01-31

    Causes of macroevolutionary trends in body size, such as Cope's Rule, the tendency of body size to increase over time, remain poorly understood. We used size measurements from Cenozoic populations of the ostracode genus Poseidonamicus, in conjunction with phylogeny and paleotemperature estimates, to show that climatic cooling leads to significant increases in body size, both overall and within individual lineages. The magnitude of size increase due to Cenozoic cooling is consistent with temperature-size relationships in geographically separated modern populations (Bergmann's Rule). Thus population-level phenotypic evolution in response to climate change can be an important determinant of macroevolutionary trends in body size. PMID:16432187

  13. Latitudinal patterns in plant defense: evolution of cardenolides, their toxicity and induction following herbivory.

    PubMed

    Rasmann, Sergio; Agrawal, Anurag A

    2011-05-01

    Attempts over the past 50 years to explain variation in the abundance, distribution and diversity of plant secondary compounds gave rise to theories of plant defense. Remarkably, few phylogenetically robust tests of these long-standing theories have been conducted. Using >50 species of milkweed (Asclepias spp.), we show that variation among plant species in the induction of toxic cardenolides is explained by latitude, with higher inducibility evolving more frequently at lower latitudes. We also found that: (1) the production of cardenolides showed positive-correlated evolution with the diversity of cardenolides, (2) greater cardenolide investment by a species is accompanied by an increase in an estimate of toxicity (measured as chemical polarity) and (3) instead of trading off, constitutive and induced cardenolides were positively correlated. Analyses of root and shoot cardenolides showed concordant patterns. Thus, milkweed species from lower latitudes are better defended with higher inducibility, greater diversity and added toxicity of cardenolides. PMID:21371232

  14. Microstructural evolution of Al-Cu thin-film conducting lines during post-pattern annealing

    NASA Astrophysics Data System (ADS)

    Kang, S. H.; Morris, J. W., Jr.

    1997-07-01

    This work reports a statistical analysis of the evolution of polygranular segment lengths during high-temperature annealing of Al(Cu) thin-film interconnects with quasi-bamboo microstructures. To create samples of Al(Cu) lines that could be imaged by transmission electron microscopy without breaking or thinning, the lines were deposited on electron-transparent silicon nitride films (the "silicon nitride window" technique). The microstructures of the lines were studied as a function of annealing time and temperature. In particular, the distribution of polygranular segment lengths was measured. The results show that the longer polyglranular segments are preferentially eliminated during post-pattern annealing. As a consequence, the segment-length distribution narrows monotonically during annealing, and changes in shape. The preferential loss of the longest polygranular segments leads to a dramatic increase in resistance to electromigration failure.

  15. Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi).

    PubMed

    Lloyd, Graeme T; Wang, Steve C; Brusatte, Stephen L

    2012-02-01

    Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a cladogram (branches or entire clades) that are characterized by significantly high or low rates of change. These methods include a randomization approach that identifies branches with significantly high rates and likelihood ratio tests that pinpoint either branches or clades that have significantly higher or lower rates than the pooled rate of the remainder of the tree. As a test case for these methods, we analyze a discrete character dataset of lungfish, which have long been regarded as "living fossils" due to an apparent slowdown in rates since the Devonian. We find that morphological rates are highly heterogeneous across the phylogeny and recover a general pattern of decreasing rates along the phylogenetic backbone toward living taxa, from the Devonian until the present. Compared with previous work, we are able to report a more nuanced picture of lungfish evolution using these new methods. PMID:22276532

  16. Pattern evolution caused by dynamic coupling between wetting and phase separation in binary liquid mixture containing glass particles

    NASA Astrophysics Data System (ADS)

    Tanaka, Hajime; Lovinger, Andew J.; Davis, Don D.

    1994-04-01

    We demonstrate here that the pattern evolution in a binary liquid mixture containing glass spheres is strongly affected by the dynamic coupling between phase separation and wetting. Because of the difference in the wettability to glass between the two phases, the glass particles are preferentially included in the more wettable phase. The resulting pattern is strongly dependent on whether the spheres are mobile or immobile. For a high density of mobile particles, we find that an initially random pattern of spheres transforms into an ordered pattern because of geometrical confinement of particles into the more wettable phase.

  17. The development and evolution of insect mouthparts as revealed by the expression patterns of gnathocephalic genes.

    PubMed

    Rogers, Bryan T; Peterson, Michael D; Kaufman, Thomas C

    2002-01-01

    To understand better both the development and evolution of insect mouthparts, we have compared the expression pattern of several developmentally important genes in insects with either mandibulate or stylate-haustellate mouthparts. Specifically, we examined the expression of the proboscipedia (pb) and Distal-less (Dll) gene products as well as three regulators of pb, Sex combs reduced (Scr), Deformed (Dfd), and cap 'n' collar (cnc). These genes are known to control the identity of cells in the gnathal segments of Drosophila melanogaster and would appear to have similar conserved functions in other insects. Together we have made an atlas of gene expression in the heads of three insects: Thermobia domestica and Acheta domestica, which likely exemplify the mandibulate mouthparts present in the common insect ancestor, and Oncopeltus fasciatus, which has piercing-sucking mouth parts that are typical of the Hemiptera. At the earliest stages of embryogenesis, only the expression of pb was found to differ dramatically between Oncopeltus and the other insects examined, although significant differences were observed later in development. This difference in pb expression reflects an apparent divergence in the specification of gnathal identity between mandibulate and stylate-haustellate mouthparts, which may result from a "phylogenetic homeosis" that occurred during the evolution of the Hemiptera. PMID:12004967

  18. Distinct patterns of gene-specific methylation in mammalian placentas: implications for placental evolution and function.

    PubMed

    Ng, H K; Novakovic, B; Hiendleder, S; Craig, J M; Roberts, C T; Saffery, R

    2010-04-01

    The placenta has arisen relatively recently and is among the most rapidly evolving tissues in mammals. Several different placental barrier and structure types appear to have independently evolved common functional features. Specific patterns of gene expression that determine placental development in humans are predicted to be accompanied by specific profiles of epigenetic modification. However, the stratification of epigenetic modifications into those involved in conserved aspects of placental function, versus those involved in divergent placental features, has yet to begin. As a first step towards this goal, we have investigated the methylation status of a small number of gene-specific methylation events recently identified in human placenta, in a panel of placental tissue from baboon, marmoset, cow, cat, guinea pig and mouse. These represent disparate placental barrier types and structures. In this study we hypothesized that specific epigenetic markings may be associated with placental barrier type or function, independent of phylogeny. However, in contrast to our predictions, the majority of gene-specific methylation appears to track with phylogeny, independent of placental barrier type or other structural features. This suggests that despite the likelihood of epigenetic modification playing a role in the functioning and evolution of different placental subtypes, there is no evidence for an involvement of the gene-specific methylation profiles we have identified, in specifying these differences. Further studies, examining larger numbers of epigenetic modifications across phylogeny, are required to define the role of specific epigenetic modifications in the evolution of distinct placental structures. PMID:20167366

  19. Evolution of osmoregulatory patterns and gill ion transport mechanisms in the decapod Crustacea: a review.

    PubMed

    McNamara, John Campbell; Faria, Samuel Coelho

    2012-12-01

    Decapod crustaceans exhibit a wide range of osmoregulatory patterns and capabilities from marine osmoconformers to brackish and freshwater hyperregulators to terrestrial hyporegulators. The principal gill salt transport mechanisms proposed to underlie the ability of the better-known taxa to occupy these specific habitats are examined here. Traditional thinking suggests that a graduated series of successively stronger adaptive mechanisms may have driven the occupation of ever more dilute osmotic niches, culminating in the conquest of freshwater and dry land. However, when habitat and osmoregulatory parameters are analyzed quantitatively against the phylogenies of the taxa examined, as illustrated here using a palaemonid shrimp clade, their association becomes questionable and may hold true only in specific cases. We also propose a putative evolution for gill epithelial ion pump and transporter arrangement in a eubrachyuran crab clade whose lineages occupy distinct osmotic niches. By including the systematics of these selected groups, this review incorporates the notion of a protracted time scale, here termed 'phylophysiology', into decapod osmoregulation, allowing the examination of putative physiological transformations and their underlying evolutionary processes. This approach assumes that species are temporally linked, a factor that can impart phylogenetic structuring, which must be considered in comparative studies. Future experimental models in decapod osmoregulatory physiology should contemplate the phylogenetic relationships among the taxa chosen to better allow comprehension of the transformations arising during their evolution. PMID:22534792

  20. Inferring directions of evolution from patterns of variation: The legacy of Sergei Meyen

    PubMed Central

    Sharov, Alexei A.; Igamberdiev, Abir U.

    2014-01-01

    In the era of the Extended Evolutionary Synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935-1987), a paleobotanist who argued that the theory of evolution should incorporate a “nomothetical” approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of “repeated polymorphic sets” (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioural capacities. Meyen's theory is compatible with Darwin's natural selection; however Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviours) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations. PMID:25072709

  1. Amphioxus and lamprey AP-2 genes: implications for neural crest evolution and migration patterns

    NASA Technical Reports Server (NTRS)

    Meulemans, Daniel; Bronner-Fraser, Marianne

    2002-01-01

    The neural crest is a uniquely vertebrate cell type present in the most basal vertebrates, but not in cephalochordates. We have studied differences in regulation of the neural crest marker AP-2 across two evolutionary transitions: invertebrate to vertebrate, and agnathan to gnathostome. Isolation and comparison of amphioxus, lamprey and axolotl AP-2 reveals its extensive expansion in the vertebrate dorsal neural tube and pharyngeal arches, implying co-option of AP-2 genes by neural crest cells early in vertebrate evolution. Expression in non-neural ectoderm is a conserved feature in amphioxus and vertebrates, suggesting an ancient role for AP-2 genes in this tissue. There is also common expression in subsets of ventrolateral neurons in the anterior neural tube, consistent with a primitive role in brain development. Comparison of AP-2 expression in axolotl and lamprey suggests an elaboration of cranial neural crest patterning in gnathostomes. However, migration of AP-2-expressing neural crest cells medial to the pharyngeal arch mesoderm appears to be a primitive feature retained in all vertebrates. Because AP-2 has essential roles in cranial neural crest differentiation and proliferation, the co-option of AP-2 by neural crest cells in the vertebrate lineage was a potentially crucial event in vertebrate evolution.

  2. Inferring directions of evolution from patterns of variation: the legacy of Sergei Meyen.

    PubMed

    Sharov, Alexei A; Igamberdiev, Abir U

    2014-09-01

    In the era of the extended evolutionary synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935-1987), a paleobotanist who argued that the theory of evolution should incorporate a "nomothetical" approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of "repeated polymorphic sets" (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioral capacities. Meyen's theory is compatible with Darwin's natural selection; however, Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviors) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations. PMID:25072709

  3. Experimental Evolution under Fluctuating Thermal Conditions Does Not Reproduce Patterns of Adaptive Clinal Differentiation in Drosophila melanogaster.

    PubMed

    Kellermann, Vanessa; Hoffmann, Ary A; Kristensen, Torsten Nygaard; Moghadam, Neda Nasiri; Loeschcke, Volker

    2015-11-01

    Experimental evolution can be a useful tool for testing the impact of environmental factors on adaptive changes in populations, and this approach is being increasingly used to understand the potential for evolutionary responses in populations under changing climates. However, selective factors will often be more complex in natural populations than in laboratory environments and produce different patterns of adaptive differentiation. Here we test the ability of laboratory experimental evolution under different temperature cycles to reproduce well-known patterns of clinal variation in Drosophila melanogaster. Six fluctuating thermal regimes mimicking the natural temperature conditions along the east coast of Australia were initiated. Contrary to expectations, on the basis of field patterns there was no evidence for adaptation to thermal regimes as reflected by changes in cold and heat resistance after 1-3 years of laboratory natural selection. While laboratory evolution led to changes in starvation resistance, development time, and body size, patterns were not consistent with those seen in natural populations. These findings highlight the complexity of factors affecting trait evolution in natural populations and indicate that caution is required when inferring likely evolutionary responses from the outcome of experimental evolution studies. PMID:26655772

  4. Controllable synthesis of Cu2O petalody octahedral microcrystals and multi-patterned evolution.

    PubMed

    Ding, Yanbo; Ge, Dengteng; Yang, Lili; Li, Zhenyu; Xin, Wuhong; Li, Yao; Wu, Xiaohong; Zhao, Jiupeng

    2013-02-15

    The fabrication of cuprous oxide (Cu(2)O) with various morphologies has attracted extensive interest due to its applications in solar energy conversion, electrode materials, sensors, and catalysts. Herein, we report a facile controllable route for Cu(2)O microcrystals with various architectures via a hydrothermal method without using templates or surfactants. Six types of Cu(2)O microcrystals including petalody octahedral, concave truncated octahedron, truncated octahedron, octahedron, sphere-like, and sphere are obtained accompanying with Cu precipitation or urchin-like CuO particles due to the modifying of pH values. The petalody octahedral pattern of Cu(2)O is for the first time found here under the condition of pH 7-8. Additionally, possible growth mechanism for multi-patterned Cu(2)O and compositional evolution is discussed via preferential growths induced by selective absorption of acrylic acid and decomposition of lactic acid in the present reaction system. These experimental results prove a versatile and facile strategy for Cu(2)O microcrystals with special and complex architectures, which may highlights their potential applications due to the improved surface activity, catalytic, or photoelectric performance. PMID:23127874

  5. Aging and fertility patterns in wild chimpanzees provide insights into the evolution of menopause

    PubMed Central

    Thompson, Melissa Emery; Jones, James H.; Pusey, Anne E.; Brewer-Marsden, Stella; Goodall, Jane; Marsden, David; Matsuzawa, Tetsuro; Nishida, Toshisada; Reynolds, Vernon; Sugiyama, Yukimaru; Wrangham, Richard W.

