Trait-based diversification shifts reflect differential extinction among fossil taxa

PubMed Central

Wagner, Peter J.; Estabrook, George F.

2014-01-01

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models. PMID:25331898

Trait-based diversification shifts reflect differential extinction among fossil taxa.

PubMed

Wagner, Peter J; Estabrook, George F

2014-11-18

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

Taxa-area relationship of aquatic fungi on deciduous leaves.

PubMed

Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Bärlocher, Felix

2017-01-01

One of the fundamental patterns in macroecology is the increase in the number of observed taxa with size of sampled area. For microbes, the shape of this relationship remains less clear. The current study assessed the diversity of aquatic fungi, by the traditional approach based on conidial morphology (captures reproducing aquatic hyphomycetes) and next generation sequencing (NGS; captures other fungi as well), on graded sizes of alder leaves (0.6 to 13.6 cm2). Leaves were submerged in two streams in geographically distant locations: the Oliveira Stream in Portugal and the Boss Brook in Canada. Decay rates of alder leaves and fungal sporulation rates did not differ between streams. Fungal biomass was higher in Boss Brook than in Oliveira Stream, and in both streams almost 100% of the reads belonged to active fungal taxa. In general, larger leaf areas tended to harbour more fungi, but these findings were not consistent between techniques. Morphospecies-based diversity increased with leaf area in Boss Brook, but not in Oliveira Stream; metabarcoding data showed an opposite trend. The higher resolution of metabarcoding resulted in steeper taxa-accumulation curves than morphospecies-based assessments (fungal conidia morphology). Fungal communities assessed by metabarcoding were spatially structured by leaf area in both streams. Metabarcoding promises greater resolution to assess biodiversity patterns in aquatic fungi and may be more accurate for assessing taxa-area relationships and local to global diversity ratios.

Zulma Ageitos de Castellanos: Publications and status of described taxa.

PubMed

Signorelli, Javier H; Urteaga, Diego; Teso, Valeria

2015-10-28

Zulma Ageitos de Castellanos was an Argentinian malacologist working in the "Facultad de Ciencias Naturales y Museo" at La Plata University where she taught invertebrate zoology between 1947 and 1990. Her scientific publications are listed in chronological order. Described genus-group and species-group taxa are listed. Information about the type locality and type material, and taxonomic remarks are also provided. Finally, type material of all described taxa was requested and, when located, illustrated.

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

DOE PAGES

Shade, Ashley; Jones, Stuart E.; Caporaso, J. Gregory; ...

2014-07-15

Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT mademore » up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. In conclusion, this observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.« less

Response of Marine Taxa to Climate Variability in the Southeast U.S.

NASA Astrophysics Data System (ADS)

Morley, J. W.; Pinsky, M. L.; Batt, R. D.

2016-02-01

Climate change has led to large-scale redistributions of marine taxa in many coastal regions around North America. Specifically, marine populations respond to spatial shifts in their preferred temperature conditions, or thermal envelope, as they shift across a seascape. The influence of climate change on the coastal fisheries of the southeast U.S. has been largely unexplored. We analyzed 25 years of trawl survey data (1990-2014) from the Southeast Area Monitoring and Assessment Program (SEAMAP), which samples the nearshore continental shelf of the South Atlantic Bight during spring, summer, and fall. Bottom temperatures exhibited no trend over this period and the assemblage showed no net shift north or south. However, taxa distributions were sensitive to interannual temperature variation. Annual projections of taxa thermal envelopes explained variation in centroid location for many species, particularly during spring. Accordingly, long-term latitudinal shifts in taxa-specific thermal envelopes, which trended to the north or south depending on the species, were highly correlated with centroid shifts during spring. One explanation for our results is that the phenology of taxa migration is adaptable to temperature variation. In particular, the inshore-offshore movement of species during spring and fall appears quite responsive to interannual temperature variability.

Polyhedral geometry of phylogenetic rogue taxa.

PubMed

Cueto, María Angélica; Matsen, Frederick A

2011-06-01

It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

PubMed Central

Aberer, Andre J.; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

Abstract The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees. PMID:22962004

Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice.

PubMed

Aberer, Andre J; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees.

Differentiating Iconella from Surirella (Bacillariophyceae): typifying four Ehrenberg names and a preliminary checklist of the African taxa

PubMed Central

Jahn, Regine; Kusber, Wolf-Henning; Cocquyt, Christine

2017-01-01

Abstract To comply with the new phylogeny within the Surirellales as supported by molecular and morphological data, re-evaluations and re-combinations of taxa from and within the genera Surirella, Cymatopleura, and Stenopterobia and with the re-established genus Iconella are necessary. Since the African diatom flora is rich with taxa from these genera, especially Iconella, and the authors have studied these taxa recently, describing also new taxa, a preliminary checklist of African Iconella and Surirella is here presented. 94 names are contained on this list. 57 taxa have been transferred to Iconella; 55 taxa were formerly ranked within Surirella and two taxa within Stenopterobia. 10 taxa have stayed within Surirella and six taxa have been transferred from Cymatopleura to Surirella. 20 Surirella and 1 Stenopterobia names are listed which are either unrevised or unrevisable since morphological data is missing. Four names and taxa described by Ehrenberg are here typified. Two had been transferred to Iconella already: Iconella bifrons (Ehrenb.) Ruck & Nakov and Iconella splendida (Ehrenb.) Ruck & Nakov. Two are re-transferred from Cymatopleura to Surirella: Surirella librile (Ehrenb.) Ehrenb. and Surirella undulata (Ehrenb.) Ehrenb.; both taxa are currently known by their younger synonyms: Cymatopleura solea (Bréb.) W. Smith and Cymatopleura elliptica (Bréb. ex Kützing) W. Smith. Lectotypes for Iconella bifrons, I. splendida, Surirella librile, and S. undulata were designated. PMID:28794683

High congruence of isotope sewage signals in multiple marine taxa.

PubMed

Connolly, Rod M; Gorman, Daniel; Hindell, Jeremy S; Kildea, Timothy N; Schlacher, Thomas A

2013-06-15

Assessments of sewage pollution routinely employ stable nitrogen isotope analysis (δ(15)N) in biota, but multiple taxa are rarely used. This single species focus leads to underreporting of whether derived spatial N patterns are consistent. Here we test the question of 'reproducibility', incorporating 'taxonomic replication' in the measurement of δ(15)N gradients in algae, seagrasses, crabs and fish with distance from a sewage outfall on the Adelaide coast (southern Australia). Isotopic sewage signals were equally strong in all taxa and declined at the same rate. This congruence amongst taxa has not been reported previously. It implies that sewage-N propagates to fish via a tight spatial coupling between production and consumption processes, resulting from limited animal movement that closely preserves the spatial pollution imprint. In situations such as this where consumers mirror pollution signals of primary producers, analyses of higher trophic levels will capture a broader ambit of ecological effects. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quaternary disappearance of tree taxa from Southern Europe: Timing and trends

NASA Astrophysics Data System (ADS)

Magri, Donatella; Di Rita, Federico; Aranbarri, Josu; Fletcher, William; González-Sampériz, Penélope

2017-05-01

A hundred pollen and plant macrofossil records from the Iberian Peninsula, Southern France, the Italian Peninsula, Greece and the Aegean, and the southwestern Black Sea area formed the basis for a review of the Quaternary distribution and extirpation of tree populations from Southern Europe. Following a discussion of the caveats/challenges about using pollen data, the Quaternary history of tree taxa has been reconstructed with attention to Taxodium/Glyptostrobus, Sciadopitys, Cathaya, Cedrus, Tsuga, Eucommia, Engelhardia, Carya, Pterocarya, Parrotia, Liquidambar, and Zelkova. The timing of extinction, distributed over the whole Quaternary, appears very diverse from one region to the other, in agreement with current biodiversity in Southern Europe. The geographical patterns of persistence/disappearance of taxa show unexpected trends and rule out a simple North to South and/or West to East trend in extirpations. In particular, it is possible to detect disjunct populations (Engelhardia), long-term persistence of taxa in restricted regions (Sciadopitys), distinct populations/species/genera in different geographical areas (Taxodium type). Some taxa that are still widespread in Europe have undergone extirpation in Mediterranean areas in the lateglacial period and Holocene (Buxus, Carpinus betulus, Picea); they provide an indication of the modes of disappearance of tree populations that may be useful to evaluate correctly the vulnerability of modern fragmented plant populations. The demographic histories of tree taxa obtained by combined palaeobotanical and genetic studies is a most challenging field of research needed not only to assess species/population differentiation, but also to reach a better understanding of extinction processes, an essential task in the current global change scenario.

Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses.

PubMed

Guillerme, Thomas; Cooper, Natalie

2016-05-01

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies. © 2016 The Authors.

Ambiguous taxa: Effects on the characterization and interpretation of invertebrate assemblages

USGS Publications Warehouse

Cuffney, T.F.; Bilger, Michael D.; Haigler, A.M.

2007-01-01

Damaged and immature specimens often result in macroinvertebrate data that contain ambiguous parent-child pairs (i.e., abundances associated with multiple related levels of the taxonomic hierarchy such as Baetis pluto and the associated ambiguous parent Baetis sp.). The choice of method used to resolve ambiguous parent-child pairs may have a very large effect on the characterization of invertebrate assemblages and the interpretation of responses to environmental change because very large proportions of taxa richness (73-78%) and abundance (79-91%) can be associated with ambiguous parents. To address this issue, we examined 16 variations of 4 basic methods for resolving ambiguous taxa: RPKC (remove parent, keep child), MCWP (merge child with parent), RPMC (remove parent or merge child with parent depending on their abundances), and DPAC (distribute parents among children). The choice of method strongly affected assemblage structure, assemblage characteristics (e.g., metrics), and the ability to detect responses along environmental (urbanization) gradients. All methods except MCWP produced acceptable results when used consistently within a study. However, the assemblage characteristics (e.g., values of assemblage metrics) differed widely depending on the method used, and data should not be combined unless the methods used to resolve ambiguous taxa are well documented and are known to be comparable. The suitability of the methods was evaluated and compared on the basis of 13 criteria that considered conservation of taxa richness and abundance, consistency among samples, methods, and studies, and effects on the interpretation of the data. Methods RPMC and DPAC had the highest suitability scores regardless of whether ambiguous taxa were resolved for each sample separately or for a group of samples. Method MCWP gave consistently poor results. Methods MCWP and DPAC approximate the use of family-level identifications and operational taxonomic units (OTU), respectively. Our

New taxa, notes and new synonymy in Neoibidionini (Cerambycidae, Coleoptera).

PubMed

Martins, Ubirajara R; Galileo, Maria Helena M

2014-04-11

New taxa, notes, and new synonymy in Neoibidionini (Cerambycidae, Coleoptera) are given. New taxa are described from Ecuador: Compsibidion inflatum sp. nov., Bezarkia gen. nov. and B. suturalis sp. nov., Corimbion antennatum sp. nov. and Neocompsa muira sp. nov.; from México: Neocompsa chiapensis sp. nov., and from French Guyana: Kunaibidion giesberti sp. nov. Pygmodeon maculatum Martins & Galileo, 2012 is considered a new synonym of Heterachthes xyleus Martins, 1974 which is transferred to the genus Pygmodeon as a new combination. Notes on variability and new records of Asynapteron equatorianum (Martins, 1960) are presented.

State-of-Science Approaches to Determine Sensitive Taxa for Water Quality Criteria Derivation

EPA Science Inventory

Current Ambient Water Quality Criteria (AWQC) guidelines specify pre-defined taxa diversity requirements, which has limited chemical-specific criteria development in the U.S. to less than 100 chemicals. A priori knowledge of sensitive taxa to toxicologically similar groups of che...

New records for Albania based on taxa from the Prespa National Park

PubMed Central

2013-01-01

Abstract Twelve taxa are enumerated as new and three taxa confirmed for the flora of Albania. They were collected between 2007 and 2012 in the Prespa National Park of Albania which is part of the Prespa International Park, a biological protected area at the borders with F.Y.R. Macedonia and Greece. Four taxa, viz., Centaurea galicicae, Festuca galicicae, Laserpitium ochridanum and Micromeria cristata subsp. kosaninii are restricted to Dry and Galičica Mountains. Centaurea decora, a recently described species, is treated as a synonym of Centaurea soskae thus extending the known localities of the latter to the southeast. Detailed information on distribution, occurrence and habitats in Albania are provided for each taxon. PMID:24723753

Wood-feeding cockroaches as models for termite evolution (Insecta: Dictyoptera): Cryptocercus vs. Parasphaeria boleiriana.

PubMed

Klass, Klaus-Dieter; Nalepa, Christine; Lo, Nathan

2008-03-01

Isoptera are highly specialized cockroaches and are one of the few eusocial insect lineages. Cryptocercus cockroaches have appeared to many as ideal models for inference on the early evolution of termites, due to their possible phylogenetic relationship and several shared key attributes in life history. Recently, Pellens, Grandcolas, and colleagues have proposed the blaberid cockroach Parasphaeria boleiriana to be an alternative model for the early evolution in termites. We compare the usefulness of Cryptocercus and P. boleiriana as models for termite evolution. Cryptocercus and lower Isoptera (1) can both feed on comparatively recalcitrant wood, (2) have an obligate, rich and unique hypermastigid and oxymonadid fauna in the hindgut, (3) transfer these flagellates to the next generation by anal trophallaxis, (4) have social systems that involve long-lasting biparental care, and, finally, (5) are strongly suggested to be sister groups, so that the key attributes (1)-(4) appear to be homologous between the two taxa. On the other hand, P. boleiriana (1) feeds on soft, ephemeral wood sources, (2) shows no trace of the oxymonadid and hypermastigid hindgut fauna unique to Cryptocercus and lower Isoptera, nor does it have any other demonstrated obligate relationship with hindgut flagellates, (3) is likely to lack anal trophallaxis, (4) has only a short period of uniparental brood care, and (5) is phylogenetically remote from the Cryptocercus+Isoptera clade. These facts would argue against any reasonable usage of P. boleiriana as a model for the early evolution of Isoptera or even of the clade Cryptocercus+Isoptera. Cryptocercus thus remains an appropriate model-taxon-by-homology for early termite evolution. As compared to P. boleiriana, some other Blaberidae (such as the Panesthiinae Salganea) appear more useful as model-taxa-by-homoplasy for the early evolution of the Cryptocercus+Isoptera clade, as their brooding behavior is more elaborate than in P. boleiriana.

EXCLUSION OF RARE TAXA AFFECTS PERFORMANCE OF THE O/E INDEX IN BIOASSESSMENTS

EPA Science Inventory

The contribution of rare taxa to bioassessments based on multispecies assemblages is the subject of continued debate. As a result, users of predictive models such as River InVertebrate Prediction and Classification System (RIVPACS) disagree on whether to exclude locally rare taxa...

Taxa: An R package implementing data standards and methods for taxonomic data

PubMed Central

Foster, Zachary S.L.; Chamberlain, Scott; Grünwald, Niklaus J.