    2008-01-01

    Summary Human menopause is remarkable in that reproductive senescence is markedly accelerated relative to somatic aging, leaving an extended post-reproductive period for a large proportion of women [1, 2]. Functional explanations for this are debated [4-11], in part because comparative data from closely-related species are inadequate. Existing studies of chimpanzees are based on very small samples and have not provided clear conclusions about the reproductive function of aging females [12-19]. These studies have not examined whether reproductive senescence in chimpanzees exceeds the pace of general aging, as in humans, or occurs in parallel with declines in overall health, as in many other animals [20, 21]. In order to remedy these problems, we examined fertility and mortality patterns in 6 free-living chimpanzee populations. Chimpanzee and human birth rates show similar patterns of decline beginning in the 4th decade, suggesting that the physiology of reproductive senescence was relatively conserved in human evolution. However, in contrast to humans, chimpanzee fertility declines are consistent with declines in survivorship, and healthy females maintain high birth rates late into life. Thus, in contrast to recent claims [16], we find no evidence that menopause is a typical characteristic of chimpanzee life histories. PMID:18083515

  6. Evolution.

    ERIC Educational Resources Information Center

    Mayr, Ernst

    1978-01-01

    Traces the history of evolution theory from Lamarck and Darwin to the present. Discusses natural selection in detail. Suggests that, besides biological evolution, there is also a cultural evolution which is more rapid than the former. (MA)

  7. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

    PubMed Central

    2011-01-01

    forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities. Reviewers This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier. PMID:21639885

  8. Dynamical patterning modules: physico-genetic determinants of morphological development and evolution

    NASA Astrophysics Data System (ADS)

    Newman, Stuart A.; Bhat, Ramray

    2008-03-01

    The shapes and forms of multicellular organisms arise by the generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. While morphogenesis and pattern formation in all animal species are widely recognized to be mediated by the gene products of an evolutionarily conserved 'developmental-genetic toolkit', the link between these molecular players and the physics underlying these processes has been generally ignored. This paper introduces the concept of 'dynamical patterning modules' (DPMs), units consisting of one or more products of the 'toolkit' genes that mobilize physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems such as cell aggregates: cohesion, viscoelasticity, diffusion, spatiotemporal heterogeneity based on lateral inhibition and multistable and oscillatory dynamics. We suggest that ancient toolkit gene products, most predating the emergence of multicellularity, assumed novel morphogenetic functions due to change in the scale and context inherent to multicellularity. We show that DPMs, acting individually and in concert with each other, constitute a 'pattern language' capable of generating all metazoan body plans and organ forms. The physical dimension of developmental causation implies that multicellular forms during the explosive radiation of animal body plans in the middle Cambrian, approximately 530 million years ago, could have explored an extensive morphospace without concomitant genotypic change or selection for adaptation. The morphologically plastic body plans and organ forms generated by DPMs, and their ontogenetic trajectories, would subsequently have been stabilized and consolidated by natural selection and genetic drift. This perspective also solves the apparent 'molecular homology-analogy paradox', whereby widely divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo

  9. Ecology and evolution of mammalian biodiversity

    PubMed Central

    Jones, Kate E.; Safi, Kamran

    2011-01-01

    Mammals have incredible biological diversity, showing extreme flexibility in eco-morphology, physiology, life history and behaviour across their evolutionary history. Undoubtedly, mammals play an important role in ecosystems by providing essential services such as regulating insect populations, seed dispersal and pollination and act as indicators of general ecosystem health. However, the macroecological and macroevolutionary processes underpinning past and present biodiversity patterns are only beginning to be explored on a global scale. It is also particularly important, in the face of the global extinction crisis, to understand these processes in order to be able to use this knowledge to prevent future biodiversity loss and loss of ecosystem services. Unfortunately, efforts to understand mammalian biodiversity have been hampered by a lack of data. New data compilations on current species' distributions, ecologies and evolutionary histories now allow an integrated approach to understand this biodiversity. We review and synthesize these new studies, exploring the past and present ecology and evolution of mammalian biodiversity, and use these findings to speculate about the mammals of our future. PMID:21807728

  10. The Evolution of Tropical Precipitation Patterns During ENSO Events Using 21+ Years of GPCP Merged Data

    NASA Technical Reports Server (NTRS)

    Curtis, Scott; Adler, Robert

    2000-01-01

    The ENSO phenomenon is characterized by fluctuations in the climate system of the tropical Pacific. Quantifying changes in the precipitation component of this system is important in understanding the distribution of heating in the atmosphere which drives the large-scale circulation and affects the weather patterns in the mid-latitudes. Monitoring precipitation anomalies in the Pacific is also an important component for tracking the evolution of ENSO. The most timely and complete observations of the earth come from satellite instruments. In this study, the state of the art satellite-gauge merged monthly precipitation data set from the Global Precipitation Climatology Project (GPCP) is used to depict tropical rainfall patterns during ENSO events over the past two decades and quantify these patterns using indices. This analysis will be complemented by daily precipitation data which can resolve the Madden-Julian Oscillation and westerly wind burst events. The 1997-98 El Nino and 1998-2000 La Nina were the best observed ENSO cycle in the historic record. Prior to the El Nino (in terms of anomalous warming of the east Pacific) dry anomalies over the Maritime Continent were observed in February 1997 as a westerly wind burst advected convection to the east. The largest SST anomalies occurred around November-December 1997, which were followed by the largest precipitation anomalies in the beginning of 1998. The largest precipitation departures from normal were not colocated with the SST anomalies, but were further west, In the spring of 1998 negative precipitation anomalies to the north of the equator intensified, signaling the mature phase of the El Nino. A rapid increase in the precipitation-based La Nina index from December-January 1998 to March-April 1998 signaled the coming La Nina. The 1982-1983 El Nino was comparable in strength (according to several indices) and the precipitation patterns evolved in a similar fashion. For the 1998-2000 La Nina, the coldest anomalies

  11. Patterns of Chromosomal Evolution in Sigmodon, Evidence from Whole Chromosome Paints

    PubMed Central

    Swier, V.J.; Bradley, R.D.; Rens, W.; Elder, F.F.B.; Baker, R.J.

    2009-01-01

    Of the superfamily Muroidea (31 genera, 1578 species), the Sigmodontinae (74 genera, 377 species) is the second largest subfamily in number of species and represents a significant radiation of rodent biodiversity. Only 2 of the 74 genera are found in both North and South America (Sigmodon and Oryzomys) and the remainder are exclusively from South America. In recent molecular studies, the genus Sigmodon (Cricetidae, Sigmodontinae) has been considered sister to many other South American Sigmodontines [Steppan et al., 2004]. We examine the chromosomal evolution of 9 species of Sigmodon utilizing chromosomal paints isolated from S. hispidus, proposed to be similar to the ancestral karyotype [Elder, 1980]. Utilizing a phylogenetic hypothesis of a molecular phylogeny of Sigmodon [Henson and Bradley, 2009], we mapped shared chromosomal rearrangements of taxa on a molecular tree to estimate the evolutionary position of each rearrangement. For several species (S. hirsutus, S. leucotis, S. ochrognathus, S. peruanus, and S. toltecus), the karyotype accumulated few or no changes, but in three species (S. arizonae, S. fulviventer, and S. mascotensis) numerous karyotype rearrangements were observed. These rearrangements involved heterochromatic additions, centric fusions, tandem fusions, pericentric inversions, as well as the addition of interstitial DNA not identified by chromosome paints or C-banding. The hypothesis that the ancestral karyotype for this complex had a diploid number of 52, a fundamental number of 52, and a G-band pattern of which most, if not all are similar to that present in modern day S. hispidus fails to be rejected. This hypothesis remains viable as an explanation of chromosomal evolution in Sigmodontine rodents. PMID:19617697

  12. [Spatial pattern evolution of carbon emission intensity from energy consumption in China].

    PubMed

    Zhao, Yun-Tai; Huang, Xian-Jin; Zhong, Tai-Yang; Peng, Jia-Wen

    2011-11-01

    Using Theil index and spatial autocorrelation analysis methods, the characteristics, regional disparity and spatial pattern evolution of carbon emission intensity from energy consumption were analyzed on national, regional and provincial level from 1999 to 2007 in China. The results indicate that: (1) total energy carbon emission in China has increased from 0.91Gt in 1999 to 1.83Gt in 2007, while carbon emission intensity has decreased from 0.83 t x (10(4) yuan) (-1) to 0.79 t x (10(4) yuan) (-1); (2) carbon emission intensity of eight major economic blocks showed the trend of three-level differentiation, with that of northeast regions, the middle reaches of Yellow River regions and northwest regions above 1.0 t x (10(4) yuan)(-1); northern coastal regions, the middle reaches of Yangtze River regions and southwest regions 0.7-1.0 t x (10(4) yuan) (-1); eastern and northern regions 0.32-0.51 t x (10(4) yuan) (-1); (3) Theil index analysis indicates that the within-region carbon emission intensities were similar, and the expanding total disparity of carbon emission intensity was primarily due to between-region inequalities. (4) spatial autocorrelation analysis shows that Global Moran's I has increased from 0.19 to 0.25, indicating that there were positive spatial correlations among provincial regions in China, and regions of similar carbon emission intensity agglomerated in space. The "cold spot" areas of carbon emission intensity were relatively stable, while the "hot spot" areas has gradually shifted from northwest regions to the middle reaches of Yellow River regions and northeast regions. (5) spatial disparity of carbon emission intensity is closely related to factors such as regional resources endowment, economic development, industrial structure and energy utilization efficiency. The study of regional disparity and spatial autocorrelation provides insight into spatial heterogeneity and spatial pattern evolution of carbon emission intensity in China, and also

  13. Modeling the Shape Evolution of Enclosed Water Bodies: Pattern Formation from Emergent Interactions

    NASA Astrophysics Data System (ADS)

    Murray, A. B.; Littlewood, R.; Ashton, A. D.

    2006-12-01

    randomly varying wind directions, some shoreline segments experience wave climates dominated by high-angle waves. As finite- amplitude features develop in these areas, they affect the fetches felt by other shoreline segments. Thus, the pattern evolution on opposite shores becomes coupled. The fetch-limitation interactions lead to new modes of emergent interactions and highly entertaining shape evolutions. If the initial water body is sufficiently elongated, merging of shoreline features extending from opposite shores will ultimately segment it into multiple water bodies.

  14. Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida

    PubMed Central

    Young, Monica R; Hebert, Paul D. N.

    2015-01-01

    Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI) from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders and 43% of its families (267/625). It examines divergences at three taxonomic levels—among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10–0.39), while the mean of the Family Distances for the ten orders ranges fivefold (0.07–0.35). BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration. Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is ‘locked down’ in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in ‘locked down’ taxa. PMID:26308206

  15. Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries.

    PubMed

    Goodman, Morris; Sterner, Kirstin N; Islam, Munirul; Uddin, Monica; Sherwood, Chet C; Hof, Patrick R; Hou, Zhuo-Cheng; Lipovich, Leonard; Jia, Hui; Grossman, Lawrence I; Wildman, Derek E

    2009-12-01

    Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains and short life spans. Thus, we investigated whether the phylogenomic patterns of adaptive evolution are more similar between elephant and human than between either elephant and tenrec lineages or human and mouse lineages, and whether aerobic energy metabolism genes are especially well represented in the elephant and human patterns. Our analyses encompassed approximately 6,000 genes in each of these lineages with each gene yielding extensive coding sequence matches in interordinal comparisons. Each gene's nonsynonymous and synonymous nucleotide substitution rates and dN/dS ratios were determined. Then, from gene ontology information on genes with the higher dN/dS ratios, we identified the more prevalent sets of genes that belong to specific functional categories and that evolved adaptively. Elephant and human lineages showed much slower nucleotide substitution rates than tenrec and mouse lineages but more adaptively evolved genes. In correlation with absolute brain size and brain oxygen consumption being largest in elephants and next largest in humans, adaptively evolved aerobic energy metabolism genes were most evident in the elephant lineage and next most evident in the human lineage. PMID:19926857

  16. Development and Evolution of Dentition Pattern and Tooth Order in the Skates And Rays (Batoidea; Chondrichthyes)

    PubMed Central

    Underwood, Charlie J.; Johanson, Zerina; Welten, Monique; Metscher, Brian; Rasch, Liam J.; Fraser, Gareth J.; Smith, Moya Meredith

    2015-01-01

    Shark and ray (elasmobranch) dentitions are well known for their multiple generations of teeth, with isolated teeth being common in the fossil record. However, how the diverse dentitions characteristic of elasmobranchs form is still poorly understood. Data on the development and maintenance of the dental patterning in this major vertebrate group will allow comparisons to other morphologically diverse taxa, including the bony fishes, in order to identify shared pattern characters for the vertebrate dentition as a whole. Data is especially lacking from the Batoidea (skates and rays), hence our objective is to compile data on embryonic and adult batoid tooth development contributing to ordering of the dentition, from cleared and stained specimens and micro-CT scans, with 3D rendered models. We selected species (adult and embryonic) spanning phylogenetically significant batoid clades, such that our observations may raise questions about relationships within the batoids, particularly with respect to current molecular-based analyses. We include developmental data from embryos of recent model organisms Leucoraja erinacea and Raja clavata to evaluate the earliest establishment of the dentition. Characters of the batoid dentition investigated include alternate addition of teeth as offset successional tooth rows (versus single separate files), presence of a symphyseal initiator region (symphyseal tooth present, or absent, but with two parasymphyseal teeth) and a restriction to tooth addition along each jaw reducing the number of tooth families, relative to addition of successor teeth within each family. Our ultimate aim is to understand the shared characters of the batoids, and whether or not these dental characters are shared more broadly within elasmobranchs, by comparing these to dentitions in shark outgroups. These developmental morphological analyses will provide a solid basis to better understand dental evolution in these important vertebrate groups as well as the

  17. Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds.

    PubMed

    Benson, Roger B J; Choiniere, Jonah N

    2013-10-01

    Birds are the most diverse living tetrapod group and are a model of large-scale adaptive radiation. Neontological studies suggest a radiation within the avian crown group, long after the origin of flight. However, deep time patterns of bird evolution remain obscure because only limited fossil data have been considered. We analyse cladogenesis and limb evolution on the entire tree of Mesozoic theropods, documenting the dinosaur-bird transition and immediate origins of powered flight. Mesozoic birds inherited constraints on forelimb evolution from non-flying ancestors, and species diversification rates did not accelerate in the earliest flying taxa. However, Early Cretaceous short-tailed birds exhibit both phenotypic release of the hindlimb and increased diversification rates, unparalleled in magnitude at any other time in the first 155 Myr of theropod evolution. Thus, a Cretaceous adaptive radiation of stem-group birds was enabled by restructuring of the terrestrial locomotor module, which represents a key innovation. Our results suggest two phases of radiation in Avialae: with the Cretaceous diversification overwritten by extinctions of stem-group birds at the Cretaceous-Palaeogene boundary, and subsequent diversification of the crown group. Our findings illustrate the importance of fossil data for understanding the macroevolutionary processes generating modern biodiversity. PMID:23945695

  18. Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds

    PubMed Central

    Benson, Roger B. J.; Choiniere, Jonah N.

    2013-01-01

    Birds are the most diverse living tetrapod group and are a model of large-scale adaptive radiation. Neontological studies suggest a radiation within the avian crown group, long after the origin of flight. However, deep time patterns of bird evolution remain obscure because only limited fossil data have been considered. We analyse cladogenesis and limb evolution on the entire tree of Mesozoic theropods, documenting the dinosaur–bird transition and immediate origins of powered flight. Mesozoic birds inherited constraints on forelimb evolution from non-flying ancestors, and species diversification rates did not accelerate in the earliest flying taxa. However, Early Cretaceous short-tailed birds exhibit both phenotypic release of the hindlimb and increased diversification rates, unparalleled in magnitude at any other time in the first 155 Myr of theropod evolution. Thus, a Cretaceous adaptive radiation of stem-group birds was enabled by restructuring of the terrestrial locomotor module, which represents a key innovation. Our results suggest two phases of radiation in Avialae: with the Cretaceous diversification overwritten by extinctions of stem-group birds at the Cretaceous–Palaeogene boundary, and subsequent diversification of the crown group. Our findings illustrate the importance of fossil data for understanding the macroevolutionary processes generating modern biodiversity. PMID:23945695

  19. Skeletal development in sloths and the evolution of mammalian vertebral patterning.

    PubMed

    Hautier, Lionel; Weisbecker, Vera; Sánchez-Villagra, Marcelo R; Goswami, Anjali; Asher, Robert J

    2010-11-01

    Mammals show a very low level of variation in vertebral count, particularly in the neck. Phenotypes exhibited at various stages during the development of the axial skeleton may play a key role in testing mechanisms recently proposed to explain this conservatism. Here, we provide osteogenetic data that identify developmental criteria with which to recognize cervical vs. noncervical vertebrae in mammals. Except for sloths, all mammals show the late ossification of the caudal-most centra in the neck after other centra and neural arches. In sloths with 8-10 ribless neck vertebrae, the caudal-most neck centra ossify early, matching the pattern observed in cranial thoracic vertebrae of other mammals. Accordingly, we interpret the ribless neck vertebrae of three-toed sloths caudal to V7 as thoracic based on our developmental criterion. Applied to the unusual vertebral phenotype of long-necked sloths, these data support the interpretation that elements of the axial skeleton with origins from distinct mesodermal tissues have repatterned over the course of evolution. PMID:20956304

  20. Skeletal development in sloths and the evolution of mammalian vertebral patterning

    PubMed Central

    Hautier, Lionel; Weisbecker, Vera; Sánchez-Villagra, Marcelo R.; Goswami, Anjali; Asher, Robert J.

    2010-01-01

    Mammals show a very low level of variation in vertebral count, particularly in the neck. Phenotypes exhibited at various stages during the development of the axial skeleton may play a key role in testing mechanisms recently proposed to explain this conservatism. Here, we provide osteogenetic data that identify developmental criteria with which to recognize cervical vs. noncervical vertebrae in mammals. Except for sloths, all mammals show the late ossification of the caudal-most centra in the neck after other centra and neural arches. In sloths with 8–10 ribless neck vertebrae, the caudal-most neck centra ossify early, matching the pattern observed in cranial thoracic vertebrae of other mammals. Accordingly, we interpret the ribless neck vertebrae of three-toed sloths caudal to V7 as thoracic based on our developmental criterion. Applied to the unusual vertebral phenotype of long-necked sloths, these data support the interpretation that elements of the axial skeleton with origins from distinct mesodermal tissues have repatterned over the course of evolution. PMID:20956304

  1. Patterns of Evolutionary Conservation of Microsatellites (SSRs) Suggest a Faster Rate of Genome Evolution in Hymenoptera Than in Diptera

    PubMed Central

    Stolle, Eckart; Kidner, Jonathan H.; Moritz, Robin F.A.

    2013-01-01

    Microsatellites, or simple sequence repeats (SSRs), are common and widespread DNA elements in genomes of many organisms. However, their dynamics in genome evolution is unclear, whereby they are thought to evolve neutrally. More available genome sequences along with dated phylogenies allowed for studying the evolution of these repetitive DNA elements along evolutionary time scales. This could be used to compare rates of genome evolution. We show that SSRs in insects can be retained for several hundred million years. Different types of microsatellites seem to be retained longer than others. By comparing Dipteran with Hymenopteran species, we found very similar patterns of SSR loss during their evolution, but both taxa differ profoundly in the rate. Relative to divergence time, Diptera lost SSRs twice as fast as Hymenoptera. The loss of SSRs on the Drosophila melanogaster X-chromosome was higher than on the other chromosomes. However, accounting for generation time, the Diptera show an 8.5-fold slower rate of SSR loss than the Hymenoptera, which, in contrast to previous studies, suggests a faster genome evolution in the latter. This shows that generation time differences can have a profound effect. A faster genome evolution in these insects could be facilitated by several factors very different to Diptera, which is discussed in light of our results on the haplodiploid D. melanogaster X-chromosome. Furthermore, large numbers of SSRs can be found to be in synteny and thus could be exploited as a tool to investigate genome structure and evolution. PMID:23292136

  2. ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera.

    PubMed

    Lewis, James J; van der Burg, Karin R L; Mazo-Vargas, Anyi; Reed, Robert D

    2016-09-13

    Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq) annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution. PMID:27626657

  3. Macroevolutionary consequences of profound climate change on niche evolution in marine molluscs over the past three million years.

    PubMed

    Saupe, E E; Hendricks, J R; Portell, R W; Dowsett, H J; Haywood, A; Hunter, S J; Lieberman, B S

    2014-11-22

    In order to predict the fate of biodiversity in a rapidly changing world, we must first understand how species adapt to new environmental conditions. The long-term evolutionary dynamics of species' physiological tolerances to differing climatic regimes remain obscure. Here, we unite palaeontological and neontological data to analyse whether species' environmental tolerances remain stable across 3 Myr of profound climatic changes using 10 phylogenetically, ecologically and developmentally diverse mollusc species from the Atlantic and Gulf Coastal Plains, USA. We additionally investigate whether these species' upper and lower thermal tolerances are constrained across this interval. We find that these species' environmental preferences are stable across the duration of their lifetimes, even when faced with significant environmental perturbations. The results suggest that species will respond to current and future warming either by altering distributions to track suitable habitat or, if the pace of change is too rapid, by going extinct. Our findings also support methods that project species' present-day environmental requirements to future climatic landscapes to assess conservation risks. PMID:25297868

  4. Macroevolutionary consequences of profound climate change on niche evolution in marine molluscs over the past three million years

    USGS Publications Warehouse

    Saupe, E.E.; Hendricks, J.R.; Portell, R.W.; Dowsett, Harry J.; Haywood, A. M.; Hunter, S.J.; Lieberman, B.S.

    2014-01-01

    In order to predict the fate of biodiversity in a rapidly changing world, we must first understand how species adapt to new environmental conditions. The long-term evolutionary dynamics of species' physiological tolerances to differing climatic regimes remain obscure. Here, we unite palaeontological and neontological data to analyse whether species' environmental tolerances remain stable across 3 Myr of profound climatic changes using 10 phylogenetically, ecologically and developmentally diverse mollusc species from the Atlantic and Gulf Coastal Plains, USA. We additionally investigate whether these species' upper and lower thermal tolerances are constrained across this interval. We find that these species' environmental preferences are stable across the duration of their lifetimes, even when faced with significant environmental perturbations. The results suggest that species will respond to current and future warming either by altering distributions to track suitable habitat or, if the pace of change is too rapid, by going extinct. Our findings also support methods that project species' present-day environmental requirements to future climatic landscapes to assess conservation risks.

  5. Macroevolutionary consequences of profound climate change on niche evolution in marine molluscs over the past three million years

    PubMed Central

    Saupe, E. E.; Hendricks, J. R.; Portell, R. W.; Dowsett, H. J.; Haywood, A.; Hunter, S. J.; Lieberman, B. S.

    2014-01-01

    In order to predict the fate of biodiversity in a rapidly changing world, we must first understand how species adapt to new environmental conditions. The long-term evolutionary dynamics of species' physiological tolerances to differing climatic regimes remain obscure. Here, we unite palaeontological and neontological data to analyse whether species' environmental tolerances remain stable across 3 Myr of profound climatic changes using 10 phylogenetically, ecologically and developmentally diverse mollusc species from the Atlantic and Gulf Coastal Plains, USA. We additionally investigate whether these species' upper and lower thermal tolerances are constrained across this interval. We find that these species' environmental preferences are stable across the duration of their lifetimes, even when faced with significant environmental perturbations. The results suggest that species will respond to current and future warming either by altering distributions to track suitable habitat or, if the pace of change is too rapid, by going extinct. Our findings also support methods that project species' present-day environmental requirements to future climatic landscapes to assess conservation risks. PMID:25297868

  6. Handling and Use of Oxygen by Pancrustaceans: Conserved Patterns and the Evolution of Respiratory Structures.

    PubMed

    Harrison, Jon F

    2015-11-01

    The handling and use of oxygen are central to physiological function of all pancrustaceans. Throughout the Pancrustacea, ventilation is controlled by a central oxygen-sensitive pattern generator. The ancestral condition was likely to achieve ventilation of the gills via leg-associated or mouth-associated muscles, but in insects and some air-breathing crustaceans, new muscles were recruited for this purpose, including intersegmental muscles likely used previously for posture and locomotion. Many aspects of the sensing of oxygen and the occurrence of responses to hypoxia (increased ventilation, depressed growth and metabolic rate, developmental changes that enhance the delivery of oxygen) appear common across most pancrustaceans, but there is tremendous variation across species. Some of this can be explained by habitat (e.g., ventilation of the internal medium occurs in terrestrial species and of the external medium in aquatic species; rearing under hypoxia induces tracheal proliferation in terrestrial insects and hemocyanin production in aquatic crustaceans); some plausibly by evolutionary origin of some responses to hypoxia within the Pancrustacea (the most basal arthropods may lack a ventilatory response to hypoxia); and some by the availability of environmental oxygen (animals adapted to survive hypoxia turn on the response to hypoxia at a lower PO2). On average, crustaceans and insects have similar tolerances to prolonged anoxia, but species or life stages from habitats with a danger of being trapped in hypoxia can tolerate longer durations of anoxia. Lactate is the primary anaerobic end-product in crustaceans but some insects have evolved a more diverse array of anaerobic end-products, including ethanol, alanine, succinate, and acetate. Most clades of Pancrustacea are small and lack obvious respiratory structures. Gilled stem-pancrustaceans likely evolved in the Cambrian, and gills persist in large Ostracoda, Malacostraca, and Branchiopoda. Based on currently

  7. SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in warblers.

    PubMed

    Bloch, Natasha I; Morrow, James M; Chang, Belinda S W; Price, Trevor D

    2015-02-01

    Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors-historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short-wavelength-sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between clades. We show SWS2 is short-wavelength shifted in birds that occupy open environments, such as finches, compared to those in closed environments, including warblers. Phylogenetic reconstructions indicate New World warblers were derived from a finch-like form that colonized from the Old World 15-20 Ma. During this process, the SWS2 gene accumulated six substitutions in branches leading to New World warblers, inviting the hypothesis that passage through a finch-like ancestor resulted in SWS2 evolution. In fact, we show spectral tuning remained similar across warblers as well as the finch ancestor. Results reject the hypothesis of historical contingency based on opsin spectral tuning, but point to evolution of other aspects of visual pigment function. Using the approach outlined here, historical contingency becomes a generally testable theory in systems where genotype and phenotype can be connected. PMID:25496318

  8. SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in Warblers

    PubMed Central

    Bloch, Natasha I.; Morrow, James M.; Chang, Belinda S.W.; Price, Trevor D.

    2014-01-01

    Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors – historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short-wavelength sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between clades. We show SWS2 is short-wavelength shifted in birds that occupy open environments, such as finches, compared to those in closed environments, including warblers. Phylogenetic reconstructions indicate New World warblers were derived from a finch-like form that colonized from the Old World 15-20Ma. During this process the SWS2 gene accumulated 6 substitutions in branches leading to New World warblers, inviting the hypothesis that passage through a finch-like ancestor resulted in SWS2 evolution. In fact, we show spectral tuning remained similar across warblers as well as the finch ancestor. Results reject the hypothesis of historical contingency based on opsin spectral tuning, but point to evolution of other aspects of visual pigment function. Using the approach outlined here, historical contingency becomes a generally testable theory in systems where genotype and phenotype can be connected. PMID:25496318

  9. Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

    SciTech Connect

    Lapidus, Alla; Kettler, Gregory C.; Martiny, Adam C.; Huang, Katherine; Zucker, Jeremy; Coleman, Maureen L.; Rodrigue, Sebastien; Chen, Feng; Lapidus, Alla; Ferriera, Steven; Johnson, Justin; Steglich, Claudia; Church, George M.; Richardson, Paul; Chisholm, Sallie W.

    2007-07-30

    Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolatesfrom diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3percent, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer

  10. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus.

    PubMed

    Kettler, Gregory C; Martiny, Adam C; Huang, Katherine; Zucker, Jeremy; Coleman, Maureen L; Rodrigue, Sebastien; Chen, Feng; Lapidus, Alla; Ferriera, Steven; Johnson, Justin; Steglich, Claudia; Church, George M; Richardson, Paul; Chisholm, Sallie W

    2007-12-01

    Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3%, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane

  11. Peritumoral Brain Edema after Stereotactic Radiosurgery for Asymptomatic Intracranial Meningiomas: Risks and Pattern of Evolution

    PubMed Central

    Hoe, Yeon; Choi, Young Jae; Kim, Jeong Hoon; Kwon, Do Hoon; Kim, Chang Jin

    2015-01-01

    Objective To investigate the risks and pattern of evolution of peritumoral brain edema (PTE) after stereotactic radiosurgery (SRS) for asymptomatic intracranial meningiomas. Methods A retrospective study was conducted on 320 patients (median age 56 years, range 24-87 years) who underwent primary Gamma Knife radiosurgery for asymptomatic meningiomas between 1998 and 2012. The median tumor volume was 2.7 cc (range 0.2-10.5 cc) and the median follow-up was 48 months (range 24-168 months). Volumetric data sets for tumors and PTE on serial MRIs were analyzed. The edema index (EI) was defined as the ratio of the volume of PTE including tumor to the tumor volume, and the relative edema indices (rEIs) were calculated from serial EIs normalized against the baseline EI. Risk factors for PTE were analyzed using logistic regression. Results Newly developed or increased PTE was noted in 49 patients (15.3%), among whom it was symptomatic in 28 patients (8.8%). Tumor volume larger than 4.2 cc (p<0.001), hemispheric tumor location (p=0.005), and pre-treatment PTE (p<0.001) were associated with an increased risk of PTE. rEI reached its maximum value at 11 months after SRS and decreased thereafter, and symptoms resolved within 24 months in most patients (85.7%). Conclusion Caution should be exercised in decision-making on SRS for asymptomatic meningiomas of large volume (>4.2 cc), of hemispheric location, or with pre-treatment PTE. PTE usually develops within months, reaches its maximum degree until a year, and resolves within 2 years after SRS. PMID:26587194

  12. Patterns of molecular evolution of RNAi genes in social and socially parasitic bumblebees.

    PubMed

    Helbing, Sophie; Lattorff, H Michael G

    2016-08-01

    The high frequency of interactions amongst closely related individuals in social insect colonies enhances pathogen transmission. Group-mediated behavior supporting immune defenses tends to decrease selection acting on immune genes. Along with low effective population sizes this might result in relaxed constraint and rapid evolution of immune system genes. Here, we show that antiviral siRNA genes show high rates of molecular evolution with argonaute 2, armitage and maelstrom evolving faster in social bumblebees compared to their socially parasitic cuckoo bumblebees that lack a worker caste. RNAi genes show frequent positive selection at the codon level additionally supported by the occurrence of parallel evolution. Their evolutionary rate is linked to their pathway specific position with genes directly interacting with viruses showing the highest rates of molecular evolution. We suggest that higher pathogen load in social insects indeed drives the molecular evolution of immune genes including antiviral siRNA, if not compensated by behavior. PMID:27117935

  13. Larval body patterning and apical organs are conserved in animal evolution

    PubMed Central

    2014-01-01

    Background Planktonic ciliated larvae are characteristic for the life cycle of marine invertebrates. Their most prominent feature is the apical organ harboring sensory cells and neurons of largely undetermined function. An elucidation of the relationships between various forms of primary larvae and apical organs is key to understanding the evolution of animal life cycles. These relationships have remained enigmatic due to the scarcity of comparative molecular data. Results To compare apical organs and larval body patterning, we have studied regionalization of the episphere, the upper hemisphere of the trochophore larva of the marine annelid Platynereis dumerilii. We examined the spatial distribution of transcription factors and of Wnt signaling components previously implicated in anterior neural development. Pharmacological activation of Wnt signaling with Gsk3β antagonists abolishes expression of apical markers, consistent with a repressive role of Wnt signaling in the specification of apical tissue. We refer to this Wnt-sensitive, six3- and foxq2-expressing part of the episphere as the ‘apical plate’. We also unraveled a molecular signature of the apical organ - devoid of six3 but expressing foxj, irx, nkx3 and hox - that is shared with other marine phyla including cnidarians. Finally, we characterized the cell types that form part of the apical organ by profiling by image registration, which allows parallel expression profiling of multiple cells. Besides the hox-expressing apical tuft cells, this revealed the presence of putative light- and mechanosensory as well as multiple peptidergic cell types that we compared to apical organ cell types of other animal phyla. Conclusions The similar formation of a six3+, foxq2+ apical plate, sensitive to Wnt activity and with an apical tuft in its six3-free center, is most parsimoniously explained by evolutionary conservation. We propose that a simple apical organ - comprising an apical tuft and a basal plexus

  14. Temporal evolution and alternation of mechanisms of electric-field-induced patterns at ultralow-frequency driving

    NASA Astrophysics Data System (ADS)

    Éber, Nándor; Palomares, Laura O.; Salamon, Péter; Krekhov, Alexei; Buka, Ágnes

    2012-08-01

    The temporal evolution of patterns within the driving period of the ac voltage was studied in the 10-mHz-250-Hz frequency range. It was shown that the stationary electroconvection pattern of the conductive regime transforms into a flashing one at ultralow frequencies, existing only in narrow time windows within the period. Furthermore a transition between electroconvection and flexoelectric domains was detected which is repeating in each half period. The two patterns are well separated in time and in Fourier space. Simultaneous current measurements uncovered that the electric properties of the polyimide orienting layers influence the redistribution of the applied voltage. The experimental findings are in good qualitative agreement with the theoretical predictions based on an extended standard model including flexoelectricity.