2018-01-01

The taxa R package provides a set of tools for defining and manipulating taxonomic data. The recent and widespread application of DNA sequencing to community composition studies is making large data sets with taxonomic information commonplace. However, compared to typical tabular data, this information is encoded in many different ways and the hierarchical nature of taxonomic classifications makes it difficult to work with. There are many R packages that use taxonomic data to varying degrees but there is currently no cross-package standard for how this information is encoded and manipulated. We developed the R package taxa to provide a robust and flexible solution to storing and manipulating taxonomic data in R and any application-specific information associated with it. Taxa provides parsers that can read common sources of taxonomic information (taxon IDs, sequence IDs, taxon names, and classifications) from nearly any format while preserving associated data. Once parsed, the taxonomic data and any associated data can be manipulated using a cohesive set of functions modeled after the popular R package dplyr. These functions take into account the hierarchical nature of taxa and can modify the taxonomy or associated data in such a way that both are kept in sync. Taxa is currently being used by the metacoder and taxize packages, which provide broadly useful functionality that we hope will speed adoption by users and developers. PMID:29707201

Discrete taxa of saprotrophic fungi respire different ages of carbon from Antarctic soils.

PubMed

Newsham, Kevin K; Garnett, Mark H; Robinson, Clare H; Cox, Filipa

2018-05-18

Different organic compounds have distinct residence times in soil and are degraded by specific taxa of saprotrophic fungi. It hence follows that specific fungal taxa should respire carbon of different ages from these compounds to the atmosphere. Here, we test whether this is the case by radiocarbon ( 14 C) dating CO 2 evolved from two gamma radiation-sterilised maritime Antarctic soils inoculated with pure single cultures of four fungi. We show that a member of the Helotiales, which accounted for 41-56% of all fungal sequences in the two soils, respired soil carbon that was aged up to 1,200 years BP and which was 350-400 years older than that respired by the other three taxa. Analyses of the enzyme profile of the Helotialean fungus and the fluxes and δ 13 C values of CO 2 that it evolved suggested that its release of old carbon from soil was associated with efficient cellulose decomposition. Our findings support suggestions that increases in the ages of carbon respired from warmed soils may be caused by changes to the abundances or activities of discrete taxa of microbes, and indicate that the loss of old carbon from soils is driven by specific fungal taxa.

Agaricus section Xanthodermatei: a phylogenetic reconstruction with commentary on taxa.

PubMed

Kerrigan, Richard W; Callac, Philippe; Guinberteau, Jacques; Challen, Michael P; Parra, Luis A

2005-01-01

Agaricus section Xanthodermatei comprises a group of species allied to A. xanthodermus and generally characterized by basidiomata having phenolic odors, transiently yellowing discolorations in some parts of the basidiome, Schaeffer's reaction negative, and mild to substantial toxicity. The section has a global distribution, while most included species have distributions restricted to regions of single continents. Using specimens and cultures from Europe, North America, and Hawaii, we analyzed DNA sequences from the ITS1+2 region of the nuclear rDNA to identify and characterize phylogenetically distinct entities and to construct a hypothesis of relationships, both among members of the section and with representative taxa from other sections of the genus. 61 sequences from affiliated taxa, plus 20 from six (or seven) other sections of Agaricus, and one Micropsalliota sequence, were evaluated under distance, maximum parsimony and maximum likelihood methods. We recognized 21 discrete entities in Xanthodermatei, including 14 established species and 7 new ones, three of which are described elsewhere. Four species from California, New Mexico, and France deserve further study before they are described. Type studies of American taxa are particularly emphasized, and a lectotype is designated for A. californicus. Section Xanthodermatei formed a single clade in most analyses, indicating that the traditional sectional characters noted above are good unifying characters that appear to have arisen only once within Agaricus. Deep divisions within the sequence-derived structure of the section could be interpreted as subsections in Xanthodermatei; however, various considerations led us to refrain from proposing new supraspecific taxa. The nearest neighbors of section Xanthodermatei are putatively in section Duploannulati.

Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data.

PubMed

Liu, Zhenqiu; Sun, Fengzhu; Braun, Jonathan; McGovern, Dermot P B; Piantadosi, Steven

2015-04-01

Identifying disease associated taxa and constructing networks for bacteria interactions are two important tasks usually studied separately. In reality, differentiation of disease associated taxa and correlation among taxa may affect each other. One genus can be differentiated because it is highly correlated with another highly differentiated one. In addition, network structures may vary under different clinical conditions. Permutation tests are commonly used to detect differences between networks in distinct phenotypes, and they are time-consuming. In this manuscript, we propose a multilevel regularized regression method to simultaneously identify taxa and construct networks. We also extend the framework to allow construction of a common network and differentiated network together. An efficient algorithm with dual formulation is developed to deal with the large-scale n ≪ m problem with a large number of taxa (m) and a small number of samples (n) efficiently. The proposed method is regularized with a general Lp (p ∈ [0, 2]) penalty and models the effects of taxa abundance differentiation and correlation jointly. We demonstrate that it can identify both true and biologically significant genera and network structures. Software MLRR in MATLAB is available at http://biostatistics.csmc.edu/mlrr/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Catalog of taxa introduced by Luitfried Salvini-Plawen (1939-2014).

PubMed

Affenzeller, Susanne; Steiner, Gerhard

2017-10-17

Luitfried Salvini-Plawen was one of the most distinguished researchers for molluscan phylogenetic systematics of the last decades. In his publications he described a total of 193 species: 134 Solenogastres, 34 Caudofoveata, 14 interstitial Gastropoda, one polyplacophoran and the remaining comprising Cnidaria, Priapulida, Kamptozoa, and Echinodermata. In addition, he introduced 47 genus-group names and 54 names for family-level and higher taxa. This catalog comprises lists of all taxon names published by Luitfried Salvini-Plawen. The catalog entries contain taxonomic information, original citations, type localities and type collections. It aims to facilitate further research on these and related taxa.

Pyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere

PubMed Central

Yousaf, Sohail; Bulgari, Daniela; Bergna, Alessandro; Pancher, Michael; Quaglino, Fabio; Casati, Paola; Campisano, Andrea

2014-01-01

Generally, plants are not considered as hosts for human and animal pathogens (HAP). The recent produce-associated outbreaks of food-borne diseases have drawn attention toward significant deficiencies in our understanding of the ecology of HAP, and their potential for interkingdom transfer. To examine the association of microorganisms classified as HAP with plants, we surveyed the presence and distribution of HAP bacterial taxa (henceforth HAPT, for brevity's sake) in the endosphere of grapevine (Vitis vinifera L.) both in the plant stems and leaves. An enrichment protocol was used on leaves to detect taxa with very low abundance in undisturbed tissues. We used pyrosequencing and phylogenetic analyses of the 16S rDNA gene. We identified several HAPT, and focused on four genera (Propionibacterium, Staphylococcus, Clostridium, and Burkholderia). The majority of the bacterial sequences in the genus Propionibacterium, from grapevine leaf and stem, were identified as P. acnes. Clostridia were detected in leaves and stems, but their number was much higher in leaves after enrichment. HAPT were indentified both in leaves and wood of grapevines. This depicts the ability of these taxa to be internalized within plant tissues and maintain their population levels in a variety of environments. Our analysis highlighted the presence of HAPT in the grapevine endosphere and unexpected occurrence of these bacterial taxa in this atypical environment. PMID:25071740

Pyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere.

PubMed

Yousaf, Sohail; Bulgari, Daniela; Bergna, Alessandro; Pancher, Michael; Quaglino, Fabio; Casati, Paola; Campisano, Andrea

2014-01-01

Generally, plants are not considered as hosts for human and animal pathogens (HAP). The recent produce-associated outbreaks of food-borne diseases have drawn attention toward significant deficiencies in our understanding of the ecology of HAP, and their potential for interkingdom transfer. To examine the association of microorganisms classified as HAP with plants, we surveyed the presence and distribution of HAP bacterial taxa (henceforth HAPT, for brevity's sake) in the endosphere of grapevine (Vitis vinifera L.) both in the plant stems and leaves. An enrichment protocol was used on leaves to detect taxa with very low abundance in undisturbed tissues. We used pyrosequencing and phylogenetic analyses of the 16S rDNA gene. We identified several HAPT, and focused on four genera (Propionibacterium, Staphylococcus, Clostridium, and Burkholderia). The majority of the bacterial sequences in the genus Propionibacterium, from grapevine leaf and stem, were identified as P. acnes. Clostridia were detected in leaves and stems, but their number was much higher in leaves after enrichment. HAPT were indentified both in leaves and wood of grapevines. This depicts the ability of these taxa to be internalized within plant tissues and maintain their population levels in a variety of environments. Our analysis highlighted the presence of HAPT in the grapevine endosphere and unexpected occurrence of these bacterial taxa in this atypical environment.

Roles of epi-anecic taxa of earthworms in the organic matter recycling

NASA Astrophysics Data System (ADS)

Hoeffner, Kevin; Monard, Cécile; Santonja, Mathieu; Pérès, Guénola; Cluzeau, Daniel

2017-04-01

Given their impact on soil functioning and their interactions with soil organisms, earthworms contribute to the recycling of organic matter and participate significantly in the numerous ecosystem services provided by soils. Most studies on the role of earthworms in organic matter recycling were conducted at the level of the four functional groups (epigeic, epi-anecic, anecic strict and endogeic), but their effects at taxa level remain largely unknown. Still, within a functional group, anatomic and physiologic earthworm taxa traits are different, which should impact organic matter recycling. This study aims at determining, under controlled conditions, epi-anecic taxa differences in (i) leaf litter mass loss, (ii) assimilation and (iii) impact on microorganisms communities implied in organic matter degradation. In seperate microcosms, we chose 4 epi anecic taxa (Lumbricus rubellus, Lumbricus festivus, Lumbricus centralis and Lumbricus terrestris). Each taxon was exposed separately to leaves of three different plants (Holcus lanatus, Lolium perenne and Corylus avellana). In the same microcosm, leaves of each plant was both placed on the surface and buried 10cm deep. The experiment lasted 10 days for half of the samples and 20 days for the second half. Microorganisms communities were analysed using TRFLP in each earthworm taxon burrow walls at 20 days. We observed differences between epi-anecic taxa depending on species of plant and the duration of the experiment. Results are discussed taking into account physical and chemical properties of these 3 trophic resources (e.g. C/N ratio, phenolic compounds, percentage of lignin and cellulose...).

Influence of anglers' specializations on catch, harvest, and bycatch of targeted taxa

USGS Publications Warehouse

Pope, Kevin L.; Chizinski, Christopher J.; Wiley, Christopher L.; Martin, Dustin R.

2016-01-01

Fishery managers often use catch per unit effort (CPUE) of a given taxon derived from a group of anglers, those that sought said taxon, to evaluate fishery objectives because managers assume CPUE for this group of anglers is most sensitive to changes in fish taxon density. Further, likelihood of harvest may differ for sought and non-sought taxa if taxon sought is a defining characteristic of anglers’ attitude toward harvest. We predicted that taxon-specific catch across parties and reservoirs would be influenced by targeted taxon after controlling for number of anglers in a party and time spent fishing (combine to quantify fishing effort of party); we also predicted similar trends for taxon-specific harvest. We used creel-survey data collected from anglers that varied in taxon targeted, from generalists (targeting “anything” [no primary target taxa, but rather targeting all fishes]) to target specialists (e.g., anglers targeting largemouth bass Micropterus salmoides) in 19 Nebraska reservoirs during 2009–2011 to test our predictions. Taxon-specific catch and harvest were, in general, positively related to fishing effort. More importantly, we observed differences of catch and harvest among anglers grouped by taxon targeted for each of the eight taxa assessed. Anglers targeting a specific taxon had the greatest catch for that taxon and anglers targeting anything typically had the second highest catch for that taxon. In addition, anglers tended to catch more of closely related taxa and of taxa commonly targeted with similar fishing techniques. We encourage managers to consider taxon-specific objectives of target and non-target catch and harvest.

A nomenclator of extant and fossil taxa of the Valvatidae (Gastropoda, Ectobranchia)

PubMed Central

Haszprunar, Gerhard

2014-01-01

Abstract A compilation of all supra- and (infra-) specific taxa of extant and fossil Valvatidae, a group of freshwater operculate snails, is provided, including taxa initially described in this family and subsequently classified in other families, as well as names containing errors or misspellings. The extensive reference list is directly linked to the available electronic source (digital view or pdf-download) of the respective papers. PMID:24578604

Relative differences in susceptibility of Pieris taxa (Ericaceae) to Stephanitis spp. lace bugs (Hemiptera: Tingidae).

PubMed

Nair, Shakunthala; Braman, S Kristine; Knauft, D A

2012-10-01

Over 60 Pieris taxa (Ericaceae) were measured for their susceptibility to the Andromeda lace bug, Stephanitis takeyai Drake and Maa, and the azalea lace bug, Stephanitis pyrioides (Scott) (Hemiptera: Tingidae) based on leaf damage, adult survival on leaves, and emergence of nymphs in no-choice petri dish assays. Pieris phillyreifolia (Hook.) DC. and P. japonica (Thunb.) D.Don ex G.Don 'Variegata' were consistently resistant to both species of lace bugs, whereas P. japonica 'Cavatine' was consistently susceptible to both. Pieris japonica 'Temple Bells' was highly susceptible to S. takeyai, but resistant to S. pyrioides. Nymph emergence was noted only with S. takeyai, on 46 Pieris taxa, whereas S. pyrioides nymphs were not observed on any of the Pieris taxa. Choice assays (with 10 Pieris taxa) and whole plant assays (with five Pieris taxa) using S. takeyai alone also were conducted, confirming the resistance of P. phillyreifolia and susceptibility of P. japonica Temple Bells to lace bug feeding.

Differences among Major Taxa in the Extent of Ecological Knowledge across Four Major Ecosystems

PubMed Central

Fisher, Rebecca; Knowlton, Nancy; Brainard, Russell E.; Caley, M. Julian

2011-01-01

Existing knowledge shapes our understanding of ecosystems and is critical for ecosystem-based management of the world's natural resources. Typically this knowledge is biased among taxa, with some taxa far better studied than others, but the extent of this bias is poorly known. In conjunction with the publically available World Registry of Marine Species database (WoRMS) and one of the world's premier electronic scientific literature databases (Web of Science®), a text mining approach is used to examine the distribution of existing ecological knowledge among taxa in coral reef, mangrove, seagrass and kelp bed ecosystems. We found that for each of these ecosystems, most research has been limited to a few groups of organisms. While this bias clearly reflects the perceived importance of some taxa as commercially or ecologically valuable, the relative lack of research of other taxonomic groups highlights the problem that some key taxa and associated ecosystem processes they affect may be poorly understood or completely ignored. The approach outlined here could be applied to any type of ecosystem for analyzing previous research effort and identifying knowledge gaps in order to improve ecosystem-based conservation and management. PMID:22073172

Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time

PubMed Central

O'Connor, Anne; Wills, Matthew A.

2016-01-01

The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence—however measured—also varied throughout the Phanerozoic

Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands.

PubMed

Ridley, Christina M; Voordouw, Gerrit

2018-06-01

Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8°C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment.