  15. Shape evolution and finite deformation pattern in analog experiments of lithosphere necking

    NASA Astrophysics Data System (ADS)

    Nestola, Yago; Storti, Fabrizio; Bedogni, Enrico; Cavozzi, Cristian

    2013-10-01

    necking evolution determines the 3-D architecture of crustal and upper mantle thinning and related basins, and the heat flow distribution in rifted regions. Despite a large number of studies, lithosphere necking evolution is still a matter of debate. We present the result from lithospheric-scale analog models designed for investigating the necking shape during extension and the vertical distribution of finite deformation in the mechanical lithosphere. In our experiments, lithosphere necking is asymmetric and, in particular, the 3-D distribution of thinning is cylindrical in the crust and very heterogeneous in the mantle. Overall, the evolution of rifting and necking progresses from delocalized to localized deformation.

  16. Herbivory Promotes Dental Disparification and Macroevolutionary Dynamics in Grunters (Teleostei: Terapontidae), a Freshwater Adaptive Radiation.

    PubMed

    Davis, Aaron M; Unmack, Peter J; Vari, Richard P; Betancur-R, Ricardo

    2016-03-01

    Trophic shifts into new adaptive zones have played major (although often conflicting) roles in reshaping the evolutionary trajectories of many lineages. We analyze data on diet, tooth, and oral morphology and relate these traits to phenotypic disparification and lineage diversification rates across the ecologically diverse Terapontidae, a family of Australasian fishes. In contrast to carnivores and most omnivores, which have retained relatively simple, ancestral caniniform tooth shapes, herbivorous terapontids appear to have evolved a variety of novel tooth shapes at significantly faster rates to meet the demands of plant-based diets. The evolution of herbivory prompted major disparification, significantly expanding the terapontid adaptive phenotypic continuum into an entirely novel functional morphospace. There was minimal support for our hypothesis of faster overall rates of integrated tooth shape, spacing, and jaw biomechanical evolution in herbivorous terapontids in their entirety, compared with other trophic strategies. There was, however, considerable support for accelerated disparification within a diverse freshwater clade containing a range of specialized freshwater herbivores. While the evolutionary transition to herbivorous diets has played a central role in terapontid phenotypic diversification by pushing herbivores toward novel fitness peaks, there was little support for herbivory driving significantly higher lineage diversification compared with background rates across the family. PMID:26913945

  17. The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq

    PubMed Central

    Renaut, Sébastien; Grassa, Christopher J.; Moyers, Brook T.; Kane, Nolan C.; Rieseberg, Loren H.

    2012-01-01

    Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq) to refine our understanding of the population genomics of wild species of sunflowers (Helianthus spp.) and the factors that affect rates of protein evolution. We aligned 35 GB of transcriptome sequencing data and identified 433,257 polymorphic sites (SNPs) in a reference transcriptome comprising 16,312 genes. Using SNP markers, we identified strong population clustering largely corresponding to the three species analyzed here (Helianthus annuus, H. petiolaris, H. debilis), with one distinct early generation hybrid. Then, we calculated the proportions of adaptive substitution fixed by selection (alpha) and identified gene ontology categories with elevated values of alpha. The “response to biotic stimulus” category had the highest mean alpha across the three interspecific comparisons, implying that natural selection imposed by other organisms plays an important role in driving protein evolution in wild sunflowers. Finally, we examined the relationship between protein evolution (dN/dS ratio) and several genomic factors predicted to co-vary with protein evolution (gene expression level, divergence and specificity, genetic divergence [FST], and nucleotide diversity pi). We find that variation in rates of protein divergence was correlated with gene expression level and specificity, consistent with results from a broad range of taxa and timescales. This would in turn imply that these factors govern protein evolution both at a microevolutionary and macroevolutionary timescale. Our results contribute to a general understanding of the determinants

  18. Temporal and phylogenetic evolution of the sauropod dinosaur body plan

    PubMed Central

    Bates, Karl T.; Mannion, Philip D.; Falkingham, Peter L.; Brusatte, Stephen L.; Hutchinson, John R.; Otero, Alejandro; Sellers, William I.; Sullivan, Corwin; Stevens, Kent A.; Allen, Vivian

    2016-01-01

    The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean absolute body shape predictions. However, applying any consistent skeleton : body volume ratio to all taxa does yield changes in body shape that appear concurrent with major macroevolutionary events in sauropod history. A caudad shift in centre-of-mass (CoM) in Middle Triassic Saurischia, associated with the evolution of bipedalism in various dinosaur lineages, was reversed in Late Triassic sauropodomorphs. A craniad CoM shift coincided with the evolution of quadrupedalism in the Late Triassic, followed by a more striking craniad shift in Late Jurassic–Cretaceous titanosauriforms, which included the largest sauropods. These craniad CoM shifts are strongly correlated with neck enlargement, a key innovation in sauropod evolution and pivotal to their gigantism. By creating a much larger feeding envelope, neck elongation is thought to have increased feeding efficiency and opened up trophic niches that were inaccessible to other herbivores. However, we find that relative neck size and CoM position are not strongly correlated with inferred feeding habits. Instead the craniad CoM positions of titanosauriforms appear closely linked with locomotion and environmental distributions, potentially contributing to the continued success of this group until the end-Cretaceous, with all other sauropods having gone extinct by the early Late Cretaceous. PMID:27069652

  19. Temporal and phylogenetic evolution of the sauropod dinosaur body plan.

    PubMed

    Bates, Karl T; Mannion, Philip D; Falkingham, Peter L; Brusatte, Stephen L; Hutchinson, John R; Otero, Alejandro; Sellers, William I; Sullivan, Corwin; Stevens, Kent A; Allen, Vivian

    2016-03-01

    The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean absolute body shape predictions. However, applying any consistent skeleton : body volume ratio to all taxa does yield changes in body shape that appear concurrent with major macroevolutionary events in sauropod history. A caudad shift in centre-of-mass (CoM) in Middle Triassic Saurischia, associated with the evolution of bipedalism in various dinosaur lineages, was reversed in Late Triassic sauropodomorphs. A craniad CoM shift coincided with the evolution of quadrupedalism in the Late Triassic, followed by a more striking craniad shift in Late Jurassic-Cretaceous titanosauriforms, which included the largest sauropods. These craniad CoM shifts are strongly correlated with neck enlargement, a key innovation in sauropod evolution and pivotal to their gigantism. By creating a much larger feeding envelope, neck elongation is thought to have increased feeding efficiency and opened up trophic niches that were inaccessible to other herbivores. However, we find that relative neck size and CoM position are not strongly correlated with inferred feeding habits. Instead the craniad CoM positions of titanosauriforms appear closely linked with locomotion and environmental distributions, potentially contributing to the continued success of this group until the end-Cretaceous, with all other sauropods having gone extinct by the early Late Cretaceous. PMID:27069652

  20. Development and evolution of the unique cetacean dentition

    PubMed Central

    Zheng, Zhengui; Bajpai, Sunil; Vinyard, Christopher J.; Thewissen, JGM

    2013-01-01

    The evolutionary success of mammals is rooted in their high metabolic rate. A high metabolic rate is sustainable thanks to efficient food processing and that in turn is facilitated by precise occlusion of the teeth and the acquisition of rhythmic mastication. These major evolutionary innovations characterize most members of the Class Mammalia. Cetaceans are one of the few groups of mammals in which precise occlusion has been secondarily lost. Most toothed whales have an increased number of simple crowned teeth that are similar along the tooth row. Evolution toward these specializations began immediately after the time cetaceans transitioned from terrestrial-to-marine environments. The fossil record documents the critical aspects of occlusal evolution of cetaceans, and allows us to pinpoint the evolutionary timing of the macroevolutionary events leading to their unusual dental morphology among mammals. The developmental controls of tooth differentiation and tooth number have been studied in a few mammalian clades, but nothing is known about how these controls differ between cetaceans and mammals that retain functional occlusion. Here we show that pigs, a cetacean relative with regionalized tooth morphology and complex tooth crowns, retain the typical mammalian gene expression patterns that control early tooth differentiation, expressing Bmp4 in the rostral (mesial, anterior) domain of the jaw, and Fgf8 caudally (distal, posterior). By contrast, dolphins have lost these regional differences in dental morphology and the Bmp4 domain is extended into the caudal region of the developing jaw. We hypothesize that the functional constraints underlying mammalian occlusion have been released in cetaceans, facilitating changes in the genetic control of early dental development. Such major developmental changes drive morphological evolution and are correlated with major shifts in diet and food processing during cetacean evolution. PMID:23638359

  1. The repeated evolution of large seeds on islands

    PubMed Central

    Kavanagh, Patrick H.; Burns, Kevin C.

    2014-01-01

    Several plant traits are known to evolve in predictable ways on islands. For example, herbaceous species often evolve to become woody and species frequently evolve larger leaves, regardless of growth form. However, our understanding of how seed sizes might evolve on islands lags far behind other plant traits. Here, we conduct the first test for macroevolutionary patterns of seed size on islands. We tested for differences in seed size between 40 island–mainland taxonomic pairings from four island groups surrounding New Zealand. Seed size data were collected in the field and then augmented by published seed descriptions to produce a more comprehensive dataset. Seed sizes of insular plants were consistently larger than mainland relatives, even after accounting for differences in growth form, dispersal mode and evolutionary history. Selection may favour seed size increases on islands to reduce dispersibility, as long-distance dispersal may result in propagule mortality at sea. Alternatively, larger seeds tend to generate larger seedlings, which are more likely to establish and outcompete neighbours. Our results indicate there is a general tendency for the evolution of large seeds on islands, but the mechanisms responsible for this evolutionary pathway have yet to be fully resolved. PMID:24850930

  2. From Central Pattern Generator to Sensory Template in the Evolution of Birdsong

    ERIC Educational Resources Information Center

    Konishi, Masakazu

    2010-01-01

    Central nervous networks, be they a part of the human brain or a group of neurons in a snail, may be designed to produce distinct patterns of movement. Central pattern generators can account for the development and production of normal vocal signals without auditory feedback in non-songbirds. Songbirds need auditory feedback to develop and…

  3. Riparian vegetation patterns in relation to fluvial landforms and channel evolution along selected rivers of Tuscany (Central Italy)

    USGS Publications Warehouse

    Hupp, C.R.; Rinaldi, M.

    2007-01-01

    Riparian vegetation distribution patterns and diversity relative to various fluvial geomorphic channel patterns, landforms, and processes are described and interpreted for selected rivers of Tuscany, Central Italy; with emphasis on channel evolution following human impacts. Field surveys were conducted along thirteen gauged reaches for species presence, fluvial landforms, and the type and amount of channel/riparian zone change. Inundation frequency of different geomorphic surfaces was determined, and vegetation data were analyzed using BDA (binary discriminate analysis) and DCA (detrended correspondence analysis) and related to hydrogeomorphology. Multivariate analyses revealed distinct quantitative vegetation patterns relative to six major fluvial geomorphic surfaces. DCA of the vegetation data also showed distinct associations of plants to processes of adjustment that are related to stage of channel evolution, and clearly separated plants along disturbance/landform/soil moisture gradients. Species richness increases from the channel bed to the terrace and on heterogeneous riparian areas, whereas species richness decreases from moderate to intense incision and from low to intense narrowing. ?? 2007 by Association of American Geographers.

  4. The Evolution of Brachiopoda

    NASA Astrophysics Data System (ADS)

    Carlson, Sandra J.

    2016-06-01

    Brachiopods are (perhaps all too) familiar to any geology student who has taken an invertebrate paleontology course; they may well be less familiar to biology students. Even though brachiopods are among the most significant components of the marine fossil record by virtue of their considerable diversity, abundance, and long evolutionary history, fewer than 500 species are extant. Reconciling the geological and biological perspectives is necessary in order to test hypotheses, not only about phylogenetic relationships among brachiopods but also about their spectacular decline in diversity in the end-Permian mass extinction, which permanently reset their evolutionary trajectory. Studying brachiopod ontogeny and development, population genetics, ecology, physiology, and biogeography, as well as molecular systematics and phylogenomics, enables us to better understand the context of evolutionary processes over the short term. Investigating brachiopod morphological, taxonomic, and stratigraphic records over the Phanerozoic Eon reveals historical patterns of long-term macroevolutionary change, patterns that are simply unknowable from a biological perspective alone.

  5. A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction.

    PubMed

    Payne, Jonathan L; Jost, Adam B; Wang, Steve C; Skotheim, Jan M

    2013-03-01

    Size is among the most important traits of any organism, yet the factors that control its evolution remain poorly understood. In this study, we investigate controls on the evolution of organismal size using a newly compiled database of nearly 25,000 foraminiferan species and subspecies spanning the past 400 million years. We find a transition in the pattern of foraminiferan size evolution from correlation with atmospheric pO2 during the Paleozoic (400-250 million years ago) to long-term stasis during the post-Paleozoic (250 million years ago to present). Thus, a dramatic shift in the evolutionary mode coincides with the most severe biotic catastrophe of the Phanerozoic (543 million years ago to present). Paleozoic tracking of pO2 was confined to Order Fusulinida, whereas Paleozoic lagenides, miliolids, and textulariids were best described by the stasis model. Stasis continued to best describe miliolids and textulariids during post-Paleozoic time, whereas random walk was the best supported mode for the other diverse orders. The shift in evolutionary dynamics thus appears to have resulted primarily from the selective elimination of fusulinids at the end of the Permian Period. These findings illustrate the potential for mass extinction to alter macroevolutionary dynamics for hundreds of millions of years. PMID:23461330

  6. Patterns of Genome Evolution among the Microsporidian Parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi

    PubMed Central

    Morrison, Hilary G.; Feng, Xiaochuan; Weiss, Louis M.; Tzipori, Saul; Keeling, Patrick J.

    2007-01-01

    Background Microsporidia are intracellular parasites that are highly-derived relatives of fungi. They have compacted genomes and, despite a high rate of sequence evolution, distantly related species can share high levels of gene order conservation. To date, only two species have been analysed in detail, and data from one of these largely consists of short genomic fragments. It is therefore difficult to determine how conservation has been maintained through microsporidian evolution, and impossible to identify whether certain regions are more prone to genomic stasis. Principal Findings Here, we analyse three large fragments of the Enterocytozoon bieneusi genome (in total 429 kbp), a species of medical significance. A total of 296 ORFs were identified, annotated and their context compared with Encephalitozoon cuniculi and Antonospora locustae. Overall, a high degree of conservation was found between all three species, and interestingly the level of conservation was similar in all three pairwise comparisons, despite the fact that A. locustae is more distantly related to E. cuniculi and E. bieneusi than either are to each other. Conclusions/Significance Any two genes that are found together in any pair of genomes are more likely to be conserved in the third genome as well, suggesting that a core of genes tends to be conserved across the entire group. The mechanisms of rearrangments identified among microsporidian genomes were consistent with a very slow evolution of their architecture, as opposed to the very rapid sequence evolution reported for these parasites. PMID:18060071

  7. Experimental evolution alters the rate and temporal pattern of population growth in Batrachochytrium dendrobatidis, a lethal fungal pathogen of amphibians

    PubMed Central

    Voyles, Jamie; Johnson, Leah R; Briggs, Cheryl J; Cashins, Scott D; Alford, Ross A; Berger, Lee; Skerratt, Lee F; Speare, Rick; Rosenblum, Erica Bree

    2014-01-01

    Virulence of infectious pathogens can be unstable and evolve rapidly depending on the evolutionary dynamics of the organism. Experimental evolution can be used to characterize pathogen evolution, often with the underlying objective of understanding evolution of virulence. We used experimental evolution techniques (serial transfer experiments) to investigate differential growth and virulence of Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes amphibian chytridiomycosis. We tested two lineages of Bd that were derived from a single cryo-archived isolate; one lineage (P10) was passaged 10 times, whereas the second lineage (P50) was passaged 50 times. We quantified time to zoospore release, maximum zoospore densities, and timing of zoospore activity and then modeled population growth rates. We also conducted exposure experiments with a susceptible amphibian species, the common green tree frog (Litoria caerulea) to test the differential pathogenicity. We found that the P50 lineage had shorter time to zoospore production (Tmin), faster rate of sporangia death (ds), and an overall greater intrinsic population growth rate (λ). These patterns of population growth in vitro corresponded with higher prevalence and intensities of infection in exposed Litoria caerulea, although the differences were not significant. Our results corroborate studies that suggest that Bd may be able to evolve relatively rapidly. Our findings also challenge the general assumption that pathogens will always attenuate in culture because shifts in Bd virulence may depend on laboratory culturing practices. These findings have practical implications for the laboratory maintenance of Bd isolates and underscore the importance of understanding the evolution of virulence in amphibian chytridiomycosis. PMID:25478154

  8. Experimental evolution alters the rate and temporal pattern of population growth in Batrachochytrium dendrobatidis, a lethal fungal pathogen of amphibians.

    PubMed

    Voyles, Jamie; Johnson, Leah R; Briggs, Cheryl J; Cashins, Scott D; Alford, Ross A; Berger, Lee; Skerratt, Lee F; Speare, Rick; Rosenblum, Erica Bree

    2014-09-01

    Virulence of infectious pathogens can be unstable and evolve rapidly depending on the evolutionary dynamics of the organism. Experimental evolution can be used to characterize pathogen evolution, often with the underlying objective of understanding evolution of virulence. We used experimental evolution techniques (serial transfer experiments) to investigate differential growth and virulence of Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes amphibian chytridiomycosis. We tested two lineages of Bd that were derived from a single cryo-archived isolate; one lineage (P10) was passaged 10 times, whereas the second lineage (P50) was passaged 50 times. We quantified time to zoospore release, maximum zoospore densities, and timing of zoospore activity and then modeled population growth rates. We also conducted exposure experiments with a susceptible amphibian species, the common green tree frog (Litoria caerulea) to test the differential pathogenicity. We found that the P50 lineage had shorter time to zoospore production (T min ), faster rate of sporangia death (d s ), and an overall greater intrinsic population growth rate (λ). These patterns of population growth in vitro corresponded with higher prevalence and intensities of infection in exposed Litoria caerulea, although the differences were not significant. Our results corroborate studies that suggest that Bd may be able to evolve relatively rapidly. Our findings also challenge the general assumption that pathogens will always attenuate in culture because shifts in Bd virulence may depend on laboratory culturing practices. These findings have practical implications for the laboratory maintenance of Bd isolates and underscore the importance of understanding the evolution of virulence in amphibian chytridiomycosis. PMID:25478154

  9. Evolution

    NASA Astrophysics Data System (ADS)

    Peter, Ulmschneider

    When we are looking for intelligent life outside the Earth, there is a fundamental question: Assuming that life has formed on an extraterrestrial planet, will it also develop toward intelligence? As this is hotly debated, we will now describe the development of life on Earth in more detail in order to show that there are good reasons why evolution should culminate in intelligent beings.

  10. The evolution of colour pattern complexity: selection for conspicuousness favours contrasting within-body colour combinations in lizards.

    PubMed

    Pérez I de Lanuza, G; Font, E

    2016-05-01

    Many animals display complex colour patterns that comprise several adjacent, often contrasting colour patches. Combining patches of complementary colours increases the overall conspicuousness of the complex pattern, enhancing signal detection. Therefore, selection for conspicuousness may act not only on the design of single colour patches, but also on their combination. Contrasting long- and short-wavelength colour patches are located on the ventral and lateral surfaces of many lacertid lizards. As the combination of long- and short-wavelength-based colours generates local chromatic contrast, we hypothesized that selection may favour the co-occurrence of lateral and ventral contrasting patches, resulting in complex colour patterns that maximize the overall conspicuousness of the signal. To test this hypothesis, we performed a comparative phylogenetic study using a categorical colour classification based on spectral data and descriptive information on lacertid coloration collected from the literature. Our results demonstrate that conspicuous ventral (long-wavelength-based) and lateral (short-wavelength-based) colour patches co-occur throughout the lacertid phylogeny more often than expected by chance, especially in the subfamily Lacertini. These results suggest that selection promotes the evolution of the complex pattern rather than the acquisition of a single conspicuous colour patch, possibly due to the increased conspicuousness caused by the combination of colours with contrasting spectral properties. PMID:26801820

  11. Onshore–offshore gradient in metacommunity turnover emerges only over macroevolutionary time-scales

    PubMed Central

    Tomašových, Adam; Dominici, Stefano; Zuschin, Martin; Merle, Didier

    2014-01-01

    Invertebrate lineages tend to originate and become extinct at a higher rate in onshore than in offshore habitats over long temporal durations (more than 10 Myr), but it remains unclear whether this pattern scales down to durations of stages (less than 5 Myr) or even sequences (less than 0.5 Myr). We assess whether onshore–offshore gradients in long-term turnover between the tropical Eocene and the warm-temperate Plio-Pleistocene can be extrapolated from gradients in short-term turnover, using abundances of molluscan species from bulk samples in the northeast Atlantic Province. We find that temporal turnover of metacommunities does not significantly decline with depth over short durations (less than 5 Myr), but significantly declines with depth between the Eocene and Plio-Pleistocene (approx. 50 Myr). This decline is determined by a higher onshore extinction of Eocene genera and families, by a higher onshore variability in abundances of genera and families, and by an onshore expansion of genera and families that were frequent offshore in the Eocene. Onshore–offshore decline in turnover thus emerges only over long temporal durations. We suggest that this emergence is triggered by abrupt and spatially extensive climatic or oceanographic perturbations that occurred between the Eocene and Plio-Pleistocene. Plio-Pleistocene metacommunities show a high proportion of bathymetric generalists, in contrast to Eocene metacommunities. Accordingly, the net cooling and weaker thermal gradients may have allowed offshore specialists to expand into onshore habitats and maintain their presence in offshore habitats. PMID:25297863

  12. Modeling bivalve diversification: the effect of interaction on a macroevolutionary system

    NASA Technical Reports Server (NTRS)

    Miller, A. I.; Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

    1988-01-01

    The global diversification of the class Bivalvia has historically received two conflicting interpretations. One is that a major upturn in diversification was associated with, and a consequence of, the Lake Permian mass extinction. The other is that mass extinctions have had little influence and that bivalves have experienced slow but nearly steady exponential diversification through most of their history, unaffected by interactions with other clades. We find that the most likely explanation lies between these two interpretations. Through most of the Phanerozoic, the diversity of bivalves did indeed exhibit slow growth, which was not substantially altered by mass extinctions. However, the presence of "hyperexponential bursts" in diversification during the initial Ordovician radiation and following the Late Permian and Late Cretaceous mass extinctions suggests a more complex history in which a higher characteristic diversification rate was dampened through most of the Phanerozoic. The observed pattern can be accounted for with a two-phase coupled (i.e., interactive) logistic model, where one phase is treated as the "bivalves" and the other phase is treated as a hypothetical group of clades with which the "bivalves" might have interacted. Results of this analysis suggest that interactions with other taxa have substantially affected bivalve global diversity through the Phanerozoic.

  13. Bees, birds and yellow flowers: pollinator-dependent convergent evolution of UV patterns.

    PubMed

    Papiorek, S; Junker, R R; Alves-Dos-Santos, I; Melo, G A R; Amaral-Neto, L P; Sazima, M; Wolowski, M; Freitas, L; Lunau, K

    2016-01-01

    Colour is one of the most obvious advertisements of flowers, and occurs in a huge diversity among the angiosperms. Flower colour is responsible for attraction from a distance, whereas contrasting colour patterns within flowers aid orientation of flower visitors after approaching the flowers. Due to the striking differences in colour vision systems and neural processing across animal taxa, flower colours evoke specific behavioural responses by different flower visitors. We tested whether and how yellow flowers differ in their spectral reflectance depending on the main pollinator. We focused on bees and birds and examined whether the presence or absence of the widespread UV reflectance pattern of yellow flowers predicts the main pollinator. Most bee-pollinated flowers displayed a pattern with UV-absorbing centres and UV-reflecting peripheries, whereas the majority of bird-pollinated flowers are entirely UV- absorbing. In choice experiments we found that bees did not show consistent preferences for any colour or pattern types. However, all tested bee species made their first antennal contact preferably at the UV-absorbing area of the artificial flower, irrespective of its spatial position within the flower. The appearance of UV patterns within flowers is the main difference in spectral reflectance between yellow bee- and bird-pollinated flowers, and affects the foraging behaviour of flower visitors. The results support the hypothesis that flower colours and the visual capabilities of their efficient pollinators are adapted to each other. PMID:25703147

  14. Evolution of Courtship Songs in Xenopus : Vocal Pattern Generation and Sound Production.

    PubMed

    Leininger, Elizabeth C; Kelley, Darcy B

    2015-01-01

    The extant species of African clawed frogs (Xenopus and Silurana) provide an opportunity to link the evolution of vocal characters to changes in the responsible cellular and molecular mechanisms. In this review, we integrate several robust lines of research: evolutionary trajectories of Xenopus vocalizations, cellular and circuit-level mechanisms of vocalization in selected Xenopus model species, and Xenopus evolutionary history and speciation mechanisms. Integrating recent findings allows us to generate and test specific hypotheses about the evolution of Xenopus vocal circuits. We propose that reduced vocal sex differences in some Xenopus species result from species-specific losses of sexually differentiated neural and neuromuscular features. Modification of sex-hormone-regulated developmental mechanisms is a strong candidate mechanism for reduced vocal sex differences. PMID:26138673

  15. Widespread Recurrent Patterns of Rapid Repeat Evolution in the Kinetochore Scaffold KNL1

    PubMed Central

    Tromer, Eelco; Snel, Berend; Kops, Geert J.P.L.

    2015-01-01

    The outer kinetochore protein scaffold KNL1 is essential for error-free chromosome segregation during mitosis and meiosis. A critical feature of KNL1 is an array of repeats containing MELT-like motifs. When phosphorylated, these motifs form docking sites for the BUB1–BUB3 dimer that regulates chromosome biorientation and the spindle assembly checkpoint. KNL1 homologs are strikingly different in both the amount and sequence of repeats they harbor. We used sensitive repeat discovery and evolutionary reconstruction to show that the KNL1 repeat arrays have undergone extensive, often species-specific array reorganization through iterative cycles of higher order multiplication in conjunction with rapid sequence diversification. The number of repeats per array ranges from none in flowering plants up to approximately 35–40 in drosophilids. Remarkably, closely related drosophilid species have independently expanded specific repeats, indicating near complete array replacement after only approximately 25–40 Myr of evolution. We further show that repeat sequences were altered by the parallel emergence/loss of various short linear motifs, including phosphosites, which supplement the MELT-like motif, signifying modular repeat evolution. These observations point to widespread recurrent episodes of concerted KNL1 repeat evolution in all eukaryotic supergroups. We discuss our findings in the light of the conserved function of KNL1 repeats in localizing the BUB1–BUB3 dimer and its role in chromosome segregation. PMID:26254484

  16. Patterns and Evolution of Nucleotide Landscapes in Seed Plants[W

    PubMed Central

    Serres-Giardi, Laurana; Belkhir, Khalid; David, Jacques; Glémin, Sylvain

    2012-01-01

    Nucleotide landscapes, which are the way base composition is distributed along a genome, strongly vary among species. The underlying causes of these variations have been much debated. Though mutational bias and selection were initially invoked, GC-biased gene conversion (gBGC), a recombination-associated process favoring the G and C over A and T bases, is increasingly recognized as a major factor. As opposed to vertebrates, evolution of GC content is less well known in plants. Most studies have focused on the GC-poor and homogeneous Arabidopsis thaliana genome and the much more GC-rich and heterogeneous rice (Oryza sativa) genome and have often been generalized as a dicot/monocot dichotomy. This vision is clearly phylogenetically biased and does not allow understanding the mechanisms involved in GC content evolution in plants. To tackle these issues, we used EST data from more than 200 species and provided the most comprehensive description of gene GC content across the seed plant phylogeny so far available. As opposed to the classically assumed dicot/monocot dichotomy, we found continuous variations in GC content from the probably ancestral GC-poor and homogeneous genomes to the more derived GC-rich and highly heterogeneous ones, with several independent enrichment episodes. Our results suggest that gBGC could play a significant role in the evolution of GC content in plant genomes. PMID:22492812

  17. Mountain uplift explains differences in Palaeogene patterns of mammalian evolution and extinction between North America and Europe

    PubMed Central

    Eronen, Jussi T.; Janis, Christine M.; Chamberlain, C. Page; Mulch, Andreas

    2015-01-01

    Patterns of late Palaeogene mammalian evolution appear to be very different between Eurasia and North America. Around the Eocene–Oligocene (EO) transition global temperatures in the Northern Hemisphere plummet: following this, European mammal faunas undergo a profound extinction event (the Grande Coupure), while in North America they appear to pass through this temperature event unscathed. Here, we investigate the role of surface uplift to environmental change and mammalian evolution through the Palaeogene (66–23 Ma). Palaeogene regional surface uplift in North America caused large-scale reorganization of precipitation patterns, particularly in the continental interior, in accord with our combined stable isotope and ecometric data. Changes in mammalian faunas reflect that these were dry and high-elevation palaeoenvironments. The scenario of Middle to Late Eocene (50–37 Ma) surface uplift, together with decreasing precipitation in higher-altitude regions of western North America, explains the enigma of the apparent lack of the large-scale mammal faunal change around the EO transition that characterized western Europe. We suggest that North American mammalian faunas were already pre-adapted to cooler and drier conditions preceding the EO boundary, resulting from the effects of a protracted history of surface uplift. PMID:26041349

  18. Multi-Input Single Output SSSC based damping controller design by a hybrid Improved Differential Evolution-Pattern Search approach.