Resistance mechanisms in Pieris taxa (Ericaceae) to Stephanitis takeyai (Hemiptera: Tingidae).

PubMed

Nair, Shakunthala; Braman, S Kristine; Knauft, D A

2012-10-01

This study examines some of the potential mechanisms of resistance in selected Pieris (Ericaceae) taxa to the Andromeda lace bug, Stephanitis takeyai Drake and Maa, based on differences in resistance to lace bug feeding, and the possible role of leaf parameters such as leaf wax, toughness, nutrient composition, and stomatal characters in plant resistance. Experiments with extracts of leaf-surface lipids revealed that Pieris leaf wax did not have a role in resistance to lace bug feeding. Leaf wax extracts from a resistant species P. phillyreifolia (Hook.) DC. applied to leaves of a susceptible cultivar P. japonica (Thunb.) D.Don ex G.Don 'Temple Bells' did not affect feeding, oviposition, or survival of S. takeyai; and neither the extracts from Temple Bells induce susceptibility in P. phillyreifolia. Leaf penetrometer measurements indicated that significantly higher force was required to puncture P. phillyreifolia leaves, which also had higher fiber, lignin, and cellulose, and lower leaf moisture contents. Ultrastructural examination of leaves of Pieris taxa revealed significant differences in the number and size of stomata. P. phillyreifolia leaves had the highest number of stomata per unit area but these were the smallest in size, whereas P. japonica (Thunb.) D.Don ex G.Don Temple Bells leaves had the fewest and largest stomata. Resistance in Pieris taxa to S. takeyai may be attributed to a combination of different factors including leaf toughness, moisture, and stomatal characters. The type of resistance may be described as antixenosis combined with antibiosis, because reduced adult survival and reproduction were observed on the taxa resistant to lace bug feeding.

Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time.

PubMed

O'Connor, Anne; Wills, Matthew A

2016-09-01

The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence-however measured-also varied throughout the Phanerozoic, reflecting

Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa.

PubMed

Wiens, John J; Kuczynski, Caitlin A; Townsend, Ted; Reeder, Tod W; Mulcahy, Daniel G; Sites, Jack W

2010-12-01

Molecular data offer great potential to resolve the phylogeny of living taxa but can molecular data improve our understanding of relationships of fossil taxa? Simulations suggest that this is possible, but few empirical examples have demonstrated the ability of molecular data to change the placement of fossil taxa. We offer such an example here. We analyze the placement of snakes among squamate reptiles, combining published morphological data (363 characters) and new DNA sequence data (15,794 characters, 22 nuclear loci) for 45 living and 19 fossil taxa. We find several intriguing results. First, some fossil taxa undergo major changes in their phylogenetic position when molecular data are added. Second, most fossil taxa are placed with strong support in the expected clades by the combined data Bayesian analyses, despite each having >98% missing cells and despite recent suggestions that extensive missing data are problematic for Bayesian phylogenetics. Third, morphological data can change the placement of living taxa in combined analyses, even when there is an overwhelming majority of molecular characters. Finally, we find strong but apparently misleading signal in the morphological data, seemingly associated with a burrowing lifestyle in snakes, amphisbaenians, and dibamids. Overall, our results suggest promise for an integrated and comprehensive Tree of Life by combining molecular and morphological data for living and fossil taxa.

Towards stressor-specific macroinvertebrate indices: Which traits and taxonomic groups are associated with vulnerable and tolerant taxa?

PubMed

Berger, Elisabeth; Haase, Peter; Schäfer, Ralf B; Sundermann, Andrea

2018-04-01

Monitoring of macroinvertebrate communities is frequently used to define the ecological health status of rivers. Ideally, biomonitoring should also give an indication on the major stressors acting on the macroinvertebrate communities supporting the selection of appropriate management measures. However, most indices are affected by more than one stressor. Biological traits (e.g. size, generation time, reproduction) could potentially lead to more stressor-specific indices. However, such an approach has rarely been tested. In this study we classify 324 macroinvertebrate taxa as vulnerable (decreasing abundances) or tolerant (increasing abundances) along 21 environmental gradients (i.e. nutrients, major ions, oxygen and micropollutants) from 422 monitoring sites in Germany using Threshold Indicator Taxa Analysis (TITAN). Subsequently, we investigate which biological traits and taxonomic groups are associated with taxa classified as vulnerable or tolerant with regard to specific gradients. The response of most taxa towards different gradients was similar and especially high for correlated gradients. Traits associated with vulnerable taxa across most gradients included: larval aquatic life stages, isolated cemented eggs, reproductive cycle per year <1, scrapers, aerial and aquatic active dispersal and plastron respiration. Traits associated with tolerant taxa included: adult aquatic life stages, polyvoltinism, ovoviviparity or egg clutches in vegetation, food preference for dead animals or living microinvertebrates, substrate preference for macrophytes, microphytes, silt or mud and a body size >2-4cm. Our results question whether stressor-specific indices based on macroinvertebrate assemblages can be achieved using single traits, because we observed that similar taxa responded to different gradients and also similar traits were associated with vulnerable and tolerant taxa across a variety of water quality gradients. Future studies should examine whether combinations of

Benefits to poorly studied taxa of conservation of bird and mammal diversity on islands.

PubMed

Aslan, Clare; Holmes, Nick; Tershy, Bernie; Spatz, Dena; Croll, Donald A

2015-02-01

Protected area delineation and conservation action are urgently needed on marine islands, but the potential biodiversity benefits of these activities can be difficult to assess due to lack of species diversity information for lesser known taxa. We used linear mixed effects modeling and simple spatial analyses to investigate whether conservation activities based on the diversity of well-known insular taxa (birds and mammals) are likely to also capture the diversity of lesser known taxa (reptiles, amphibians, vascular land plants, ants, land snails, butterflies, and tenebrionid beetles). We assembled total, threatened, and endemic diversity data for both well-known and lesser known taxa and combined these with physical island biogeography characteristics for 1190 islands from 109 archipelagos. Among physical island biogeography factors, island area was the best indicator of diversity of both well-known and little-known taxa. Among taxonomic factors, total mammal species richness was the best indicator of total diversity of lesser known taxa, and the combination of threatened mammal and threatened bird diversity was the best indicator of lesser known endemic richness. The results of other intertaxon diversity comparisons were highly variable, however. Based on our results, we suggest that protecting islands above a certain minimum threshold area may be the most efficient use of conservation resources. For example, using our island database, if the threshold were set at 10 km(2) and the smallest 10% of islands greater than this threshold were protected, 119 islands would be protected. The islands would range in size from 10 to 29 km(2) and would include 268 lesser known species endemic to a single island, along with 11 bird and mammal species endemic to a single island. Our results suggest that for islands of equivalent size, prioritization based on total or threatened bird and mammal diversity may also capture opportunities to protect lesser known species endemic to

Dendrothele griseocana (Corticiaceae) and related taxa with hyphal pegs

Treesearch

Karen K. Nakasone

2006-01-01

Four Dendrothele (Corticiaceae, Polyporales) species with hyphal pegs are described and illustrated. Type specimens of Corticium griseocanum and Dendrothele papillosa were examined and found to be conspecific. Two new taxa, D. americana and D. tanzaniana, are described and illustrated, and the new combination, Dendrothele andina, is proposed. A key to D. griseocana and...

Twelve invasive plant taxa in U.S. western riparian ecosystems

EPA Science Inventory

Assessments of stream ecosystems often include an evaluation of riparian condition; a key stressor in riparian ecosystems is the presence of invasive plants. We analyzed the distribution of 12 invasive taxa (common burdock [Arctium minus], giant reed [Arundo donax], cheatgrass [B...

Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

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

Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.

2011-04-18

Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeledmore » DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial

Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa.

PubMed

Choudoir, Mallory J; Buckley, Daniel H

2018-06-07

The latitudinal diversity gradient is a pattern of biogeography observed broadly in plants and animals but largely undocumented in terrestrial microbial systems. Although patterns of microbial biogeography across broad taxonomic scales have been described in a range of contexts, the mechanisms that generate biogeographic patterns between closely related taxa remain incompletely characterized. Adaptive processes are a major driver of microbial biogeography, but there is less understanding of how microbial biogeography and diversification are shaped by dispersal limitation and drift. We recently described a latitudinal diversity gradient of species richness and intraspecific genetic diversity in Streptomyces by using a geographically explicit culture collection. Within this geographically explicit culture collection, we have identified Streptomyces sister-taxa whose geographic distribution is delimited by latitude. These sister-taxa differ in geographic distribution, genomic diversity, and ecological traits despite having nearly identical SSU rRNA gene sequences. Comparative genomic analysis reveals genomic differentiation of these sister-taxa consistent with restricted gene flow across latitude. Furthermore, we show phylogenetic conservatism of thermal traits between the sister-taxa suggesting that thermal trait adaptation limits dispersal and gene flow across climate regimes as defined by latitude. Such phylogenetic conservatism of thermal traits is commonly associated with latitudinal diversity gradients for plants and animals. These data provide further support for the hypothesis that the Streptomyces latitudinal diversity gradient was formed as a result of historical demographic processes defined by dispersal limitation and driven by paleoclimate dynamics.

Floral traits driving reproductive isolation of two co-flowering taxa that share vertebrate pollinators

PubMed Central

Queiroz, Joel A.; Quirino, Zelma G. M.; Machado, Isabel C.

2015-01-01

Floral attributes evolve in response to frequent and efficient pollinators, which are potentially important drivers of floral diversification and reproductive isolation. In this context, we asked, how do flowers evolve in a bat–hummingbird pollination system? Hence, we investigated the pollination ecology of two co-flowering Ipomoea taxa (I. marcellia and I. aff. marcellia) pollinated by bats and hummingbirds, and factors favouring reproductive isolation and pollinator sharing in these plants. To identify the most important drivers of reproductive isolation, we compared the flowers of the two Ipomoea taxa in terms of morphometry, anthesis and nectar production. Pollinator services were assessed using frequency of visits, fruit set and the number of seeds per fruit after visits. The studied Ipomoea taxa differed in corolla size and width, beginning and duration of anthesis, and nectar attributes. However, they shared the same diurnal and nocturnal visitors. The hummingbird Heliomaster squamosus was more frequent in I. marcellia (1.90 visits h−1) than in I. aff. marcellia (0.57 visits h−1), whereas glossophagine bats showed similar visit rates in both taxa (I. marcellia: 0.57 visits h−1 and I. aff. marcellia: 0.64 visits h−1). Bat pollination was more efficient in I. aff. marcellia, whereas pollination by hummingbirds was more efficient in I. marcellia. Differences in floral attributes between Ipomoea taxa, especially related to the anthesis period, length of floral parts and floral arrangement in the inflorescence, favour reproductive isolation from congeners through differential pollen placement on pollinators. This bat–hummingbird pollination system seems to be advantageous in the study area, where the availability of pollinators and floral resources changes considerably throughout the year, mainly as a result of rainfall seasonality. This interaction is beneficial for both sides, as it maximizes the number of potential pollen vectors for plants and

Cephalopod embryonic shells as a tool to reconstruct reproductive strategies in extinct taxa.

PubMed

Laptikhovsky, Vladimir; Nikolaeva, Svetlana; Rogov, Mikhail

2018-02-01

An exhaustive study of existing data on the relationship between egg size and maximum size of embryonic shells in 42 species of extant cephalopods demonstrated that these values are approximately equal regardless of taxonomy and shell morphology. Egg size is also approximately equal to mantle length of hatchlings in 45 cephalopod species with rudimentary shells. Paired data on the size of the initial chamber versus embryonic shell in 235 species of Ammonoidea, 46 Bactritida, 13 Nautilida, 22 Orthocerida, 8 Tarphycerida, 4 Oncocerida, 1 Belemnoidea, 4 Sepiida and 1 Spirulida demonstrated that, although there is a positive relationship between these parameters in some taxa, initial chamber size cannot be used to predict egg size in extinct cephalopods; the size of the embryonic shell may be more appropriate for this task. The evolution of reproductive strategies in cephalopods in the geological past was marked by an increasing significance of small-egged taxa, as is also seen in simultaneously evolving fish taxa. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape

PubMed Central

Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

2015-01-01

Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km2, by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape.

PubMed

Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

2015-06-01

Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km(2) , by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships

Unsegmented annelids? Possible origins of four lophotrochozoan worm taxa.

PubMed

Halanych, Kenneth M; Dahlgren, Thomas G; McHugh, Damhnait

2002-07-01

In traditional classification schemes, the Annelida consists of the Polychaeta and the Clitellata (the latter including the Oligochaeta and Hirudinida). However, recent analyses suggest that annelids are much more diverse than traditionally believed, and that polychaetes are paraphyletic. Specifically, some lesser-known taxa (previously regarded as separate phyla) appear to fall within the annelid radiation. Abundant molecular, developmental, and morphological data show that the Siboglinidae, which includes the formerly recognized Pogonophora and Vestimentifera, are derived annelids; recent data from the Elongation Factor-1α (EF-1α) gene also suggest that echiurids are of annelid ancestry. Further, the phylogenetic origins of two other lesser-known groups of marine worms, the Myzostomida and Sipuncula, have recently been called into question. Whereas some authors advocate annelid affinities, others argue that these taxa do not fall within the annelid radiation. With advances in our understanding of annelid phylogeny, our perceptions of body plan evolution within the Metazoa are changing. The evolution of segmentation probably is more plastic than traditionally believed. However, as our understanding of organismal evolution is being revised, we are also forced to reconsider the specific characters being examined. Should segmentation be considered a developmental process or an ontological endpoint?

Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

PubMed Central

Jeffries, Thomas C.; Ijaz, Umer Z.; Hamonts, Kelly

2017-01-01

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients. PMID:29038749

Comparative ITS and AFLP Analysis of Diploid Cardamine (Brassicaceae) Taxa from Closely Related Polyploid Complexes

PubMed Central

MARHOLD, KAROL; LIHOVÁ, JUDITA; PERNÝ, MARIÁN; BLEEKER, WALTER

2004-01-01

• Background and Aims Diploid representatives from the related polyploid complexes of Cardamine amara, C. pratensis and C. raphanifolia (Brassicaceae), were studied to elucidate phylogenetic relationships among the complexes and among the individual taxa included. • Methods Two independent molecular data sets were used: nucleotide sequences from the internal transcribed spacers (ITS) of nrDNA, and amplified fragment length polymorphism (AFLP) markers. Seventeen diploid taxa from the studied groups were sampled. • Key Results Both ITS and AFLP analyses provided congruent results in inferred relationships, and revealed two main lineages. While the C. amara group, consisting of C. wiedemanniana and four subspecies of C. amara, was resolved as a well‐supported monophyletic group, taxa from the C. pratensis and C. tenera groups (the latter representing diploid taxa of the complex of C. raphanifolia) all appeared together in a single clade/cluster with no support for the recognition of either of the groups. Intra‐individual polymorphisms and patterns of nucleotide variation in the ITS region in C. uliginosa and C. tenera, together with the distribution of AFLP bands, indicate ancient hybridization and introgression among these Caucasian diploids. • Conclusions The lack of supported hierarchical structure suggests that extensive reticulate evolution between these groups, even at the diploid level, has occurred (although an alternative explanation, namely ancestral polymorphism in ITS data, cannot be completely excluded). Several implications for the investigation of the polyploid complexes of concern are drawn. When tracing origins of polyploid taxa, a much more complex scenario should be expected, taking into account all relatives as potential parents, irrespective of the group in which they are classified. PMID:15037449

Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams.