    PubMed

    Panda, Sidhartha; Yegireddy, Narendra Kumar

    2015-09-01

    In this paper, a hybrid Improved Differential Evolution and Pattern Search (hIDEPS) approach is proposed for the design of a PI-Type Multi-Input Single Output (MISO) Static Synchronous Series Compensator (SSSC) based damping controller. The improvement in Differential Evolution (DE) algorithm is introduced by a simple but effective scheme of changing two of its most important control parameters i.e. step size and crossover probability with an objective of achieving improved performance. Pattern Search (PS) is subsequently employed to fine tune the best solution provided by modified DE algorithm. The superiority of a proposed hIDEPS technique over DE and improved DE has also been demonstrated. At the outset, this concept is applied to a SSSC connected in a Single Machine Infinite Bus (SMIB) power system and then extended to a multi-machine power system. To show the effectiveness and robustness of the proposed design approach, simulation results are presented and compared with DE and Particle Swarm Optimization (PSO) optimized Single Input Single Output (SISO) SSSC based damping controllers. It is observed that the proposed approach yield superior damping performance compared to some approaches available in the literature. PMID:25864132

  19. Mosaic patterns of diversification dynamics following the colonization of Melanesian islands.

    PubMed

    Toussaint, Emmanuel F A; Hendrich, Lars; Shaverdo, Helena; Balke, Michael

    2015-01-01

    The fate of newly settled dispersers on freshly colonized oceanic islands is a central theme of island biogeography. The emergence of increasingly sophisticated methods of macroevolutionary pattern inference paves the way for a deeper understanding of the mechanisms governing these diversification patterns on lineages following their colonization of oceanic islands. Here we infer a comprehensive molecular phylogeny for Melanesian Exocelina diving beetles. Recent methods in historical biogeography and diversification rate inference were then used to investigate the evolution of these insects in space and time. An Australian origin in the mid-Miocene was followed by independent colonization events towards New Guinea and New Caledonia in the late Miocene. One colonization of New Guinea led to a large radiation of >150 species and 3 independent colonizations of New Caledonia gave rise to about 40 species. The comparably late colonizations of Vanuatu, Hawaii and China left only one or two species in each region. The contrasting diversification trajectories of these insects on Melanesian islands are likely accounted for by island size, age and availability of ecological opportunities during the colonization stage. PMID:26526041

  20. Mosaic patterns of diversification dynamics following the colonization of Melanesian islands

    PubMed Central

    Toussaint, Emmanuel F. A.; Hendrich, Lars; Shaverdo, Helena; Balke, Michael

    2015-01-01

    The fate of newly settled dispersers on freshly colonized oceanic islands is a central theme of island biogeography. The emergence of increasingly sophisticated methods of macroevolutionary pattern inference paves the way for a deeper understanding of the mechanisms governing these diversification patterns on lineages following their colonization of oceanic islands. Here we infer a comprehensive molecular phylogeny for Melanesian Exocelina diving beetles. Recent methods in historical biogeography and diversification rate inference were then used to investigate the evolution of these insects in space and time. An Australian origin in the mid-Miocene was followed by independent colonization events towards New Guinea and New Caledonia in the late Miocene. One colonization of New Guinea led to a large radiation of >150 species and 3 independent colonizations of New Caledonia gave rise to about 40 species. The comparably late colonizations of Vanuatu, Hawaii and China left only one or two species in each region. The contrasting diversification trajectories of these insects on Melanesian islands are likely accounted for by island size, age and availability of ecological opportunities during the colonization stage. PMID:26526041

  1. Evolution of pattern complexity in the Cahn-Hilliard theory of phase separation

    SciTech Connect

    Gameiro, Marcio; Mischaikow, Konstantin; Wanner, Thomas . E-mail: wanner@math.gmu.edu

    2005-02-01

    Phase separation processes in compound materials can produce intriguing and complicated patterns. Yet, characterizing the geometry of these patterns quantitatively can be quite challenging. In this paper we propose the use of computational algebraic topology to obtain such a characterization. Our method is illustrated for the complex microstructures observed during spinodal decomposition and early coarsening in both the deterministic Cahn-Hilliard theory, as well as in the stochastic Cahn-Hilliard-Cook model. While both models produce microstructures that are qualitatively similar to the ones observed experimentally, our topological characterization points to significant differences. One particular aspect of our method is its ability to quantify boundary effects in finite size systems.

  2. Domestication and the Mitochondrial Genome: Comparing Patterns and Rates of Molecular Evolution in Domesticated Mammals and Birds and Their Wild Relatives

    PubMed Central

    Moray, Camile; Lanfear, Robert; Bromham, Lindell

    2014-01-01

    Studies of domesticated animals have led to the suggestion that domestication could have significant effects on patterns of molecular evolution. In particular, analyses of mitochondrial genome sequences from domestic dogs and yaks have yielded higher ratios of non-synonymous to synonymous substitutions in the domesticated lineages than in their wild relatives. These results are important because they imply that changes to selection or population size operating over a short timescale can cause significant changes to the patterns of mitochondrial molecular evolution. In this study, our aim is to test whether the impact on mitochondrial genome evolution is a general feature of domestication or whether it is specific to particular examples. We test whether domesticated mammals and birds have consistently different patterns of molecular evolution than their wild relatives for 16 phylogenetically independent comparisons of mitochondrial genome sequences. We find no consistent difference in branch lengths or dN/dS between domesticated and wild lineages. We also find no evidence that our failure to detect a consistent pattern is due to the short timescales involved or low genetic distance between domesticated lineages and their wild relatives. However, removing comparisons where the wild relative may also have undergone a bottleneck does reveal a pattern consistent with reduced effective population size in domesticated lineages. Our results suggest that, although some domesticated lineages may have undergone changes to selective regime or effective population size that could have affected mitochondrial evolution, it is not possible to generalize these patterns over all domesticated mammals and birds. PMID:24459286

  3. Clinicopathogenomic analysis of mismatch repair proficient colorectal adenocarcinoma uncovers novel prognostic subgroups with differing patterns of genetic evolution.

    PubMed

    Braxton, David R; Zhang, Ray; Morrissette, Jennifer D; Loaiza-Bonilla, Arturo; Furth, Emma E

    2016-10-01

    Cancer somatic genetic evolution is a direct contributor to heterogeneity at the clonal and molecular level in colorectal adenocarcinoma (COAD). We sought to determine the extent to which genetic evolution may be detected in COAD in routinely obtained single clinical specimens and establish clinical significance with regard to clinicopathologic and outcome data. One hundred and twenty three cases of routinely collected mismatch repair proficient COAD were sequenced on the Illumina Truseq Amplicon assay. Measures of intratumoral heterogeneity and the preferential timing of mutational events were assessed and compared to clinicopathologic data. Survival subanalysis was performed on 55 patients. Patient age (p = 0.013) and specimen percent tumor (p = 0.033) was associated with clonal diversity, and biopsy (p = 0.044) and metastasis (p = 0.044) returned fewer mutations per case. APC and TP53 mutations preferentially occurred early while alterations in FBXW7, FLT3, SMAD4, GNAS and PTEN preferentially occurred as late events. Temporal heterogeneity was evident in KRAS and PIK3CA mutations. Hierarchical clustering revealed a TP53 mutant subtype and a MAPK-PIK3CA subtype with differing patterns of late mutational events. Survival subanalysis showed a decreased median progression free survival for the MAPK-PIK3CA subtype (8 months vs. 13 months; univariate logrank p = 0.0380, cox model p= 0.018). Neoadjuvant therapy associated mutations were found for ERBB2 (p = 0.0481) and FBXW7 (p = 0.015). Our data indicate novel molecular subtypes of mismatch repair proficient COAD display differing patterns of genetic evolution which correlate with clinical outcomes. Furthermore, we report treatment acquired and/or selected mutations in ERBB2 and FBXW7. PMID:27194209

  4. Oxygen and evolutionary patterns in the sea: onshore/offshore trends and recent recruitment of deep-sea faunas

    NASA Technical Reports Server (NTRS)

    Jacobs, D. K.; Lindberg, D. R.

    1998-01-01

    Over the last 15 years a striking pattern of diversification has been documented in the fossil record of benthic marine invertebrates. Higher taxa (orders) tend to originate onshore, diversify offshore, and retreat into deep-water environments. Previous studies attribute this macroevolutionary pattern to a variety of causes, foremost among them the role of nearshore disturbance in providing opportunities for the evolution of novel forms accorded ordinal rank. Our analysis of the post-Paleozoic record of ordinal first appearances indicates that the onshore preference of ordinal origination occurred only in the Mesozoic prior to the Turonian stage of the Cretaceous, a period characterized by relatively frequent anoxic/dysoxic bottom conditions in deeper marine environments. Later, in the Cretaceous and Cenozoic, ordinal origination of benthic organisms did not occur exclusively, or even preferentially, in onshore environments. This change in environmental pattern of ordinal origination roughly correlates with Late Cretaceous: (i) decline in anoxia/dysoxia in offshore benthic environments; (ii) extinction of faunas associated with dysoxic conditions; (iii) increase in bioturbation with the expansion of deep burrowing forms into offshore environments; and (iv) offshore expansion of bryozoan diversity. We also advance a separate argument that the Cenomanian/Turonian and latest Paleocene global events eliminated much of the deep-water benthos. This requires a more recent origin of modern vent and deep-sea faunas, from shallower water refugia, than the Paleozoic or early Mesozoic origin of these faunas suggested by other workers.

  5. Oxygen and evolutionary patterns in the sea: Onshore/offshore trends and recent recruitment of deep-sea faunas

    PubMed Central

    Jacobs, David K.; Lindberg, David R.

    1998-01-01

    Over the last 15 years a striking pattern of diversification has been documented in the fossil record of benthic marine invertebrates. Higher taxa (orders) tend to originate onshore, diversify offshore, and retreat into deep-water environments. Previous studies attribute this macroevolutionary pattern to a variety of causes, foremost among them the role of nearshore disturbance in providing opportunities for the evolution of novel forms accorded ordinal rank. Our analysis of the post-Paleozoic record of ordinal first appearances indicates that the onshore preference of ordinal origination occurred only in the Mesozoic prior to the Turonian stage of the Cretaceous, a period characterized by relatively frequent anoxic/dysoxic bottom conditions in deeper marine environments. Later, in the Cretaceous and Cenozoic, ordinal origination of benthic organisms did not occur exclusively, or even preferentially, in onshore environments. This change in environmental pattern of ordinal origination roughly correlates with Late Cretaceous: (i) decline in anoxia/dysoxia in offshore benthic environments; (ii) extinction of faunas associated with dysoxic conditions; (iii) increase in bioturbation with the expansion of deep burrowing forms into offshore environments; and (iv) offshore expansion of bryozoan diversity. We also advance a separate argument that the Cenomanian/Turonian and latest Paleocene global events eliminated much of the deep-water benthos. This requires a more recent origin of modern vent and deep-sea faunas, from shallower water refugia, than the Paleozoic or early Mesozoic origin of these faunas suggested by other workers. PMID:11541238

  6. Evolution of stationary wave patterns in mesospheric water vapor due to climate change

    NASA Astrophysics Data System (ADS)

    Demirhan Barı, Deniz; Gabriel, Axel; Sezginer Ünal, Yurdanur

    2016-07-01

    The variability in the observed stationary wave patterns of the mesospheric water vapor (H2O) is investigated using CMIP5 RCP 4.5 and RCP 8.5 projections. The change in the vertical and meridional wave structure at northern mid- and polar latitudes associated to the zonal and meridional eddy heat fluxes is discussed by analyzing the advection of H2O due to residual wind components. The alteration in the characteristics of the stationary wave-1 pattern of the lower mesospheric H2O (up to about 75km) related to change in the projected radiative forcing is observed for the years from 2006 to 2100. Additionally the remarkable effect of the increase in global temperature on the zonal asymmetries in small-scale transient waves and parameterized gravity waves, which largely contribute to the observed stationary wave patterns of H2O in the upper mesosphere, is analyzed. For validation purposes, the derived stratospheric patterns are verified against the eddy heat fluxes and residual advection terms derived from Aura/MLS satellite data between 2004-2010 and the reference period of the CMIP5 MPI dataset (1976-2005) providing confidence in the applied method.

  7. The pattern of hominin postcranial evolution reconsidered in light of size-related shape variation of the distal humerus.

    PubMed

    Lague, Michael R

    2014-10-01

    Previous research suggests that some hominin postcranial features do not follow a linear path of increasing modernization through geological time. With respect to the distal humerus, in particular, the earliest known hominin specimens are reportedly among the most modern in morphology, while some later humeri appear further removed from the average modern human shape. Although Plio-Pleistocene humeri vary widely in size, previous studies have failed to account for size-related shape variation when making morphometric comparisons. This study reexamines hominin postcranial evolution in light of distal humeral allometry. Using two-dimensional landmark data, the relationship between specimen size and shape among modern humans is quantified using multivariate regression and principal components analysis of size-shape space. Fossils are compared with modern human shapes expected at a given size, as well as with the overall average human shape. The null hypothesis of humeral isometry in modern humans is rejected. Subsequently, if one takes allometry into account, the apparent pattern of hominin humeral evolution does not resemble the pattern described above. All 14 of the Plio-Pleistocene hominin fossils examined here share a similar pattern of shape differences from equivalently-sized modern humans, though they vary in the extent to which these differences are expressed. The oldest specimen in the sample (KNM-KP 271; Australopithecus anamensis) exhibits the least human-like elbow morphology. Similarly primitive morphology characterizes all younger species of Australopithecus as well as Paranthropus robustus. After 2 Ma, a subtly more human-like elbow morphology is apparent among specimens attributed to early Homo, as well as among isolated specimens that may represent either Homo or Paranthropus boisei. This study emphasizes the need to consider size-related shape variation when individual fossil specimens are compared with the average shape of a comparative group

  8. Evolution of the F-Box Gene Family in Euarchontoglires: Gene Number Variation and Selection Patterns

    PubMed Central

    Wang, Ailan; Fu, Mingchuan; Jiang, Xiaoqian; Mao, Yuanhui; Li, Xiangchen; Tao, Shiheng

    2014-01-01

    F-box proteins are substrate adaptors used by the SKP1–CUL1–F-box protein (SCF) complex, a type of E3 ubiquitin ligase complex in the ubiquitin proteasome system (UPS). SCF-mediated ubiquitylation regulates proteolysis of hundreds of cellular proteins involved in key signaling and disease systems. However, our knowledge of the evolution of the F-box gene family in Euarchontoglires is limited. In the present study, 559 F-box genes and nine related pseudogenes were identified in eight genomes. Lineage-specific gene gain and loss events occurred during the evolution of Euarchontoglires, resulting in varying F-box gene numbers ranging from 66 to 81 among the eight species. Both tandem duplication and retrotransposition were found to have contributed to the increase of F-box gene number, whereas mutation in the F-box domain was the main mechanism responsible for reduction in the number of F-box genes, resulting in a balance of expansion and contraction in the F-box gene family. Thus, the Euarchontoglire F-box gene family evolved under a birth-and-death model. Signatures of positive selection were detected in substrate-recognizing domains of multiple F-box proteins, and adaptive changes played a role in evolution of the Euarchontoglire F-box gene family. In addition, single nucleotide polymorphism (SNP) distributions were found to be highly non-random among different regions of F-box genes in 1092 human individuals, with domain regions having a significantly lower number of non-synonymous SNPs. PMID:24727786

  9. Large-scale pattern of mantle evolution through rifting in hyper-extended margins

    NASA Astrophysics Data System (ADS)

    Picazo, Suzanne; Müntener, Othmar; Manatschal, Gianreto; Bauville, Arthur

    2016-04-01

    New ideas and concepts have been developed to understand and be able to give a simplified large-scale view of the evolution of the mantle lithosphere in hyper-extended magma-poor rifted margins based on the ancient Alpine Tethys rifted margin. In contrast to the classical assumption assuming a simple, isotropic mantle lithosphere, these new models integrate observations from exposed and drilled mantle rocks and propose that the mantle lithosphere evolved and was modified during an extensional cycle from post-orogenic collapse through several periods of rifting to embryonic oceanic (ultra-) slow seafloor spreading. But it is, at present, unclear how far these ideas can be generalized at Atlantic type rifted margins. In our presentation, we review the available mantle data from dredged samples in the North Atlantic and from ophiolite massifs and xenoliths in preserved and reactivated passive margins i.e. the Alpine Tethys, the Pyrenean domain, and the Dinarides and Hellenides. We revisit the available terminology concerning mantle massifs and xenoliths and compile the available data to identify different mantle domains. We define chemical and petrological characteristics of mantle domains based on clinopyroxene and spinel compositions and compile them on present-day and paleo-geographic maps of Western Europe. Finally we link the observed distribution of mantle domains to the post-Variscan extensional cycle and link domains to processes related to the late post-Variscan extension, the rift evolution and refertilization associated to hyper-extension and the development of embryonic oceanic domains.

  10. Patterns of molecular evolution of an avian neo-sex chromosome.

    PubMed

    Pala, Irene; Hasselquist, Dennis; Bensch, Staffan; Hansson, Bengt

    2012-12-01

    Newer parts of sex chromosomes, neo-sex chromosomes, offer unique possibilities for studying gene degeneration and sequence evolution in response to loss of recombination and population size decrease. We have recently described a neo-sex chromosome system in Sylvioidea passerines that has resulted from a fusion between the first half (10 Mb) of chromosome 4a and the ancestral sex chromosomes. In this study, we report the results of molecular analyses of neo-Z and neo-W gametologs and intronic parts of neo-Z and autosomal genes on the second half of chromosome 4a in three species within different Sylvioidea lineages (Acrocephalidea, Timaliidae, and Alaudidae). In line with hypotheses of neo-sex chromosome evolution, we observe 1) lower genetic diversity of neo-Z genes compared with autosomal genes, 2) moderate synonymous and weak nonsynonymous sequence divergence between neo-Z and neo-W gametologs, and 3) lower GC content on neo-W than neo-Z gametologs. Phylogenetic reconstruction of eight neo-Z and neo-W gametologs suggests that recombination continued after the split of Alaudidae from the rest of the Sylvioidea lineages (i.e., after ~42.2 Ma) and with some exceptions also after the split of Acrocephalidea and Timaliidae (i.e., after ~39.4 Ma). The Sylvioidea neo-sex chromosome shares classical evolutionary features with the ancestral sex chromosomes but, as expected from its more recent origin, shows weaker divergence between gametologs. PMID:22826461

  11. Origins of adult pigmentation: diversity in pigment stem cell lineages and implications for pattern evolution

    PubMed Central

    Spiewak, Jessica E.

    2014-01-01

    Summary Teleosts comprise about half of all vertebrate species and exhibit an extraordinary diversity of adult pigment patterns that function in shoaling, camouflage and mate choice and have played important roles in speciation. Here, we review recent studies that have identified several distinct neural crest lineages, with distinct genetic requirements, that give rise to adult pigment cells in fishes. These lineages include post-embryonic, peripheral nerve associated stem cells that generate black melanophores and iridescent iridophores, cells derived directly from embryonic neural crest cells that generate yellow-orange xanthophores, and bipotent stem cells that generate both melanophores and xanthophores. This complexity in adult chromatophore lineages has implications for our understanding of adult traits, melanoma, and the evolutionary diversification of pigment cell lineages and patterns. PMID:25421288

  12. Unraveling a generic growth pattern in structure evolution of thiolate-protected gold nanoclusters

    NASA Astrophysics Data System (ADS)

    Xu, Wen Wu; Li, Yadong; Gao, Yi; Zeng, Xiao Cheng

    2016-03-01

    Precise control of the growth of thiolate-protected gold nanoclusters is a prerequisite for their applications in catalysis and bioengineering. Here, we bring to bear a new series of thiolate-protected nanoclusters with a unique growth pattern, i.e., Au20(SR)16, Au28(SR)20, Au36(SR)24, Au44(SR)28, and Au52(SR)32. These nanoclusters can be viewed as resulting from the stepwise addition of a common structural motif [Au8(SR)4]. The highly negative values of the nucleus-independent chemical shift (NICS) in the center of the tetrahedral Au4 units suggest that the overall stabilities of these clusters stem from the local stability of each tetrahedral Au4 unit. Generalization of this growth-pattern rule to large-sized nanoclusters allows us to identify the structures of three new thiolate-protected nanoclusters, namely, Au60(SR)36, Au68(SR)40, and Au76(SR)44. Remarkably, all three large-sized nanoclusters possess relatively large HOMO-LUMO gaps and negative NICS values, suggesting their high chemical stability. Further extension of the growth-pattern rule to the infinitely long nanowire limit results in a one-dimensional (1D) thiolate-protected gold nanowire (RS-AuNW) with a band gap of 0.78 eV. Such a unique growth-pattern rule offers a guide for precise synthesis of a new class of large-sized thiolate-protected gold nanoclusters or even RS-AuNW which, to our knowledge, has not been reported in the literature.Precise control of the growth of thiolate-protected gold nanoclusters is a prerequisite for their applications in catalysis and bioengineering. Here, we bring to bear a new series of thiolate-protected nanoclusters with a unique growth pattern, i.e., Au20(SR)16, Au28(SR)20, Au36(SR)24, Au44(SR)28, and Au52(SR)32. These nanoclusters can be viewed as resulting from the stepwise addition of a common structural motif [Au8(SR)4]. The highly negative values of the nucleus-independent chemical shift (NICS) in the center of the tetrahedral Au4 units suggest that the overall

  13. Structural patterns, evolution, and seismic expression of Montague County, Texas - Implications concerning past discoveries and future exploration

    SciTech Connect

    Font, R.G. )

    1990-02-01

    North Texas is a mature province that has yielded abundant hydrocarbons. Opportunities still exist for discovering large reserves by applying new technology and developing innovative concepts for frontier type plays. Montague County can be used to illustrate this point. Analysis of seismic and petrologic data reveals a fascinating scenario concerning structural patterns and tectonic evolution. The Proterozoic and early Paleozoic history is related to the development of the Wichita aulacogen. Similar structural architecture is found on the southern side of the Wichita-Amarillo uplift from the Hardeman basin to Montague County. The early history reflects rifting. Subsequent tectonism relates to the Hercynian orogeny, plate convergence, and collision. Fault patterns mapped from seismic and subsurface data may be explained through reorientation of the principal stresses. Of the major patterns mapped, the northwest-trending system is dominant. Normal faults formed during rifting were selectively reactivated as upthrusts during convergence. Past discoveries are almost invariably related to seismic expression. New Carboniferous reserves will be discovered in subtle traps. State-of-the-art seismic and seismic stratigraphy will equate to exploratory success. New play concepts involve the petroleum potential of the deep Ellenburger, similar to the deep pay found in Oklahoma. Recent deep wells drilled in the county affirm the presence of structure and reservoir, but fail to find the indigenous source potential present north of the Red River. Best opportunities for deep Ellenburger discoveries in Texas lie where faulting juxtaposes Carboniferous source rocks to the Cambrian-Ordovician reservoirs.

  14. The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes).

    PubMed

    Dornburg, Alex; Moore, Jon; Beaulieu, Jeremy M; Eytan, Ron I; Near, Thomas J

    2015-01-01

    One of the most striking biodiversity patterns is the uneven distribution of marine species richness, with species diversity in the Indo-Australian Archipelago (IAA) exceeding all other areas. However, the IAA formed fairly recently, and marine biodiversity hotspots have shifted across nearly half the globe since the Paleogene. Understanding how lineages have responded to shifting biodiversity hotspots represents a necessary historic perspective on the formation and maintenance of global marine biodiversity. Such evolutionary inferences are often challenged by a lack of fossil evidence that provide insights into historic patterns of abundance and diversity. The greatest diversity of squirrelfishes and soldierfishes (Holocentridae) is in the IAA, yet these fishes also represent some of the most numerous fossil taxa in deposits of the former West Tethyan biodiversity hotspot. We reconstruct the pattern of holocentrid range evolution using time-calibrated phylogenies that include most living species and several fossil lineages, demonstrating the importance of including fossil species as terminal taxa in ancestral area reconstructions. Holocentrids exhibit increased range fragmentation following the West Tethyan hotspot collapse. However, rather than originating within the emerging IAA hotspot, the IAA has acted as a reservoir for holocentrid diversity that originated in adjacent regions over deep evolutionary time scales. PMID:25407924

  15. Chromosomal rearrangements and evolution of recombination: comparison of chiasma distribution patterns in standard and robertsonian populations of the house mouse.

    PubMed Central

    Dumas, David; Britton-Davidian, Janice

    2002-01-01

    The effects of chromosomal rearrangements on recombination rates were tested by the analysis of chiasma distribution patterns in wild house mice. Males and females of two chromosomal races from Tunisia differing by nine pairs of Robertsonian (Rb) fusions (standard all-acrocentric, 2N = 40 and 2N = 22) were studied. A significant decrease in chiasma number (CN) was observed in Rb mice compared to standard ones for both sexes. The difference in CN was due to a reduction in the number of proximal chiasmata and was associated with an overall more distal redistribution. These features were related to distance of chiasmata to the centromere, suggesting that the centromere effect was more pronounced in Rb fusions than in acrocentric chromosomes. These modifications were interpreted in terms of structural meiotic constraints, although genic factors were likely involved in patterning the observed differences between sexes within races. Thus, the change in chromosomal structure in Rb mice was associated with a generalized decrease in recombination due to a reduction in diploid number, a lower CN, and a decrease in the efficiency of recombination. The effects of such modifications on patterns of genic diversity are discussed in the light of models of evolution of recombination. PMID:12454079

  16. Design of Spiking Central Pattern Generators for Multiple Locomotion Gaits in Hexapod Robots by Christiansen Grammar Evolution.

    PubMed

    Espinal, Andres; Rostro-Gonzalez, Horacio; Carpio, Martin; Guerra-Hernandez, Erick I; Ornelas-Rodriguez, Manuel; Sotelo-Figueroa, Marco

    2016-01-01

    This paper presents a method to design Spiking Central Pattern Generators (SCPGs) to achieve locomotion at different frequencies on legged robots. It is validated through embedding its designs into a Field-Programmable Gate Array (FPGA) and implemented on a real hexapod robot. The SCPGs are automatically designed by means of a Christiansen Grammar Evolution (CGE)-based methodology. The CGE performs a solution for the configuration (synaptic weights and connections) for each neuron in the SCPG. This is carried out through the indirect representation of candidate solutions that evolve to replicate a specific spike train according to a locomotion pattern (gait) by measuring the similarity between the spike trains and the SPIKE distance to lead the search to a correct configuration. By using this evolutionary approach, several SCPG design specifications can be explicitly added into the SPIKE distance-based fitness function, such as looking for Spiking Neural Networks (SNNs) with minimal connectivity or a Central Pattern Generator (CPG) able to generate different locomotion gaits only by changing the initial input stimuli. The SCPG designs have been successfully implemented on a Spartan 6 FPGA board and a real time validation on a 12 Degrees Of Freedom (DOFs) hexapod robot is presented. PMID:27516737

  17. Design of Spiking Central Pattern Generators for Multiple Locomotion Gaits in Hexapod Robots by Christiansen Grammar Evolution

    PubMed Central

    Espinal, Andres; Rostro-Gonzalez, Horacio; Carpio, Martin; Guerra-Hernandez, Erick I.; Ornelas-Rodriguez, Manuel; Sotelo-Figueroa, Marco

    2016-01-01

    This paper presents a method to design Spiking Central Pattern Generators (SCPGs) to achieve locomotion at different frequencies on legged robots. It is validated through embedding its designs into a Field-Programmable Gate Array (FPGA) and implemented on a real hexapod robot. The SCPGs are automatically designed by means of a Christiansen Grammar Evolution (CGE)-based methodology. The CGE performs a solution for the configuration (synaptic weights and connections) for each neuron in the SCPG. This is carried out through the indirect representation of candidate solutions that evolve to replicate a specific spike train according to a locomotion pattern (gait) by measuring the similarity between the spike trains and the SPIKE distance to lead the search to a correct configuration. By using this evolutionary approach, several SCPG design specifications can be explicitly added into the SPIKE distance-based fitness function, such as looking for Spiking Neural Networks (SNNs) with minimal connectivity or a Central Pattern Generator (CPG) able to generate different locomotion gaits only by changing the initial input stimuli. The SCPG designs have been successfully implemented on a Spartan 6 FPGA board and a real time validation on a 12 Degrees Of Freedom (DOFs) hexapod robot is presented. PMID:27516737

  18. Evolution of Canada’s Boreal Forest Spatial Patterns as Seen from Space

    PubMed Central

    Pickell, Paul D.; Coops, Nicholas C.; Gergel, Sarah E.; Andison, David W.; Marshall, Peter L.

    2016-01-01

    Understanding the development of landscape patterns over broad spatial and temporal scales is a major contribution to ecological sciences and is a critical area of research for forested land management. Boreal forests represent an excellent case study for such research because these forests have undergone significant changes over recent decades. We analyzed the temporal trends of four widely-used landscape pattern indices for boreal forests of Canada: forest cover, largest forest patch index, forest edge density, and core (interior) forest cover. The indices were computed over landscape extents ranging from 5,000 ha (n = 18,185) to 50,000 ha (n = 1,662) and across nine major ecozones of Canada. We used 26 years of Landsat satellite imagery to derive annualized trends of the landscape pattern indices. The largest declines in forest cover, largest forest patch index, and core forest cover were observed in the Boreal Shield, Boreal Plain, and Boreal Cordillera ecozones. Forest edge density increased at all landscape extents for all ecozones. Rapidly changing landscapes, defined as the 90th percentile of forest cover change, were among the most forested initially and were characterized by four times greater decrease in largest forest patch index, three times greater increase in forest edge density, and four times greater decrease in core forest cover compared with all 50,000 ha landscapes. Moreover, approximately 18% of all 50,000 ha landscapes did not change due to a lack of disturbance. The pattern database results provide important context for forest management agencies committed to implementing ecosystem-based management strategies. PMID:27383055

  19. Evolution and functional significance of derived sternal ossification patterns in ornithothoracine birds.

    PubMed

    O'Connor, J K; Zheng, X-T; Sullivan, C; Chuong, C-M; Wang, X-L; Li, A; Wang, Y; Zhang, X-M; Zhou, Z-H

    2015-08-01

    The midline pattern of sternal ossification characteristic of the Cretaceous enantiornithine birds is unique among the Ornithodira, the group containing birds, nonavian dinosaurs and pterosaurs. This has been suggested to indicate that Enantiornithes is not the sister group of Ornithuromorpha, the clade that includes living birds and their close relatives, which would imply rampant convergence in many nonsternal features between enantiornithines and ornithuromorphs. However, detailed comparisons reveal greater similarity between neornithine (i.e. crown group bird) and enantiornithine modes of sternal ossification than previously recognized. Furthermore, a new subadult enantiornithine specimen demonstrates that sternal ossification followed a more typically ornithodiran pattern in basal members of the clade. This new specimen, referable to the Pengornithidae, indicates that the unique ossification pattern observed in other juvenile enantiornithines is derived within Enantiornithes. A similar but clearly distinct pattern appears to have evolved in parallel in the ornithuromorph lineage. The atypical mode of sternal ossification in some derived enantiornithines should be regarded as an autapomorphic condition rather than an indication that enantiornithines are not close relatives of ornithuromorphs. Based on what is known about molecular mechanisms for morphogenesis and the possible selective advantages, the parallel shifts to midline ossification that took place in derived enantiornithines and living neognathous birds appear to have been related to the development of a large ventral keel, which is only present in ornithuromorphs and enantiornithines. Midline ossification can serve to medially reinforce the sternum at a relatively early ontogenetic stage, which would have been especially beneficial during the protracted development of the superprecocial Cretaceous enantiornithines. PMID:26079847