PubMed

Wilhelm, Linda; Besemer, Katharina; Fasching, Christina; Urich, Tim; Singer, Gabriel A; Quince, Christopher; Battin, Tom J

2014-08-01

Glaciers harbour diverse microorganisms, which upon ice melt can be released downstream. In glacier-fed streams microorganisms can attach to stones or sediments to form benthic biofilms. We used 454-pyrosequencing to explore the bulk (16S rDNA) and putatively active (16S rRNA) microbial communities of stone and sediment biofilms across 26 glacier-fed streams. We found differences in community composition between bulk and active communities among streams and a stronger congruence between biofilm types. Relative abundances of rRNA and rDNA were positively correlated across different taxa and taxonomic levels, but at lower taxonomic levels, the higher abundance in either the active or the bulk communities became more apparent. Here, environmental variables played a minor role in structuring active communities. However, we found a large number of rare taxa with higher relative abundances in rRNA compared with rDNA. This suggests that rare taxa contribute disproportionately to microbial community dynamics in glacier-fed streams. Our findings propose that high community turnover, where taxa repeatedly enter and leave the 'seed bank', contributes to the maintenance of microbial biodiversity in harsh ecosystems with continuous environmental perturbations, such as glacier-fed streams. © 2014 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications.

PubMed

Espinosa, Avelina; Paz-Y-Miño-C, Guillermo

2014-11-01

Unicellular eukaryotes, or protists, are among the most ancient organisms on Earth. Protists belong to multiple taxonomic groups; they are widely distributed geographically and in all environments. Their ability to discriminate among con- and heterospecifics has been documented during the past decade. Here we discuss exemplar cases of taxa-, clone-, and possible kin-discrimination in five major lineages: Mycetozoa ( Dictyostelium , Polysphondylium ), Dikarya ( Saccharomyces ), Ciliophora ( Tetrahymena ), Apicomplexa ( Plasmodium ) and Archamoebae ( Entamoeba ). We summarize the proposed genetic mechanisms involved in discrimination-mediated aggregation (self versus different), including the csA , FLO and trg (formerly lag ) genes, and the Proliferation Activation Factors (PAFs), which facilitate clustering in some protistan taxa. We caution about the experimental challenges intrinsic to studying recognition in protists, and highlight the opportunities for exploring the ecology and evolution of complex forms of cell-cell communication, including social behavior, in a polyphyletic, still superficially understood group of organisms. Because unicellular eukaryotes are the evolutionary precursors of multicellular life, we infer that their mechanisms of taxa-, clone-, and possible kin-discrimination gave origin to the complex diversification and sophistication of traits associated with species and kin recognition in plants, fungi, invertebrates and vertebrates.

Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications

PubMed Central

Espinosa, Avelina; Paz-y-Miño-C, Guillermo

2014-01-01

Unicellular eukaryotes, or protists, are among the most ancient organisms on Earth. Protists belong to multiple taxonomic groups; they are widely distributed geographically and in all environments. Their ability to discriminate among con- and heterospecifics has been documented during the past decade. Here we discuss exemplar cases of taxa-, clone-, and possible kin-discrimination in five major lineages: Mycetozoa (Dictyostelium, Polysphondylium), Dikarya (Saccharomyces), Ciliophora (Tetrahymena), Apicomplexa (Plasmodium) and Archamoebae (Entamoeba). We summarize the proposed genetic mechanisms involved in discrimination-mediated aggregation (self versus different), including the csA, FLO and trg (formerly lag) genes, and the Proliferation Activation Factors (PAFs), which facilitate clustering in some protistan taxa. We caution about the experimental challenges intrinsic to studying recognition in protists, and highlight the opportunities for exploring the ecology and evolution of complex forms of cell-cell communication, including social behavior, in a polyphyletic, still superficially understood group of organisms. Because unicellular eukaryotes are the evolutionary precursors of multicellular life, we infer that their mechanisms of taxa-, clone-, and possible kin-discrimination gave origin to the complex diversification and sophistication of traits associated with species and kin recognition in plants, fungi, invertebrates and vertebrates. PMID:25400313

Diversity among Cynodon accessions and taxa based on DNA amplification fingerprinting.

PubMed

Assefa, S; Taliaferro, C M; Anderson, M P; de los Reyes, B G; Edwards, R M

1999-06-01

The genus Cynodon (Gramineae), comprised of 9 species, is geographically widely distributed and genetically diverse. Information on the amounts of molecular genetic variation among and within Cynodon taxa is needed to enhance understanding of phylogenetic relations and facilitate germplasm management and breeding improvement efforts. Genetic relatedness among 62 Cynodon accessions, representing eight species, was assessed using DNA amplification fingerprinting (DAF). Ten 8-mer oligonucleotides were used to amplify specific Cynodon genomic sequences. The DNA amplification products of individual accessions were scored for presence (1) or absence (0) of bands. Similarity matrices were developed and the accessions were grouped by cluster (UPGMA) and principal coordinate analysis. Analyses were conducted within ploidy level (2x = 18 and 4x = 36) and over ploidy levels. Each primer revealed polymorphic loci among accessions within species. Of 539 loci (bands) scored, 496 (92%) were polymorphic. Cynodon arcuatus was clearly separated from other species by numerous monomorphic bands. The strongest species similarities were between C. aethiopicus and C. arcuatus, C. transvaalensis and C. plectostachyus, and C. incompletus and C. nlemfuensis. Intraspecific variation was least for C. aethiopicus, C. arcuatus, and C. transvaalensis, and greatest for C. dactylon. Accessions of like taxonomic classification were generally clustered, except the cosmopolitan C. dactylon var. dactylon and C. dactylon var. afganicus. Within taxa, accessions differing in chromosome number clustered in all instances indicating the 2x and 4x forms to be closely related. Little, if any, relationship was found between relatedness as indicated by the DAF profiles and previous estimates of hybridization potential between the different taxa.

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

PubMed

Stamatakis, Alexandros

2006-11-01

RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. icwww.epfl.ch/~stamatak

Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere

PubMed Central

Peredo, Elena L.; Simmons, Sheri L.

2018-01-01

Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents. PMID:29375531

Laticiferous taxa as a source of energy and hydrocarbon

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

Marimuthu, S.; Subramanian, R.B.; Kothari, I.L.

Twenty-nine laticiferous taxa of Apocynaceae, Asclepiadaceae, and Sapotaceae were screened for suitability as alternative sources of renewable energy, rubber, and phytochemicals and to select the most promising ones for large-scale cultivation. Of these, Allamanda violacea (14.9% protein, 13.8% polyphenol, 8.6% oil, 3.2% hydrocarbon), Catharanthus roseus (15.4% protein, 10.4% polyphenol, 11.5% oil, 1.9% hydrocarbon), and Holarrhena antidysenterica (14.2% protein, 16.4% polyphenol, 5,4% oil, 4.8% hydrocarbon) of Apocynaceae; Asclepias curassavica (19.3% protein, 6.5% polyphenol, 3.9% oil, 2.0% hydrocarbon), Calotropis gigantea (18.5% protein, 6.8% polyphenol, 7.0% oil, 2.8% hydrocarbon) of Asclepiadaceae; Mimusops elengi (11.3% protein, 9.7% polyphenol, 7.2% oil, 4.0% hydrocarbon) of Sapotaceaemore » show promising potential for future petrochemical plantations; of all these taxa, Holarrhena antidysenterica yielded an unusually high percentage (4.8%) of hydrocarbon fraction followed by Mimusops elengi (4.0%). NMR spectra confirmed the presence of cis-polyisoprene in all species studied except Nerium indicum (white-flowered var.). These data indicate that the majority of the species under investigation may be considered for large-scale cultivation as an alternative source of rubber, intermediate energy, and other phytochemicals.« less

Crisis of Japanese Vascular Flora Shown By Quantifying Extinction Risks for 1618 Taxa

PubMed Central

Kadoya, Taku; Takenaka, Akio; Ishihama, Fumiko; Fujita, Taku; Ogawa, Makoto; Katsuyama, Teruo; Kadono, Yasuro; Kawakubo, Nobumitsu; Serizawa, Shunsuke; Takahashi, Hideki; Takamiya, Masayuki; Fujii, Shinji; Matsuda, Hiroyuki; Muneda, Kazuo; Yokota, Masatsugu; Yonekura, Koji; Yahara, Tetsukazu

2014-01-01

Although many people have expressed alarm that we are witnessing a mass extinction, few projections have been quantified, owing to limited availability of time-series data on threatened organisms, especially plants. To quantify the risk of extinction, we need to monitor changes in population size over time for as many species as possible. Here, we present the world's first quantitative projection of plant species loss at a national level, with stochastic simulations based on the results of population censuses of 1618 threatened plant taxa in 3574 map cells of ca. 100 km2. More than 500 lay botanists helped monitor those taxa in 1994–1995 and in 2003–2004. We projected that between 370 and 561 vascular plant taxa will go extinct in Japan during the next century if past trends of population decline continue. This extinction rate is approximately two to three times the global rate. Using time-series data, we show that existing national protected areas (PAs) covering ca. 7% of Japan will not adequately prevent population declines: even core PAs can protect at best <60% of local populations from decline. Thus, the Aichi Biodiversity Target to expand PAs to 17% of land (and inland water) areas, as committed to by many national governments, is not enough: only 29.2% of currently threatened species will become non-threatened under the assumption that probability of protection success by PAs is 0.5, which our assessment shows is realistic. In countries where volunteers can be organized to monitor threatened taxa, censuses using our method should be able to quantify how fast we are losing species and to assess how effective current conservation measures such as PAs are in preventing species extinction. PMID:24922311

Selection of nontarget arthropod taxa for field research on transgenic insecticidal crops: using empirical data and statistical power.

PubMed

Prasifka, J R; Hellmich, R L; Dively, G P; Higgins, L S; Dixon, P M; Duan, J J

2008-02-01

One of the possible adverse effects of transgenic insecticidal crops is the unintended decline in the abundance of nontarget arthropods. Field trials designed to evaluate potential nontarget effects can be more complex than expected because decisions to conduct field trials and the selection of taxa to include are not always guided by the results of laboratory tests. Also, recent studies emphasize the potential for indirect effects (adverse impacts to nontarget arthropods without feeding directly on plant tissues), which are difficult to predict because of interactions among nontarget arthropods, target pests, and transgenic crops. As a consequence, field studies may attempt to monitor expansive lists of arthropod taxa, making the design of such broad studies more difficult and reducing the likelihood of detecting any negative effects that might be present. To improve the taxonomic focus and statistical rigor of future studies, existing field data and corresponding power analysis may provide useful guidance. Analysis of control data from several nontarget field trials using repeated-measures designs suggests that while detection of small effects may require considerable increases in replication, there are taxa from different ecological roles that are sampled effectively using standard methods. The use of statistical power to guide selection of taxa for nontarget trials reflects scientists' inability to predict the complex interactions among arthropod taxa, particularly when laboratory trials fail to provide guidance on which groups are more likely to be affected. However, scientists still may exercise judgment, including taxa that are not included in or supported by power analyses.

A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping.

PubMed

Koh, Hyunwook; Blaser, Martin J; Li, Huilin

2017-04-24

The role of the microbiota in human health and disease has been increasingly studied, gathering momentum through the use of high-throughput technologies. Further identification of the roles of specific microbes is necessary to better understand the mechanisms involved in diseases related to microbiome perturbations. Here, we introduce a new microbiome-based group association testing method, optimal microbiome-based association test (OMiAT). OMiAT is a data-driven testing method which takes an optimal test throughout different tests from the sum of powered score tests (SPU) and microbiome regression-based kernel association test (MiRKAT). We illustrate that OMiAT efficiently discovers significant association signals arising from varying microbial abundances and different relative contributions from microbial abundance and phylogenetic information. We also propose a way to apply it to fine-mapping of diverse upper-level taxa at different taxonomic ranks (e.g., phylum, class, order, family, and genus), as well as the entire microbial community, within a newly introduced microbial taxa discovery framework, microbiome comprehensive association mapping (MiCAM). Our extensive simulations demonstrate that OMiAT is highly robust and powerful compared with other existing methods, while correctly controlling type I error rates. Our real data analyses also confirm that MiCAM is especially efficient for the assessment of upper-level taxa by integrating OMiAT as a group analytic method. OMiAT is attractive in practice due to the high complexity of microbiome data and the unknown true nature of the state. MiCAM also provides a hierarchical association map for numerous microbial taxa and can also be used as a guideline for further investigation on the roles of discovered taxa in human health and disease.

Covariance in species diversity and facilitation among non-interactive parasite taxa: all against the host.

PubMed

Krasnov, B R; Mouillot, D; Khokhlova, I S; Shenbrot, G I; Poulin, R

2005-10-01

Different parasite taxa exploit different host resources and are often unlikely to interact directly. It is unclear, however, whether the diversity of any given parasite taxon is indirectly influenced by that of other parasite taxa on the same host. Some components of host immune defences may operate simultaneously against all kinds of parasites, whereas investment by the host in specific defences against one type of parasite may come at the expense of defence against other parasites. We investigated the relationships between the species diversity of 4 higher taxa of ectoparasites (fleas, sucking lice, mesostigmatid mites, and ixodid ticks), and between the species richness of ectoparasites and endoparasitic helminths, across different species of rodent hosts. Our analyses used 2 measures of species diversity, species richness and taxonomic distinctness, and controlled for the potentially confounding effects of sampling effort and phylogenetic relationships among host species. We found positive pairwise correlations between the species richness of fleas, mites and ticks; however, there was no association between species richness of any of these 3 groups and that of lice. We also found a strong positive relationship between the taxonomic distinctness of ecto- and endoparasite assemblages across host species. These results suggest the existence of a process of apparent facilitation among unrelated taxa in the organization of parasite communities. We propose explanations based on host immune responses, involving acquired cross-resistance to infection and interspecific variation in immunocompetence among hosts, to account for these patterns.

Early Cretaceous greenhouse pumped higher taxa diversification in spiders.

PubMed

Shao, Lili; Li, Shuqiang

2018-05-24

The Cretaceous experienced one of the most remarkable greenhouse periods in geological history. During this time, ecosystem reorganizations significantly impacted the diversification of many groups of organisms. The rise of angiosperms marked a major biome turnover. Notwithstanding, relatively little remains known about how the Cretaceous global ecosystem impacted the evolution of spiders, which constitute one of the most abundant groups of predators. Herein, we evaluate the transcriptomes of 91 taxa representing more than half of the spider families. We add 23 newly sequenced taxa to the existing database to obtain a robust phylogenomic assessment. Phylogenetic reconstructions using different datasets and methods obtain novel placements of some groups, especially in the Synspermiata and the group having a retrolateral tibial apophysis (RTA). Molecular analyses indicate an expansion of the RTA clade at the Early Cretaceous with a hunting predatory strategy shift. Fossil analyses show a 7-fold increase of diversification rate at the same period, but this likely owes to the first occurrences spider in amber deposits. Additional analyses of fossil abundance show an accumulation of spider lineages in the Early Cretaceous. We speculate that the establishment of a warm greenhouse climate pumped the diversification of spiders, in particular among webless forms tracking the abundance of insect prey. Our study offers a new pathway for future investigations of spider phylogeny and diversification. Copyright © 2018. Published by Elsevier Inc.

Crickets (Insecta, Orthoptera, Grylloidea) from Southern New Caledonia,
with descriptions of new taxa.

PubMed

Anso, Jérémy; Jourdan, Hervé; Desutter-Grandcolas, Laure

2016-06-15

Intensive sampling of cricket communities has been undertaken in southern New Caledonia in selected plots of vegetation, i.e. rain forest, preforest and maquis shrubland. This leads to the discovery of many new taxa, which are described in the present paper, together with closely related species from nearby areas. Descriptions are based on general morphology and characters of genitalia. Calling songs are described for all acoustic taxa but two, and observations about species habitats are given. In total, 35 species belonging to 13 genera are studied, including 21 new species and two new genera. The pattern of assemblages of cricket species in New Caledonia is discussed.

Fungal Taxa Target Different Carbon Substrates in Harvard Forest Soils

NASA Astrophysics Data System (ADS)

Hanson, C. A.; Allison, S. D.; Wallenstein, M. D.; Mellilo, J. M.; Treseder, K. K.

2006-12-01

The mineralization of soil organic carbon is a major component of the global carbon cycle and is largely controlled by soil microbial communities. However, little is known about the functional roles of soil microbes or whether different microbial taxa target different carbon substrates under natural conditions. To examine this possibility, we assessed the community composition of active fungi by using a novel nucleotide analog technique in soils from the Harvard Forest. We hypothesized that fungal community composition would shift in response to the addition of different substrates and that specific fungal taxa would respond differentially to particular carbon sources. To test this hypothesis, we added a nucleotide analog probe directly to soils in conjunction with one of five carbon compounds of increasing recalcitrance: glycine, sucrose, cellulose, tannin-protein complex, and lignin. During 48 hour incubations, the nucleotide analog was incorporated into newly replicated DNA of soil organisms that proliferated following the addition of the substrates. In this way, we labeled the DNA of microbes that respond to a particular carbon source. Labeled DNA was isolated and fungal Internal Transcribed Spacer (ITS) regions of ribosomal DNA (rDNA) were sequenced and analyzed to identify active fungi to near-species resolution. Diversity analyses at the ≥97% sequence similarity level indicated that taxonomic richness was greater under cellulose (Shannon Index: 3.23 ± 0.11 with ± 95% CI) and lignin (2.87 ± 0.15) additions than the other treatments (2.34 ± 0.16 to 2.64 ± 0.13). In addition, community composition of active fungi shifted under glycine, sucrose, and cellulose additions. Specifically, the community under glycine was significantly different from communities under control, cellulose, and tannin-protein (P<0.05). Additionally, the sucrose and cellulose communities were marginally different from the control community (P = 0.059 and 0.054, respectively) and

A nomenclator of extant and fossil taxa of the Melanopsidae (Gastropoda, Cerithioidea)

PubMed Central

Neubauer, Thomas A.

2016-01-01

Abstract This nomenclator provides details on all published names in the family-, genus-, and species-group, as well as for a few infrasubspecific names introduced for, or attributed to, the family Melanopsidae. It includes nomenclaturally valid names, as well as junior homonyms, junior objective synonyms, nomina nuda, common incorrect subsequent spellings, and as far as possible discussion on the current status in taxonomy. The catalogue encompasses three family-group names, 79 genus-group names, and 1381 species-group names. All of them are given in their original combination and spelling (except mandatory corrections requested by the Code), along with their original source. For each family- and genus-group name, the original classification and the type genus and type species, respectively, are given. Data provided for species-group taxa are type locality, type horizon (for fossil taxa), and type specimens, as far as available. PMID:27551193

Immunological Change in a Parasite-Impoverished Environment: Divergent Signals from Four Island Taxa

PubMed Central

Beadell, Jon S.; Atkins, Colm; Cashion, Erin; Jonker, Michelle; Fleischer, Robert C.

2007-01-01

Dramatic declines of native Hawaiian avifauna due to the human-mediated emergence of avian malaria and pox prompted an examination of whether island taxa share a common altered immunological signature, potentially driven by reduced genetic diversity and reduced exposure to parasites. We tested this hypothesis by characterizing parasite prevalence, genetic diversity and three measures of immune response in two recently-introduced species (Neochmia temporalis and Zosterops lateralis) and two island endemics (Acrocephalus aequinoctialis and A. rimitarae) and then comparing the results to those observed in closely-related mainland counterparts. The prevalence of blood parasites was significantly lower in 3 of 4 island taxa, due in part to the absence of certain parasite lineages represented in mainland populations. Indices of genetic diversity were unchanged in the island population of N. temporalis; however, allelic richness was significantly lower in the island population of Z. lateralis while both allelic richness and heterozygosity were significantly reduced in the two island-endemic species examined. Although parasite prevalence and genetic diversity generally conformed to expectations for an island system, we did not find evidence for a pattern of uniformly altered immune responses in island taxa, even amongst endemic taxa with the longest residence times. The island population of Z. lateralis exhibited a significantly reduced inflammatory cell-mediated response while levels of natural antibodies remained unchanged for this and the other recently introduced island taxon. In contrast, the island endemic A. rimitarae exhibited a significantly increased inflammatory response as well as higher levels of natural antibodies and complement. These measures were unchanged or lower in A. aequinoctialis. We suggest that small differences in the pathogenic landscape and the stochastic history of mutation and genetic drift are likely to be important in shaping the unique

New records of truffle taxa in Tuber and Terfezia from Turkey

Treesearch

Michael Angelo Castellano; Aziz Turkoglu

2012-01-01

Turkey has one of the richest floras in the northern hemisphere as it is located at the convergence of 3 phytogeographical regions: Euro-Siberian, Mediterranean, and Irano-Turanian. This is reflected in the high number of plant taxa, particularly plant families that have truffles associated with them. The forests of these regions are dominated by ectomycorrhizal...

Metazoan meiofauna in deep-sea canyons and adjacent open slopes: A large-scale comparison with focus on the rare taxa

NASA Astrophysics Data System (ADS)

Bianchelli, S.; Gambi, C.; Zeppilli, D.; Danovaro, R.

2010-03-01

Metazoan meiofaunal abundance, total biomass, nematode size and the richness of taxa were investigated along bathymetric gradients (from the shelf break down to ca. 5000-m depth) in six submarine canyons and on five adjacent open slopes of three deep-sea regions. The investigated areas were distributed along >2500 km, on the Portuguese to the Catalan and South Adriatic margins. The Portuguese and Catalan margins displayed the highest abundances, biomass and richness of taxa, while the lowest values were observed in the Central Mediterranean Sea. The comparison between canyons and the nearby open slopes showed the lack of significant differences in terms of meiofaunal abundance and biomass at any sampling depth. In most canyons and on most slopes, meiofaunal variables did not display consistent bathymetric patterns. Conversely, we found that the different topographic features were apparently responsible for significant differences in the abundance and distribution of the rare meiofaunal taxa (i.e. taxa accounting for <1% of total meiofaunal abundance). Several taxa belonging to the temporary meiofauna, such as larvae/juveniles of Priapulida, Holothuroidea, Ascidiacea and Cnidaria, were encountered exclusively on open slopes, while others (including the Tanaidacea and Echinodea larvae) were found exclusively in canyons sediments. Results reported here indicate that, at large spatial scales, differences in deep-sea meiofaunal abundance and biomass are not only controlled by the available food sources, but also by the region or habitat specific topographic features, which apparently play a key role in the distribution of rare benthic taxa.

Overcoming the effects of rogue taxa: Evolutionary relationships of the bee flies

PubMed Central

Trautwein, Michelle D.; Wiegmann, Brian M.; Yeates, David K

2011-01-01

Bombyliidae (5000 sp.), or bee flies, are a lower brachyceran family of flower-visiting flies that, as larvae, act as parasitoids of other insects. The evolutionary relationships are known from a morphological analysis that yielded minimal support for higher-level groupings. We use the protein-coding gene CAD and 28S rDNA to determine phylogeny and to test the monophyly of existing subfamilies, the divisions Tomophtalmae, and ‘the sand chamber subfamilies’. Additionally, we demonstrate that consensus networks can be used to identify rogue taxa in a Bayesian framework. Pruning rogue taxa post-analysis from the final tree distribution results in increased posterior probabilities. We find 8 subfamilies to be monophyletic and the subfamilies Heterotropinae and Mythicomyiinae to be the earliest diverging lineages. The large subfamily Bombyliinae is found to be polyphyletic and our data does not provide evidence for the monophyly of Tomophthalmae or the ‘sand chamber subfamilies’. PMID:21686308

Using computational fluid dynamics to test functional and ecological hypotheses in fossil taxa

NASA Astrophysics Data System (ADS)

Rahman, Imran

2016-04-01

Reconstructing how ancient organisms moved and fed is a major focus of study in palaeontology. Traditionally, this has been hampered by a lack of objective data on the functional morphology of extinct species, especially those without a clear modern analogue. However, cutting-edge techniques for characterizing specimens digitally and in three dimensions, coupled with state-of-the-art computer models, now provide a robust framework for testing functional and ecological hypotheses even in problematic fossil taxa. One such approach is computational fluid dynamics (CFD), a method for simulating fluid flows around objects that has primarily been applied to complex engineering-design problems. Here, I will present three case studies of CFD applied to fossil taxa, spanning a range of specimen sizes, taxonomic groups and geological ages. First, I will show how CFD enabled a rigorous test of hypothesized feeding modes in an enigmatic Ediacaran organism with three-fold symmetry, revealing previously unappreciated complexity of pre-Cambrian ecosystems. Second, I will show how CFD was used to evaluate hydrodynamic performance and feeding in Cambrian stem-group echinoderms, shedding light on the probable feeding strategy of the latest common ancestor of all deuterostomes. Third, I will show how CFD allowed us to explore the link between form and function in Mesozoic ichthyosaurs. These case studies serve to demonstrate the enormous potential of CFD for addressing long-standing hypotheses for a variety of fossil taxa, opening up an exciting new avenue in palaeontological studies of functional morphology.

Taxa-specific eco-sensitivity in relation to phytoplankton bloom stability and ecologically relevant lake state

NASA Astrophysics Data System (ADS)

Napiórkowska-Krzebietke, Agnieszka; Dunalska, Julita A.; Zębek, Elżbieta

2017-05-01

Phytoplankton (including plant-like, animal-like algae and Cyanobacteria) blooms have recently become a serious global threat to the sustenance of ecosystems, to human and animal health and to economy. This study focused on the composition and stability of blooms as well as their taxa-specific ecological sensitivity to the main causal factors (especially phosphorus and nitrogen) in degraded urban lakes. The analyzed lakes were assessed with respect to the trophic state as well as ecological status. Total phytoplankton biomass (ranging from 1.5 to 181.3 mg dm-3) was typical of blooms of different intensity, which can appear during a whole growing season but are the most severe in early or late summer. Our results suggested that steady-state and non-steady-state bloom assemblages including mono-, bi- and multi-species or heterogeneous blooms may occur in urban lakes. The most intense blooms were formed by the genera of Cyanobacteria: Microcystis, Limnothrix, Pseudanabaena, Planktothrix, Bacillariophyta: Cyclotella and Dinophyta mainly Ceratium and Peridinium. Considering the sensitivity of phytoplankton assemblages, a new eco-sensitivity factor was proposed (E-SF), based on the concept of Phytoplankton Trophic Index composed of trophic scores of phytoplankton taxa along the eutrophication gradient. The E-SF values of 0.5, 1.3, 6.7 and 15.1 were recognized in lakes having a high, good, moderate or poor ecological status, respectively. For lake restoration, each type of bloom should be considered separately because of different sensitivities of taxa and relationships with environmental variables. Proper recognition of the taxa-specific response to abiotic (especially to N and P enrichment) and biotic factors could have significant implications for further water protection and management.

Animal taxa contrast in their scale-dependent responses to land use change in rural Africa.

PubMed

Foord, Stefan Hendrik; Swanepoel, Lourens Hendrik; Evans, Steven William; Schoeman, Colin Stefan; Erasmus, Barend Frederik N; Schoeman, M Corrie; Keith, Mark; Smith, Alain; Mauda, Evans Vusani; Maree, Naudene; Nembudani, Nkhumeleni; Dippenaar-Schoeman, Anna Sophia; Munyai, Thinandavha Caswell; Taylor, Peter John

2018-01-01

Human-dominated landscapes comprise the bulk of the world's terrestrial surface and Africa is predicted to experience the largest relative increase over the next century. A multi-scale approach is required to identify processes that maintain diversity in these landscapes. Here we identify scales at which animal diversity responds by partitioning regional diversity in a rural African agro-ecosystem between one temporal and four spatial scales. Human land use practices are the main driver of diversity in all seven animal assemblages considered, with medium sized mammals and birds most affected. Even the least affected taxa, bats and non-volant small mammals (rodents), responded with increased abundance in settlements and agricultural sites respectively. Regional turnover was important to invertebrate taxa and their response to human land use was intermediate between that of the vertebrate extremes. Local scale (< 300 m) heterogeneity was the next most important level for all taxa, highlighting the importance of fine scale processes for the maintenance of biodiversity. Identifying the triggers of these changes within the context of functional landscapes would provide the context for the long-term sustainability of these rapidly changing landscapes.

Animal taxa contrast in their scale-dependent responses to land use change in rural Africa

PubMed Central

Swanepoel, Lourens Hendrik; Evans, Steven William; Schoeman, Colin Stefan; Erasmus, Barend Frederik N.; Schoeman, M. Corrie; Keith, Mark; Smith, Alain; Mauda, Evans Vusani; Maree, Naudene; Nembudani, Nkhumeleni; Dippenaar-Schoeman, Anna Sophia; Munyai, Thinandavha Caswell; Taylor, Peter John

2018-01-01

Human-dominated landscapes comprise the bulk of the world’s terrestrial surface and Africa is predicted to experience the largest relative increase over the next century. A multi-scale approach is required to identify processes that maintain diversity in these landscapes. Here we identify scales at which animal diversity responds by partitioning regional diversity in a rural African agro-ecosystem between one temporal and four spatial scales. Human land use practices are the main driver of diversity in all seven animal assemblages considered, with medium sized mammals and birds most affected. Even the least affected taxa, bats and non-volant small mammals (rodents), responded with increased abundance in settlements and agricultural sites respectively. Regional turnover was important to invertebrate taxa and their response to human land use was intermediate between that of the vertebrate extremes. Local scale (< 300 m) heterogeneity was the next most important level for all taxa, highlighting the importance of fine scale processes for the maintenance of biodiversity. Identifying the triggers of these changes within the context of functional landscapes would provide the context for the long-term sustainability of these rapidly changing landscapes. PMID:29738559

Fossil preservation and the stratigraphic ranges of taxa

NASA Technical Reports Server (NTRS)

Foote, M.; Raup, D. M.