  20. Evolution of Canada's Boreal Forest Spatial Patterns as Seen from Space.

    PubMed

    Pickell, Paul D; Coops, Nicholas C; Gergel, Sarah E; Andison, David W; Marshall, Peter L

    2016-01-01

    Understanding the development of landscape patterns over broad spatial and temporal scales is a major contribution to ecological sciences and is a critical area of research for forested land management. Boreal forests represent an excellent case study for such research because these forests have undergone significant changes over recent decades. We analyzed the temporal trends of four widely-used landscape pattern indices for boreal forests of Canada: forest cover, largest forest patch index, forest edge density, and core (interior) forest cover. The indices were computed over landscape extents ranging from 5,000 ha (n = 18,185) to 50,000 ha (n = 1,662) and across nine major ecozones of Canada. We used 26 years of Landsat satellite imagery to derive annualized trends of the landscape pattern indices. The largest declines in forest cover, largest forest patch index, and core forest cover were observed in the Boreal Shield, Boreal Plain, and Boreal Cordillera ecozones. Forest edge density increased at all landscape extents for all ecozones. Rapidly changing landscapes, defined as the 90th percentile of forest cover change, were among the most forested initially and were characterized by four times greater decrease in largest forest patch index, three times greater increase in forest edge density, and four times greater decrease in core forest cover compared with all 50,000 ha landscapes. Moreover, approximately 18% of all 50,000 ha landscapes did not change due to a lack of disturbance. The pattern database results provide important context for forest management agencies committed to implementing ecosystem-based management strategies. PMID:27383055

  1. Interface dynamics under nonequilibrium conditions: from a self-propelled droplet to dynamic pattern evolution.

    PubMed

    Chen, Y-J; Yoshikawa, K

    2011-04-01

    In this article, we describe the instability of a contact line under nonequilibrium conditions mainly based on the results of our recent studies. Two experimental examples are presented: the self-propelled motion of a liquid droplet and spontaneous dynamic pattern formation. For the self-propelled motion of a droplet, we introduce an experiment in which a droplet of aniline sitting on an aqueous layer moves spontaneously at an air-water interface. The spontaneous symmetry breaking of Marangoni-driven spreading causes regular motion. In a circular Petri dish, the droplet exhibits either beeline motion or circular motion. On the other hand, we show the emergence of a dynamic labyrinthine pattern caused by dewetting of a metastable thin film from the air-water interface. The contact line between the organic phase and the aqueous phase forms a unique spatio-temporal pattern characterized as a dynamic labyrinth. Motion of the contact line is controlled by diffusion processes. We propose a theoretical model to interpret essential aspects of the observed dynamic behavior. PMID:21509663

  2. Patterns of recurrent evolution and geographic parthenogenesis within apomictic polyploid Easter daises (Townsendia hookeri).

    PubMed

    Thompson, Stacey Lee; Whitton, Jeannette

    2006-10-01

    Geographic patterns of parthenogenesis and the number of transitions from sexual diploidy to asexual (apomictic) autopolyploidy were examined for 40 populations of the Easter daisy, Townsendia hookeri. Analyses of pollen diameter and stainability characterized 15 sexual diploid and 25 apomictic polyploid populations from throughout the plant's western North American range. Sexual diploids were restricted to two Wisconsin refugia: Colorado/Wyoming, south of the ice sheets, and northern Yukon/Beringia. Chloroplast DNA sequencing uncovered 17 polymorphisms within the ndhF gene and trnK intron, yielding 10 haplotypes. Phylogenetic analyses indicated that five exclusively polyploid haplotypes were derived from four haplotypes that are shared among ploidies, conservatively inferring a minimum of four origins of apomictic polyploidy. Three of these apomictic polyploid origins were derived from southern sexual diploids, while the fourth origin was derived from northern sexual diploids. Analyses of regional diversity were suggestive of a formerly broad distribution for sexual diploids that has become subsequently fragmented, possibly due to the last round of glaciation. As sexual diploids were exclusively found north and south of the glacial maximum, while formerly glaciated areas were exclusively inhabited by asexual polyploids derived from both northern and southern sexual lineages, it is more likely that patterns of glaciation, as opposed to a particular latitudinal trend, played a causal role in the establishment of the observed pattern of geographic parthenogenesis in Easter daisies. PMID:16968277

  3. Evolution of self-organized two-dimensional patterns of nanoclusters through demixing

    NASA Astrophysics Data System (ADS)

    Choudhuri, Madhumita; Iyengar, A. N. Sekar; Datta, Alokmay; Janaki, M. S.

    2015-09-01

    A mixture of dodecanethiol-capped Au nanoparticles (AuNPs) and the amphiphilic fatty acid, stearic acid, spread as a monomolecular layer on water surface, is observed with Brewster angle microscopy (BAM) to form a two-dimensional network of AuNP clusters through demixing, at concentration of AuNPs by weight (ρ ¯)>10 % and the surface pressure (π )≥10 mN m-1 . For π =15 mN m-1 , the number of nodes (n ) remains unchanged till ˜2 hours and then changes over to a lower n state, where the pattern consists of almost perfect circles with greater in-plane thickness of the AuNP lamellae. For the higher n state the mean-square fluctuation of BAM intensity remains flat and then decays as f (ξ ) =ξ2 α with α ˜0.6 (correlated fluctuations) over the length scales of 400 μ m -6 μ m and below 6 μ m , respectively. For the lower n state the fluctuation decays almost over the entire length scale with α =0.3 , indicating emergence of aperiodicity from quasiperiodicity and a changeover to anticorrelated fluctuations. These patterns can be looked at as two distinct chaotic trajectories in the I -I' phase space of the system (I being the scattered light intensity at any position of the pattern and I' its gradient) with characteristic Lyapunov exponents.

  4. Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady's slipper orchid

    PubMed Central

    2011-01-01

    Background Paphiopedilum is a horticulturally and ecologically important genus of ca. 80 species of lady's slipper orchids native to Southeast Asia. These plants have long been of interest regarding their chromosomal evolution, which involves a progressive aneuploid series based on either fission or fusion of centromeres. Chromosome number is positively correlated with genome size, so rearrangement processes must include either insertion or deletion of DNA segments. We have conducted Fluorescence In Situ Hybridization (FISH) studies using 5S and 25S ribosomal DNA (rDNA) probes to survey for rearrangements, duplications, and phylogenetically-correlated variation within Paphiopedilum. We further studied sequence variation of the non-transcribed spacers of 5S rDNA (5S-NTS) to examine their complex duplication history, including the possibility that concerted evolutionary forces may homogenize diversity. Results 5S and 25S rDNA loci among Paphiopedilum species, representing all key phylogenetic lineages, exhibit a considerable diversity that correlates well with recognized evolutionary groups. 25S rDNA signals range from 2 (representing 1 locus) to 9, the latter representing hemizygosity. 5S loci display extensive structural variation, and show from 2 specific signals to many, both major and minor and highly dispersed. The dispersed signals mainly occur at centromeric and subtelomeric positions, which are hotspots for chromosomal breakpoints. Phylogenetic analysis of cloned 5S rDNA non-transcribed spacer (5S-NTS) sequences showed evidence for both ancient and recent post-speciation duplication events, as well as interlocus and intralocus diversity. Conclusions Paphiopedilum species display many chromosomal rearrangements - for example, duplications, translocations, and inversions - but only weak concerted evolutionary forces among highly duplicated 5S arrays, which suggests that double-strand break repair processes are dynamic and ongoing. These results make the genus

  5. Tracking pattern evolution through extended center manifold reduction and singular perturbations

    NASA Astrophysics Data System (ADS)

    Sewalt, L.; Doelman, A.; Meijer, H. G. E.; Rottschäfer, V.; Zagaris, A.

    2015-04-01

    In this paper we develop an extended center manifold reduction method: a methodology to analyze the formation and bifurcations of small-amplitude patterns in certain classes of multi-component, singularly perturbed systems of partial differential equations. We specifically consider systems with a spatially homogeneous state whose stability spectrum partitions into eigenvalue groups with distinct asymptotic properties. One group of successive eigenvalues in the bifurcating group are widely interspaced, while the eigenvalues in the other are stable and cluster asymptotically close to the origin along the stable semi-axis. The classical center manifold reduction provides a rigorous framework to analyze destabilizations of the trivial state, as long as there is a spectral gap of sufficient width. When the bifurcating eigenvalue becomes commensurate to the stable eigenvalues clustering close to the origin, the center manifold reduction breaks down. Moreover, it cannot capture subsequent bifurcations of the bifurcating pattern. Through our methodology, we formally derive expressions for low-dimensional manifolds exponentially attracting the full flow for parameter combinations that go beyond those allowed for the (classical) center manifold reduction, i.e. to cases in which the spectral gap condition no longer can be satisfied. Our method also provides an explicit description of the flow on these manifolds and thus provides an analytical tool to study subsequent bifurcations. Our analysis centers around primary bifurcations of transcritical type-that can be either of co-dimension 1 or 2-in two- and three-component PDE systems. We employ our method to study bifurcation scenarios of small-amplitude patterns and the possible appearance of low-dimensional spatio-temporal chaos. We also exemplify our analysis by a number of characteristic reaction-diffusion systems with disparate diffusivities.

  6. Evolution of Xylan Substitution Patterns in Gymnosperms and Angiosperms: Implications for Xylan Interaction with Cellulose.

    PubMed

    Busse-Wicher, Marta; Li, An; Silveira, Rodrigo L; Pereira, Caroline S; Tryfona, Theodora; Gomes, Thiago C F; Skaf, Munir S; Dupree, Paul

    2016-08-01

    The interaction between cellulose and xylan is important for the load-bearing secondary cell wall of flowering plants. Based on the precise, evenly spaced pattern of acetyl and glucuronosyl (MeGlcA) xylan substitutions in eudicots, we recently proposed that an unsubstituted face of xylan in a 2-fold helical screw can hydrogen bond to the hydrophilic surfaces of cellulose microfibrils. In gymnosperm cell walls, any role for xylan is unclear, and glucomannan is thought to be the important cellulose-binding polysaccharide. Here, we analyzed xylan from the secondary cell walls of the four gymnosperm lineages (Conifer, Gingko, Cycad, and Gnetophyta). Conifer, Gingko, and Cycad xylan lacks acetylation but is modified by arabinose and MeGlcA. Interestingly, the arabinosyl substitutions are located two xylosyl residues from MeGlcA, which is itself placed precisely on every sixth xylosyl residue. Notably, the Gnetophyta xylan is more akin to early-branching angiosperms and eudicot xylan, lacking arabinose but possessing acetylation on alternate xylosyl residues. All these precise substitution patterns are compatible with gymnosperm xylan binding to hydrophilic surfaces of cellulose. Molecular dynamics simulations support the stable binding of 2-fold screw conifer xylan to the hydrophilic face of cellulose microfibrils. Moreover, the binding of multiple xylan chains to adjacent planes of the cellulose fibril stabilizes the interaction further. Our results show that the type of xylan substitution varies, but an even pattern of xylan substitution is maintained among vascular plants. This suggests that 2-fold screw xylan binds hydrophilic faces of cellulose in eudicots, early-branching angiosperm, and gymnosperm cell walls. PMID:27325663

  7. Energetic constraints, not predation, influence the evolution of sleep patterning in mammals.

    PubMed

    Capellini, I; Nunn, C L; McNamara, P; Preston, B T; Barton, R A

    2008-10-01

    Mammalian sleep is composed of two distinct states - rapid-eye-movement (REM) and non-REM (NREM) sleep - that alternate in cycles over a sleep bout. The duration of these cycles varies extensively across mammalian species. Because the end of a sleep cycle is often followed by brief arousals to waking, a shorter sleep cycle has been proposed to function as an anti-predator strategy. Similarly, higher predation risk could explain why many species exhibit a polyphasic sleep pattern (division of sleep into several bouts per day), as having multiple sleep bouts avoids long periods of unconsciousness, potentially reducing vulnerability.Using phylogenetic comparative methods, we tested these predictions in mammals, and also investigated the relationships among sleep phasing, sleep-cycle length, sleep durations and body mass.Neither sleep-cycle length nor phasing of sleep was significantly associated with three different measures of predation risk, undermining the idea that they represent anti-predator adaptations.Polyphasic sleep was associated with small body size, shorter sleep cycles and longer sleep durations. The correlation with size may reflect energetic constraints: small animals need to feed more frequently, preventing them from consolidating sleep into a single bout. The reduced daily sleep quotas in monophasic species suggests that the consolidation of sleep into one bout per day may deliver the benefits of sleep more efficiently and, since early mammals were small-bodied and polyphasic, a more efficient monophasic sleep pattern could be a hitherto unrecognized advantage of larger size. PMID:20428321

  8. The nocturnal bottleneck and the evolution of activity patterns in mammals.

    PubMed

    Gerkema, Menno P; Davies, Wayne I L; Foster, Russell G; Menaker, Michael; Hut, Roelof A

    2013-08-22

    In 1942, Walls described the concept of a 'nocturnal bottleneck' in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail. PMID:23825205

  9. Long-distance communication by specialized cellular projections during pigment pattern development and evolution

    PubMed Central

    Eom, Dae Seok; Bain, Emily J; Patterson, Larissa B; Grout, Megan E; Parichy, David M

    2015-01-01

    Changes in gene activity are essential for evolutionary diversification. Yet, elucidating the cellular behaviors that underlie modifications to adult form remains a profound challenge. We use neural crest-derived adult pigmentation of zebrafish and pearl danio to uncover cellular bases for alternative pattern states. We show that stripes in zebrafish require a novel class of thin, fast cellular projection to promote Delta-Notch signaling over long distances from cells of the xanthophore lineage to melanophores. Projections depended on microfilaments and microtubules, exhibited meandering trajectories, and stabilized on target cells to which they delivered membraneous vesicles. By contrast, the uniformly patterned pearl danio lacked such projections, concomitant with Colony stimulating factor 1-dependent changes in xanthophore differentiation that likely curtail signaling available to melanophores. Our study reveals a novel mechanism of cellular communication, roles for differentiation state heterogeneity in pigment cell interactions, and an unanticipated morphogenetic behavior contributing to a striking difference in adult form. DOI: http://dx.doi.org/10.7554/eLife.12401.001 PMID:26701906

  10. Phylogenetic Patterns of Codon Evolution in the ACTIN-DEPOLYMERIZING FACTOR/COFILIN (ADF/CFL) Gene Family

    PubMed Central

    Roy-Zokan, Eileen M.; Dyer, Kelly A.; Meagher, Richard B.

    2015-01-01

    The actin-depolymerizing factor/cofilin (ADF/CFL) gene family encodes a diverse group of relatively small proteins. Once known strictly as modulators of actin filament dynamics, recent research has demonstrated that these proteins are involved in a variety of cellular processes, from signal transduction to the cytonuclear trafficking of actin. In both plant and animal lineages, expression patterns of paralogs in the ADF/CFL gene family vary among tissue types and developmental stages. In this study we use computational approaches to investigate the evolutionary forces responsible for the diversification of the ADF/CFL gene family. Estimating the rate of non-synonymous to synonymous mutations (dN/dS) across phylogenetic lineages revealed that the majority of ADF/CFL codon positions were under strong purifying selection, with rare episodic events of accelerated protein evolution. In both plants and animals these instances of accelerated evolution were ADF/CFL subclass specific, and all of the sites under selection were located in regions of the protein that could serve in new functional roles. We suggest these sites may have been important in the functional diversification of ADF/CFL proteins. PMID:26717562