1996-01-01

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of

Assessing the completeness of the fossil record using brachiopod Lazarus taxa

NASA Astrophysics Data System (ADS)

Gearty, W.; Payne, J.

2012-12-01

Lazarus taxa, organisms that disappear from the fossil record only to reappear later, provide a unique opportunity to assess the completeness of the fossil record. In this study, we apply logistic regression to quantify the associations of body size, geographic extent, and species diversity with the probability of being a Lazarus genus using the Phanerozoic fossil record of brachiopods. We find that both the geographic range and species diversity of a genus are inversely associated with the probability of being a Lazarus taxon in the preceding or succeeding stage. In contrast, body size exhibits little association with the probability of becoming a Lazarus taxon. A model including species diversity and geographic extent as predictors performs best among all combinations examined, whereas a model including only shell size as a predictor performs the worst - even worse than a model that assumes Lazarus taxa are randomly drawn from all available genera. These findings suggest that geographic range and species richness data can be used to improve estimates of extensions on the observed fossil ranges of genera and, thereby, better correct for sampling effects in estimates of taxonomic diversity change through the Phanerozoic.

Brachyceran Diptera (Insecta) in Cretaceous ambers, Part IV, Significant New Orthorrhaphous Taxa

PubMed Central

Grimaldi, David A.; Arillo, Antonio; Cumming, Jeffrey M.; Hauser, Martin

2011-01-01

Abstract Thirteen species of basal Brachycera (11 described as new) are reported, belonging to nine families and three infraorders. They are preserved in amber from the Early Cretaceous (Neocomian) of Lebanon, Albian of northern Spain, upper Albian to lower Cenomanian of northern Myanmar, and Late Cretaceous of New Jersey USA (Turonian) and Alberta, Canada (Campanian). Taxa are as follows, with significance as noted: In Stratiomyomorpha: Stratiomyidae (Cretaceogaster pygmaeus Teskey [2 new specimens in Canadian amber], Lysistrata emerita Grimaldi & Arillo, gen. et sp. n. [stem-group species of the family in Spanish amber]), and Xylomyidae (Cretoxyla azari Grimaldi & Cumming, gen. et sp. n. [in Lebanese amber], and an undescribed species from Spain). In Tabanomorpha: Tabanidae (Cratotabanus newjerseyensis Grimaldi, sp. n., in New Jersey amber). In Muscomorpha: Acroceridae (Schlingeromyia minuta Grimaldi & Hauser, gen. et sp. n. and Burmacyrtus rusmithi Grimaldi & Hauser gen. et sp. n., in Burmese amber, the only definitive species of the family from the Cretaceous); Mythicomyiidae (Microburmyia analvena Grimaldi & Cumming gen. et sp. n. and Microburmyia veanalvena Grimaldi & Cumming, sp. n., stem-group species of the family, both in Burmese amber); Apsilocephalidae or near (therevoid family-group) (Kumaromyia burmitica Grimaldi & Hauser, gen. et sp. n. [in Burmese amber]); Apystomyiidae (Hilarimorphites burmanica Grimaldi & Cumming, sp. n. [in Burmese amber], whose closest relatives are from the Late Jurassic of Kazachstan, the Late Cretaceous of New Jersey, and Recent of California). Lastly, two species belonging to families incertae sedis, both in Burmese amber: Tethepomyiidae (Tethepomyia zigrasi Grimaldi & Arillo sp. n., the aculeate oviscapt of which indicates this family was probably parasitoidal and related to Eremochaetidae); and unplaced to family is Myanmyia asteiformia Grimaldi, gen. et sp. n., a minute fly with highly reduced venation. These new taxa

Brachyceran Diptera (Insecta) in Cretaceous ambers, Part IV, Significant New Orthorrhaphous Taxa.

PubMed

Grimaldi, David A; Arillo, Antonio; Cumming, Jeffrey M; Hauser, Martin

2011-01-01

Thirteen species of basal Brachycera (11 described as new) are reported, belonging to nine families and three infraorders. They are preserved in amber from the Early Cretaceous (Neocomian) of Lebanon, Albian of northern Spain, upper Albian to lower Cenomanian of northern Myanmar, and Late Cretaceous of New Jersey USA (Turonian) and Alberta, Canada (Campanian). Taxa are as follows, with significance as noted: In Stratiomyomorpha: Stratiomyidae (Cretaceogaster pygmaeus Teskey [2 new specimens in Canadian amber], Lysistrata emerita Grimaldi & Arillo, gen. et sp. n. [stem-group species of the family in Spanish amber]), and Xylomyidae (Cretoxyla azari Grimaldi & Cumming, gen. et sp. n. [in Lebanese amber], and an undescribed species from Spain). In Tabanomorpha: Tabanidae (Cratotabanus newjerseyensis Grimaldi, sp. n., in New Jersey amber). In Muscomorpha: Acroceridae (Schlingeromyia minuta Grimaldi & Hauser, gen. et sp. n. and Burmacyrtus rusmithi Grimaldi & Hauser gen. etsp. n., in Burmese amber, the only definitive species of the family from the Cretaceous); Mythicomyiidae (Microburmyia analvena Grimaldi & Cumming gen. et sp. n. and Microburmyia veanalvena Grimaldi & Cumming, sp. n., stem-group species of the family, both in Burmese amber); Apsilocephalidae or near (therevoid family-group) (Kumaromyia burmitica Grimaldi & Hauser, gen. et sp. n. [in Burmese amber]); Apystomyiidae (Hilarimorphites burmanica Grimaldi & Cumming, sp. n. [in Burmese amber], whose closest relatives are from the Late Jurassic of Kazachstan, the Late Cretaceous of New Jersey, and Recent of California). Lastly, two species belonging to families incertae sedis, both in Burmese amber: Tethepomyiidae (Tethepomyia zigrasi Grimaldi & Arillo sp. n., the aculeate oviscapt of which indicates this family was probably parasitoidal and related to Eremochaetidae); and unplaced to family is Myanmyia asteiformia Grimaldi, gen. et sp. n., a minute fly with highly reduced venation. These new taxa significantly

Temporal consistency in background mortality of four dominant coral taxa along Australia's Great Barrier Reef

NASA Astrophysics Data System (ADS)

Pisapia, C.; Anderson, K. D.; Pratchett, M. S.

2016-09-01

Studies on the population and community dynamics of scleractinian corals typically focus on catastrophic mortality associated with acute disturbances (e.g., coral bleaching and outbreaks of crown-of-thorns starfish), though corals are subject to high levels of background mortality and injuries caused by routine and chronic processes. This study quantified prevalence (proportion of colonies with injuries) and severity (areal extent of injuries on individual colonies) of background mortality and injuries for four common coral taxa (massive Porites, encrusting Montipora, Acropora hyacinthus and branching Pocillopora) on the Great Barrier Reef, Australia. Sampling was conducted over three consecutive years during which there were no major acute disturbances. A total of 2276 adult colonies were surveyed across 27 sites, within nine reefs and three distinct latitudinal sectors. The prevalence of injuries was very high (>83%) across all four taxa, but highest for Porites (91%) and Montipora (85%). For these taxa ( Montipora and Pocillopora), there was also significant temporal and spatial variation in prevalence of partial mortality. The severity of injuries ranged from 3% to more than 80% and varied among coral taxa, but was fairly constant spatially and temporally. This shows that some injuries have considerable longevity and that corals may invest relatively little in regenerating tissue over sites of previous injuries. Inter-colony variation in the severity of injury also had no apparent effect on the realized growth of individual colonies, suggesting that energy diverted to regeneration has a limited bearing on overall energetic allocation, or impacts on other life-history processes (e.g., reproduction) rather than growth. Establishing background levels of injury and regeneration is important for understanding energy investment and life-history consequences for reef-building corals as well as for predicting susceptibility to, and capacity to recover from, acute

Genome size of termites (Insecta, Dictyoptera, Isoptera) and wood roaches (Insecta, Dictyoptera, Cryptocercidae)

NASA Astrophysics Data System (ADS)

Koshikawa, Shigeyuki; Miyazaki, Satoshi; Cornette, Richard; Matsumoto, Tadao; Miura, Toru

2008-09-01

The evolution of genome size has been discussed in relation to the evolution of various biological traits. In the present study, the genome sizes of 22 dictyopteran species were estimated by Feulgen image analysis densitometry and 6-diamidino-2-phenylindole (DAPI)-based flow cytometry. The haploid genome sizes ( C-values) of termites (Isoptera) ranged from 0.58 to 1.90 pg, and those of Cryptocercus wood roaches (Cryptocercidae) were 1.16 to 1.32 pg. Compared to known values of other cockroaches (Blattaria) and mantids (Mantodea), these values are low. A relatively small genome size appears to be a (syn)apomorphy of Isoptera + Cryptocercus, together with their sociality. In some phylogenetic groups, genome size evolution is thought to be influenced by selective pressure on a particular trait, such as cell size or rate of development. The present results raise the possibility that genome size is influenced by selective pressures on traits associated with the evolution of sociality.

Genome size of termites (Insecta, Dictyoptera, Isoptera) and wood roaches (Insecta, Dictyoptera, Cryptocercidae).

PubMed

Koshikawa, Shigeyuki; Miyazaki, Satoshi; Cornette, Richard; Matsumoto, Tadao; Miura, Toru

2008-09-01

The evolution of genome size has been discussed in relation to the evolution of various biological traits. In the present study, the genome sizes of 22 dictyopteran species were estimated by Feulgen image analysis densitometry and 6-diamidino-2-phenylindole (DAPI)-based flow cytometry. The haploid genome sizes (C-values) of termites (Isoptera) ranged from 0.58 to 1.90 pg, and those of Cryptocercus wood roaches (Cryptocercidae) were 1.16 to 1.32 pg. Compared to known values of other cockroaches (Blattaria) and mantids (Mantodea), these values are low. A relatively small genome size appears to be a (syn)apomorphy of Isoptera + Cryptocercus, together with their sociality. In some phylogenetic groups, genome size evolution is thought to be influenced by selective pressure on a particular trait, such as cell size or rate of development. The present results raise the possibility that genome size is influenced by selective pressures on traits associated with the evolution of sociality.

Surrogate taxa and fossils as reliable proxies of spatial biodiversity patterns in marine benthic communities.

PubMed

Tyler, Carrie L; Kowalewski, Michał

2017-03-15

Rigorous documentation of spatial heterogeneity (β-diversity) in present-day and preindustrial ecosystems is required to assess how marine communities respond to environmental and anthropogenic drivers. However, the overwhelming majority of contemporary and palaeontological assessments have centred on single higher taxa. To evaluate the validity of single taxa as community surrogates and palaeontological proxies, we compared macrobenthic communities and sympatric death assemblages at 52 localities in Onslow Bay (NC, USA). Compositional heterogeneity did not differ significantly across datasets based on live molluscs, live non-molluscs, and all live organisms. Death assemblages were less heterogeneous spatially, likely reflecting homogenization by time-averaging. Nevertheless, live and dead datasets were greater than 80% congruent in pairwise comparisons to the literature estimates of β-diversity in other marine ecosystems, yielded concordant bathymetric gradients, and produced nearly identical ordinations consistently delineating habitats. Congruent estimates from molluscs and non-molluscs suggest that single groups can serve as reliable community proxies. High spatial fidelity of death assemblages supports the emerging paradigm of Conservation Palaeobiology. Integrated analyses of ecological and palaeontological data based on surrogate taxa can quantify anthropogenic changes in marine ecosystems and advance our understanding of spatial and temporal aspects of biodiversity. © 2017 The Author(s).

Darwin's diagram of divergence of taxa as a causal model for the origin of species.

PubMed

Bouzat, Juan L

2014-03-01

On the basis that Darwin's theory of evolution encompasses two logically independent processes (common descent and natural selection), the only figure in On the Origin of Species (the Diagram of Divergence of Taxa) is often interpreted as illustrative of only one of these processes: the branching patterns representing common ancestry. Here, I argue that Darwin's Diagram of Divergence of Taxa represents a broad conceptual model of Darwin's theory, illustrating the causal efficacy of natural selection in producing well-defined varieties and ultimately species. The Tree Diagram encompasses the idea that natural selection explains common descent and the origin of organic diversity, thus representing a comprehensive model of Darwin's theory on the origin of species. I describe Darwin's Tree Diagram in relation to his argumentative strategy under the vera causa principle, and suggest that the testing of his theory based on the evidence from the geological record, the geographical distribution of organisms, and the mutual affinities of organic beings can be framed under the hypothetico-deductive method. Darwin's Diagram of Divergence of Taxa therefore represents a broad conceptual model that helps understanding the causal construction of Darwin's theory of evolution, the structure of his argumentative strategy, and the nature of his scientific methodology.

Gene Flow Among Different Teosinte Taxa and Into the Domesticated Maize Gene Pool

USDA-ARS?s Scientific Manuscript database

Maize (Zea mays ssp. mays) was domesticated from one wild species ancestor, the Balsas teosinte (Zea mays ssp. parviglumis) about 9000 years ago. Higher levels of gene diversity are found in teosinte taxa compared to maize following domestication and selection bottlenecks. Diversity in maize can b...

Climate-driven C4 plant distributions in China: divergence in C4 taxa

PubMed Central

Wang, Renzhong; Ma, Linna

2016-01-01

There have been debates on the driving factors of C4 plant expansion, such as PCO2 decline in the late Micocene and warmer climate and precipitation at large-scale modern ecosystems. These disputes are mainly due to the lack of direct evidence and extensive data analysis. Here we use mass flora data to explore the driving factors of C4 distribution and divergent patterns for different C4 taxa at continental scale in China. The results display that it is mean annual climate variables driving C4 distribution at present-day vegetation. Mean annual temperature is the critical restriction of total C4 plants and the precipitation gradients seem to have much less impact. Grass and sedge C4 plants are largely restricted to mean annual temperature and precipitation respectively, while Chenopod C4 plants are strongly restricted by aridity in China. Separate regression analysis can succeed to detect divergences of climate distribution patterns of C4 taxa at global scale. PMID:27302686

Comparative Analysis of Native Crocus Taxa as a Great Source of Flavonoids with High Antioxidant Activity.

PubMed

Šola, Ivana; Stipaničev, Mirta; Vujčić, Valerija; Mitić, Božena; Huđek, Ana; Rusak, Gordana

2018-06-02

Native Crocus taxa are abundant in regions with moderate and dry climate; however, their potential in the food industry has thus far been neglected. The objective of this study was to compare the quantitative and qualitative flavonoid content and antioxidant and cytotoxic activity in organs of several populations of Croatian native taxa and assess their potential for application in the food industry. The dominant flavonoids in the native Crocus taxa were kaempferol and quercetin. Tepals contained similar or higher concentrations of flavonoid-glycosides than other organs. Tepals from Cvv1 and Cvv2 populations contained more flavonoid-glycosides than the commonly used spice saffron (C. sativus stigmas). The FRAP antioxidant activity of Cvv1 and Cvv5 tepals was similar to that of standard Trolox. DPPH inhibition of Cvv1 and Cvv3 tepals was within the range of that recorded for saffron. Cvv1 tepals significantly reduced reactive oxygen species in the broadest concentration range (50-1000 μg/ml), and showed considerable antioxidant activity in the ABTS assay, equal to 82% of standard Trolox antioxidant activity. A significantly higher concentration of kaempferol-rutinoside was recorded in this than in other taxa. The flavonoid showed a very strong or strong correlation with antioxidant assays results, and a negative correlation with cellular reactive oxygen species concentration. We therefore presumed that kaempferol-rutinoside is one of the main antioxidant phenolics in Crocus tepals. None of the tested extracts showed cytotoxicity toward Caco-2 cells. The results revealed that Cvv tepals have potential as a food supplement and are a promising material for further food safety tests.

A microarray for assessing transcription from pelagic marine microbial taxa

PubMed Central

Shilova, Irina N; Robidart, Julie C; James Tripp, H; Turk-Kubo, Kendra; Wawrik, Boris; Post, Anton F; Thompson, Anne W; Ward, Bess; Hollibaugh, James T; Millard, Andy; Ostrowski, Martin; J Scanlan, David; Paerl, Ryan W; Stuart, Rhona; Zehr, Jonathan P

2014-01-01

Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions. PMID:24477198

Bathymetric distribution patterns of Southern Ocean macrofaunal taxa: Bivalvia, Gastropoda, Isopoda and Polychaeta

NASA Astrophysics Data System (ADS)

Brandt, Angelika; Linse, Katrin; Schüller, Myriam

2009-11-01

The aim of this study is to compare the depth distributions of four major Southern Ocean macrobenthic epi- and infaunal taxa, the Bivalvia, Gastropoda, Isopoda, and Polychaeta, from subtidal to abyssal depth. All literature data up to summer 2008, as well as the unpublished data from the most recent ANDEEP I-III (Antarctic benthic deep-sea biodiversity: colonisation history and recent community patterns) expeditions to the Southern Ocean deep sea are included in the analysis. Benthic invertebrates in the Southern Ocean are known for their wide bathymetric ranges. We analysed the distributions of four of the most abundant and species-rich taxa from intertidal to abyssal (5200 m) depths in depth zones of 100 m. The depth distributions of three macrofaunal classes (Bivalvia, Gastropoda, Polychaeta) and one order (Isopoda) showed distinct differences. In the case of bivalves, gastropods and polychaetes, the number of species per depth zone decreased from the shelf to the slope at around 1000 m depth and then showed stable low numbers. The isopods showed the opposite trend; they were less species rich in the upper 1000 m but increased in species numbers from the slope to bathyal and abyssal depths. Depth ranges of families of the studied taxa (Bivalvia: 31 families, Gastropoda: 60, Isopoda: 32, and Polychaeta: 46 families) were compiled and illustrated. At present vast areas of the deep sea in the Southern Ocean remain unexplored and species accumulation curves showed that only a fraction of the species have been discovered to date. We anticipate that further investigations will greatly increase the number of species known in the Southern Ocean deep sea.

Nine endangered taxa, one recovering ecosystem: Identifying common ground for recovery on Santa Cruz Island, California

USGS Publications Warehouse

McEachern, A. Kathryn; Wilken, Dieter H.

2011-01-01

It is not uncommon to have several rare and listed taxa occupying habitats in one landscape or management area where conservation amounts to defense against the possibility of further loss. It is uncommon and extremely exciting, however, to have several listed taxa occupying one island that is managed cooperatively for conservation and recovery. On Santa Cruz Island, the largest of the northern California island group in the Santa Barbara Channel, we have a golden opportunity to marry ecological knowledge and institutional "good will" in a field test of holistic rare plant conservation. Here, the last feral livestock have been removed, active weed control is underway, and management is focused on understanding and demonstrating system response to conservation management. Yet funding limitations still exist and we need to plan the most fiscally conservative and marketable approach to rare plant restoration. We still experience the tension between desirable quick results and the ecological pace of system recovery. Therefore, our research has focused on identifying fundamental constraints on species recovery at individual, demographic, habitat, and ecosystem levels, and then developing suites of actions that might be taken across taxa and landscapes. At the same time, we seek a performance middle ground that balances an institutional need for quick demonstration of hands-on positive results with a contrasting approach that allows ecosystem recovery to facilitate species recovery in the long term. We find that constraints vary across breeding systems, life-histories, and island locations. We take a hybrid approach in which we identify several actions that we can take now to enhance population size or habitat occupancy for some taxa by active restoration, while allowing others to recover at the pace of ecosystem change. We make our recommendations on the basis of data we have collected over the last decade, so that management is firmly grounded in ecological observation.

Bias and sensitivity in the placement of fossil taxa resulting from interpretations of missing data.

PubMed

Sansom, Robert S

2015-03-01

The utility of fossils in evolutionary contexts is dependent on their accurate placement in phylogenetic frameworks, yet intrinsic and widespread missing data make this problematic. The complex taphonomic processes occurring during fossilization can make it difficult to distinguish absence from non-preservation, especially in the case of exceptionally preserved soft-tissue fossils: is a particular morphological character (e.g., appendage, tentacle, or nerve) missing from a fossil because it was never there (phylogenetic absence), or just happened to not be preserved (taphonomic loss)? Missing data have not been tested in the context of interpretation of non-present anatomy nor in the context of directional shifts and biases in affinity. Here, complete taxa, both simulated and empirical, are subjected to data loss through the replacement of present entries (1s) with either missing (?s) or absent (0s) entries. Both cause taxa to drift down trees, from their original position, toward the root. Absolute thresholds at which downshift is significant are extremely low for introduced absences (two entries replaced, 6% of present characters). The opposite threshold in empirical fossil taxa is also found to be low; two absent entries replaced with presences causes fossil taxa to drift up trees. As such, only a few instances of non-preserved characters interpreted as absences will cause fossil organisms to be erroneously interpreted as more primitive than they were in life. This observed sensitivity to coding non-present morphology presents a problem for all evolutionary studies that attempt to use fossils to reconstruct rates of evolution or unlock sequences of morphological change. Stem-ward slippage, whereby fossilization processes cause organisms to appear artificially primitive, appears to be a ubiquitous and problematic phenomenon inherent to missing data, even when no decay biases exist. Absent characters therefore require explicit justification and taphonomic

Larger ejaculate volumes are associated with a lower degree of polyandry across bushcricket taxa

PubMed Central

Vahed, Karim

2006-01-01

In numerous insects, including bushcrickets (Tettigoniidae), males are known to transfer substances in the ejaculate that inhibit the receptivity of females to further matings, but it has not yet been established whether these substances reduce the lifetime degree of polyandry of the female. The aim of this study was to test the hypothesis that larger ejaculate volumes should be associated with a lower degree of polyandry across tettigoniid taxa, controlling for male body mass and phylogeny. Data on ejaculate mass, sperm number, nuptial gift mass and male mass were taken primarily from the literature. The degree of polyandry for 14 species of European bushcrickets was estimated by counting the number of spermatodoses within the spermathecae of field-caught females towards the end of their adult lifespans. Data for four further species were obtained from the literature. Data were analysed by using both species regression and independent contrasts to control for phylogeny. Multiple regression analysis revealed that, as predicted, there was a significant negative association between the degree of polyandry and ejaculate mass, relative to male body mass, across bushcricket taxa. Nuptial gift size and sperm number, however, did not contribute further to interspecific variation in the degree of polyandry. A positive relationship was found, across bushcricket taxa, between relative nuptial gift size and relative ejaculate mass, indicating that larger nuptial gifts allow the male to overcome female resistance to accepting large ejaculates. This appears to be the first comparative evidence that males can manipulate the lifetime degree of polyandry of their mates through the transfer of large ejaculates. PMID:16928643

Identifying sighting clusters of endangered taxa with historical records.

PubMed

Duffy, Karl J

2011-04-01

The probability and time of extinction of taxa is often inferred from statistical analyses of historical records. Many of these analyses require the exclusion of multiple records within a unit of time (i.e., a month or a year). Nevertheless, spatially explicit, temporally aggregated data may be useful for identifying clusters of sightings (i.e., sighting clusters) in space and time. Identification of sighting clusters highlights changes in the historical recording of endangered taxa. I used two methods to identify sighting clusters in historical records: the Ederer-Myers-Mantel (EMM) test and the space-time permutation scan (STPS). I applied these methods to the spatially explicit sighting records of three species of orchids that are listed as endangered in the Republic of Ireland under the Wildlife Act (1976): Cephalanthera longifolia, Hammarbya paludosa, and Pseudorchis albida. Results with the EMM test were strongly affected by the choice of the time interval, and thus the number of temporal samples, used to examine the records. For example, sightings of P. albida clustered when the records were partitioned into 20-year temporal samples, but not when they were partitioned into 22-year temporal samples. Because the statistical power of EMM was low, it will not be useful when data are sparse. Nevertheless, the STPS identified regions that contained sighting clusters because it uses a flexible scanning window (defined by cylinders of varying size that move over the study area and evaluate the likelihood of clustering) to detect them, and it identified regions with high and regions with low rates of orchid sightings. The STPS analyses can be used to detect sighting clusters of endangered species that may be related to regions of extirpation and may assist in the categorization of threat status. ©2010 Society for Conservation Biology.

Diel, Seasonal, and Interannual Variability in Abundance of Major Mesozooplankton Taxa in the Sargasso Sea as Related to Changing Environmental Parameters

NASA Astrophysics Data System (ADS)

Ivory, J.; Steinberg, D. K.; Latour, R. J.

2016-02-01

Temporal changes in mesozooplankton community structure affect planktonic food web interactions and biogeochemical cycling. Epipelagic mesozooplankton biomass in the Sargasso Sea has increased over the last two decades, with a related increase in zooplankton-mediated carbon export. Unknown, however, is what are the patterns and variability at different temporal scales (diel, seasonal, and interannual) in abundance of each major zooplankton taxon, and how do these patterns relate to physical and other environmental changes? We enumerated major taxa of mesozooplankton collected from monthly day and night net tows in the epipelagic zone at the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea from 1999 to 2010. Abundances of each taxon were determined using a ZooScan optical imaging system and microscopy. Generalized Linear Models (GLMs) were used to determine what environmental parameters best explain abundance of major taxa. We used annual averages to consider broader patterns. Zooplankton taxa with the most pronounced diel vertical migration (i.e., night:day ratio, N:D, >>1) included Limacina spp. pteropods (N:D=2.02), euphausiids (1.93), calanoid copepods (1.34), and heteropods (1.34). Taxa with a pronounced spring abundance peak included chaetognaths, larvaceans, and Limacina spp. pteropods, while harpacticoid copepods peaked in late summer, and calanoid copepods in both spring and summer. Environmental variables affecting abundance differed amongst taxa. For example, calanoid copepod density was highly influenced by the abundance of a major predator- chaetognaths. Multi-year densities of calanoid copepods and ostracods both increased with increasing Water Column Stratification Index and the Atlantic Multidecadal Oscillation (AMO) index, indicating warmer sea surface temperatures are favorable for these taxa. We discuss how these temporal patterns at different scales help predict effects of global climate change on the zooplankton community.

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards.

PubMed

Streicher, Jeffrey W; Schulte, James A; Wiens, John J

2016-01-01

Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or to minimize the inclusion of missing data cells. Here, we explore this question for an ancient, rapid radiation of lizards, the pleurodont iguanians. Pleurodonts include many well-known clades (e.g., anoles, basilisks, iguanas, and spiny lizards) but relationships among families have proven difficult to resolve strongly and consistently using traditional sequencing approaches. We generated up to 4921 ultraconserved elements with sampling strategies including 16, 29, and 44 taxa, from 1179 to approximately 2.4 million characters per matrix and approximately 30% to 60% total missing data. We then compared mean branch support for interfamilial relationships under these 15 different sampling strategies for both concatenated (maximum likelihood) and species tree (NJst) approaches (after showing that mean branch support appears to be related to accuracy). We found that both approaches had the highest support when including loci with up to 50% missing taxa (matrices with ~40-55% missing data overall). Thus, our results show that simply excluding all missing data may be highly problematic as the primary guiding principle for the inclusion or exclusion of taxa and genes. The optimal strategy was somewhat different for each approach, a pattern that has not been shown previously. For concatenated analyses, branch support was maximized when including many taxa (44) but fewer characters (1.1 million). For species-tree analyses, branch support was maximized with minimal taxon sampling (16) but many loci (4789 of 4921). We also show that the choice of these sampling

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

PubMed Central

Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C.; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A.G.; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J.M.; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H. Thorsten; Schmull, Michaela; Schoch, Conrad; Sérusiaux, Emmanuël; Maddison, David R.; Arnold, A. Elizabeth; Lutzoni, François; Stenroos, Soili

2014-01-01

The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, ‘Candelariomycetidae’). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed

Phalangopsidae crickets from Tropical Africa (Orthoptera, Grylloidea), with descriptions of new taxa and an identification key for African genera.

PubMed

Desutter-Grandcolas, Laure

2015-04-22

New Phalangopsidae crickets are described from tropical Africa, including three new genera and ten new species: Afrophaloria Desutter-Grandcolas, n.gen., Afrophaloria amani Desutter-Grandcolas, n. sp., type species, Afrophaloria apiariensis Desutter-Grandcolas, n. sp., Afrophaloria hempae Desutter-Grandcolas, n. sp., Kameruloria gabonensis Desutter-Grandcolas, n. sp., Kameruloria nigricornis Desutter-Grandcolas, n. sp., Kameruloria trimaculata Desutter-Grandcolas, n. sp., Paragryllodes amani Desutter-Grandcolas, n. sp., Phasmagryllus Desutter-Grandcolas, n.gen., Phasmagryllus elegans Desutter-Grandcolas, n. sp., type species, Upupagryllus Desutter-Grandcolas, n.gen., Upupagryllus subalatus Desutter-Grandcolas, n. sp., type species, and Upupagryllus alatus Desutter-Grandcolas, n. sp. All these taxa, except Paragryllodes amani Desutter-Grandcolas, n. sp., belong to the subfamily Phaloriinae. The subfamily is redefined, to take into account their morphological (apterous taxa) and ecological (straminicolous taxa) diversity. A key for phalangopsid African genera is proposed, and the status of Larandeicus Chopard, 1937 briefly discussed.

Do the rich get richer? Varying effects of tree species identity and diversity on the richness of understory taxa

USGS Publications Warehouse

Champagne, Juilette; Paine, C. E. Timothy; Schoolmaster, Donald; Stejskal, Robert; Volařík, Daniel; Šebesta, Jan; Trnka, Filip; Koutecký, Tomáš; Švarc, Petr; Svátek, Martin; Hector, Andy; Matula, Radim

2016-01-01

Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in forests. Studies suggest that diversity in the canopy and in the understory are positively associated, but these studies often confound the effects of tree species diversity with those of tree species identity and abiotic conditions. We combined extensive field sampling with structural equation modeling to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs, beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and positively associated with tree diversity, presumably because species of both these taxa specialize on certain species of trees. Tree identity also strongly affected diversity in the understory, especially for herbs, likely as a result of interspecific differences in canopy light transmittance or litter decomposition rates. Our results suggest that changes in forest management will disproportionately affect certain understory taxa. For instance, changes in canopy diversity will affect the diversity of earthworms and saproxylic beetles more than changes in tree species composition, whereas the converse would be expected for understory herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa can vary from positive to negative and may affect biogeochemical cycling in temperate forests. Thus, maintaining high diversity in temperate forests can promote the diversity of multiple taxa in the understory.

Do the rich get richer? Varying effects of tree species identity and diversity on the richness of understory taxa.

PubMed

Chamagne, Juliette; Paine, C E Timothy; Schoolmaster, Donald R; Stejskal, Robert; Volarřík, Daniel; Šebesta, Jan; Trnka, Filip; Koutecký, Tomáš; Švarc, Petr; Svátek, Martin; Hector, Andy; Matula, Radim

2016-09-01

Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in forests. Studies suggest that diversity in the canopy and in the understory are positively associated, but these studies often confound the effects of tree species diversity with those of tree species identity and abiotic conditions. We combined extensive field sampling with structural equation modeling to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs, beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and positively associated with tree diversity, presumably because species of both these taxa specialize on certain species of trees. Tree identity also strongly affected diversity in the understory, especially for herbs, likely as a result of interspecific differences in canopy light transmittance or litter decomposition rates. Our results suggest that changes in forest management will disproportionately affect certain understory taxa. For instance, changes in canopy diversity will affect the diversity of earthworms and saproxylic beetles more than changes in tree species composition, whereas the converse would be expected for understory herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa can vary from positive to negative and may affect biogeochemical cycling in temperate forests. Thus, maintaining high diversity in temperate forests can promote the diversity of multiple taxa in the understory. © 2016 by the Ecological Society of America.

The effects of fossil placement and calibration on divergence times and rates: an example from the termites (Insecta: Isoptera).

PubMed

Ware, Jessica L; Grimaldi, David A; Engel, Michael S

2010-01-01

Among insects, eusocial behavior occurs in termites, ants, some bees and wasps. Isoptera and Hymenoptera convergently share social behavior, and for both taxa its evolution remains poorly understood. While dating analyses provide researchers with the opportunity to date the origin of eusociality, fossil calibration methodology may mislead subsequent ecological interpretations. Using a comprehensive termite dataset, we explored the effect of fossil placement and calibration methodology. A combined molecular and morphological dataset for 42 extant termite lineages was used, and a second dataset including these 42 taxa, plus an additional 39 fossil lineages for which we had only morphological data. MrBayes doublet-model analyses recovered similar topologies, with one minor exception (Stolotermitidae is sister to the Hodotermitidae, s.s., in the 42-taxon analysis but is in a polytomy with Hodotermitidae and (Kalotermitidae + Neoisoptera) in the 81-taxon analysis). Analyses using the r8s program on these topologies were run with either minimum/maximum constraints (analysis a = 42-taxon and analysis c = 81-taxon analyses) or with the fossil taxon ages fixed (ages fixed to be the geological age of the deposit from which they came, analysis b = 81-taxon analysis). Confidence intervals were determined for the resulting ultrametric trees, and for most major clades there was significant overlap between dates recovered for analyses A and C (with exceptions, such as the nodes Neoisoptera, and Euisoptera). With the exception of isopteran and eusiopteran node ages, however, none of the major clade ages overlapped when analysis B is compared with either analysis A or C. Future studies on Dictyoptera should note that the age of Kalotermitidae was underestimated in absence of kalotermitid fossils with fixed ages. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

New light on names and naming of dark taxa

PubMed Central

Ryberg, Martin; Nilsson, R. Henrik

2018-01-01

Abstract A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as “dark taxa” or “dark matter fungi”. As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted. PMID:29681731

Nuclear DNA content and base composition in 28 taxa of Musa.

PubMed

Kamaté, K; Brown, S; Durand, P; Bureau, J M; De Nay, D; Trinh, T H

2001-08-01

The nuclear DNA content of 28 taxa of Musa was assessed by flow cytometry, using line PxPC6 of Petunia hybrida as an internal standard. The 2C DNA value of Musa balbisiana (BB genome) was 1.16 pg, whereas Musa acuminata (AA genome) had an average 2C DNA value of 1.27 pg, with a difference of 11% between its subspecies. The two haploid (IC) genomes, A and B, comprising most of the edible bananas, are therefore of similar size, 0.63 pg (610 million bp) and 0.58 pg (560 million bp), respectively. The genome of diploid Musa is thus threefold that of Arabidopsis thaliana. The genome sizes in a set of triploid Musa cultivars or clones were quite different, with 2C DNA values ranging from 1.61 to 2.23 pg. Likewise, the genome sizes of tetraploid cultivars ranged from 1.94 to 2.37 pg (2C). Apparently, tetraploids (for instance, accession I.C.2) can have a genome size that falls within the range of triploid genome sizes, and vice versa (as in the case of accession Simili Radjah). The 2C values estimated for organs such as leaf, leaf sheath, rhizome, and flower were consistent, whereas root material gave atypical results, owing to browning. The genomic base composition of these Musa taxa had a median value of 40.8% GC (SD = 0.43%).

Dominant plant taxa predict plant productivity responses to CO 2 enrichment across precipitation and soil gradients

DOE PAGES

Fay, Philip A.; Newingham, Beth A.; Polley, H. Wayne; ...

2015-03-30

The Earth’s atmosphere will continue to be enriched with carbon dioxide (CO 2) over the coming century. Carbon dioxide enrichment often reduces leaf transpiration, which in water-limited ecosystems may increase soil water content, change species abundances and increase the productivity of plant communities. The effect of increased soil water on community productivity and community change may be greater in ecosystems with lower precipitation, or on coarser-textured soils, but responses are likely absent in deserts. We tested correlations among yearly increases in soil water content, community change and community plant productivity responses to CO 2 enrichment in experiments in a mesicmore » grassland with fine- to coarse-textured soils, a semi-arid grassland and a xeric shrubland. We found no correlation between CO 2-caused changes in soil water content and changes in biomass of dominant plant taxa or total community aboveground biomass in either grassland type or on any soil in the mesic grassland (P > 0.60). Instead, increases in dominant taxa biomass explained up to 85% of the increases in total community biomass under CO 2 enrichment. The effect of community change on community productivity was stronger in the semi-arid grassland than in the mesic grassland,where community biomass change on one soil was not correlated with the change in either the soil water content or the dominant taxa. No sustained increases in soil water content or community productivity and no change in dominant plant taxa occurred in the xeric shrubland. Thus, community change was a crucial driver of community productivity responses to CO 2 enrichment in the grasslands, but effects of soil water change on productivity were not evident in yearly responses to CO 2 enrichment. In conclusion, future research is necessary to isolate and clarify the mechanisms controlling the temporal and spatial variations in the linkages among soil water, community change and plant productivity responses

Chemical composition and antioxidant activity of essential oil of six pinus taxa native to China.

PubMed

Xie, Qing; Liu, Zhihong; Li, Zhouqi

2015-05-21

The essential oils obtained by steam distillation from needles of six China endemic Pinus taxa (P. tabulaeformis, P. tabulaeformis f. shekanensis, P. tabulaeformis var. mukdensis, P. tabulaeformis var. umbraculifera, P. henryi and P. massoniana) were analysed by GC/MS. A total of 72 components were separated and identified by GC/MS from the six taxa. The major constituents of the essential oils were: α-pinene (6.78%-20.55%), bornyl acetale (3.32%-12.71%), β-caryophellene (18.26%-26.31%), α-guaiene (1.23%-8.19%), and germacrene D (1.26%-9.93%). Moreover, the essential oils were evaluated for antioxidant potential by three assays (DPPH, FRAP and ABTS) and tested for their total phenolic content. The results showed that all essential oils exhibited acceptable antioxidant activities and these strongly suggest that these pine needles may serve as a potential source of natural antioxidants for food and medical purposes.

Cambro-ordovician sea-level fluctuations and sequence boundaries: The missing record and the evolution of new taxa

USGS Publications Warehouse

Lehnert, O.; Miller, J.F.; Leslie, Stephen A.; Repetski, J.E.; Ethington, Raymond L.

2005-01-01

The evolution of early Palaeozoic conodont faunas shows a clear connection to sea-level changes. One way that this connection manifests itself is that thick successions of carbonates are missing beneath major sequence boundaries due to karstification and erosion. From this observation arises the question of how many taxa have been lost from different conodont lineages in these incomplete successions. Although many taxa suffered extinction due to the environmental stresses associated with falling sea-levels, some must have survived in these extreme conditions. The number of taxa missing in the early Palaeozoic tropics always will be unclear, but it will be even more difficult to evaluate the missing record in detrital successions of higher latitudes. A common pattern in the evolution of Cambrian-Ordovician conodont lineages is appearances of new species at sea-level rises and disappearances at sea-level drops. This simple picture can be complicated by intervals that consistently have no representatives of a particular lineage, even after extensive sampling of the most complete sections. Presumably the lineages survived in undocumented refugia. In this paper, we give examples of evolution in Cambrian-Ordovician shallowmarine conodont faunas and highlight problems of undiscovered or truly missing segments of lineages. ?? The Palaeontological Association.

Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil.

PubMed

Hesse, Cedar N; Torres-Cruz, Terry J; Tobias, Terri Billingsley; Al-Matruk, Maryam; Porras-Alfaro, Andrea; Kuske, Cheryl R

Soil fungal communities are responsible for carbon and nitrogen (N) cycling. The high complexity of the soil fungal community and the high proportion of taxonomically unidentifiable sequences confound ecological interpretations in field studies because physiological information is lacking for many organisms known only by their rRNA sequences. This situation forces experimental comparisons to be made at broader taxonomic racks where functions become difficult to infer. The objective of this study was to determine OTU (operational taxonomic units) level responses of the soil fungal community to N enrichment in a temperate pine forest experiment and to use the sequencing data to guide culture efforts of novel N-responsive fungal taxa. Replicate samples from four soil horizons (up to 10 cm depth) were obtained from ambient, enriched CO 2 and N-fertilization plots. Through a fungal large subunit rRNA gene (LSU) sequencing survey, we identified two novel fungal clades that were abundant in our soil sampling (representing up to 27% of the sequences in some samples) and responsive to changes in soil N. The two N-responsive taxa with no predicted taxonomic association were targeted for isolation and culturing from specific soil samples where their sequences were abundant. Representatives of both OTUs were successfully cultured using a filtration approach. One taxon (OTU6) was most closely related to Saccharomycotina; the second taxon (OTU69) was most closely related to Mucoromycotina. Both taxa likely represent novel species. This study shows how observation of specific OTUs level responses to altered N status in a large rRNA gene field survey provided the impetus to design targeted culture approaches for isolation of novel N-responsive fungal taxa.

Transposable elements in sexual and ancient asexual taxa

PubMed Central

Arkhipova, Irina; Meselson, Matthew

2000-01-01

Sexual reproduction allows deleterious transposable elements to proliferate in populations, whereas the loss of sex, by preventing their spread, has been predicted eventually to result in a population free of such elements [Hickey, D. A. (1982) Genetics 101, 519–531]. We tested this expectation by screening representatives of a majority of animal phyla for LINE-like and gypsy-like reverse transcriptases and mariner/Tc1-like transposases. All species tested positive for reverse transcriptases except rotifers of the class Bdelloidea, the largest eukaryotic taxon in which males, hermaphrodites, and meiosis are unknown and for which ancient asexuality is supported by molecular genetic evidence. Mariner-like transposases are distributed sporadically among species and are present in bdelloid rotifers. The remarkable lack of LINE-like and gypsy-like retrotransposons in bdelloids and their ubiquitous presence in other taxa support the view that eukaryotic retrotransposons are sexually transmitted nuclear parasites and that bdelloid rotifers evolved asexually. PMID:11121049

Host-specificity among abundant and rare taxa in the sponge microbiome.

PubMed

Reveillaud, Julie; Maignien, Loïs; Murat Eren, A; Huber, Julie A; Apprill, Amy; Sogin, Mitchell L; Vanreusel, Ann

2014-06-01

Microbial communities have a key role in the physiology of the sponge host, and it is therefore essential to understand the stability and specificity of sponge-symbiont associations. Host-specific bacterial associations spanning large geographic distance are widely acknowledged in sponges. However, the full spectrum of specificity remains unclear. In particular, it is not known whether closely related sponges host similar or very different microbiota over wide bathymetric and geographic gradients, and whether specific associations extend to the rare members of the sponge microbiome. Using the ultra-deep Illumina sequencing technology, we conducted a comparison of sponge bacterial communities in seven closely related Hexadella species with a well-resolved host phylogeny, as well as of a distantly related sponge Mycale. These samples spanned unprecedentedly large bathymetric (15-960 m) gradients and varying European locations. In addition, this study included a bacterial community analysis of the local background seawater for both Mycale and the widespread deep-sea taxa Hexadella cf. dedritifera. We observed a striking diversity of microbes associated with the sponges, spanning 47 bacterial phyla. The data did not reveal any Hexadella microbiota co-speciation pattern, but confirmed sponge-specific and species-specific host-bacteria associations, even within extremely low abundant taxa. Oligotyping analysis also revealed differential enrichment preferences of closely related Nitrospira members in closely related sponges species. Overall, these results demonstrate highly diverse, remarkably specific and stable sponge-bacteria associations that extend to members of the rare biosphere at a very fine phylogenetic scale, over significant geographic and bathymetric gradients.

prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME.

PubMed

Lakhujani, Vijay; Badapanda, Chandan

2017-06-01

QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary . py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary . py , it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts . py , to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary . py but is also very fast in terms of CPU time and user friendly.

Diversity of kelp holdfast-associated fauna in an Arctic fjord - inconsistent responses to glacial mineral sedimentation across different taxa

NASA Astrophysics Data System (ADS)

Ronowicz, Marta; Kukliński, Piotr; Włodarska-Kowalczuk, Maria

2018-05-01

Kelp forests are complex underwater habitats that support diverse assemblages of animals ranging from sessile filter feeding invertebrates to fishes and marine mammals. In this study, the diversity of invertebrate fauna associated with kelp holdfasts was surveyed in a high Arctic glacial fjord (76 N, Hornsund, Svalbard). The effects of algal host identity (three kelp species: Laminaria digitata, Saccharina latissima and Alaria esculenta), depth (5 and 10 m) and glacier-derived disturbance (three sites with varying levels of mineral sedimentation) on faunal species richness and composition were studied based on 239 collected algal holdfasts. The species pool was mostly made up by three taxa: colonial Bryozoa and Hydrozoa, and Polychaeta. While the all-taxa species richness did not differ between depths, algal hosts and sites, the patterns varied when the two colonial sessile filter-feeding taxa were analysed alone (Hydrozoa and Bryozoa). The Hydrozoa sample species richness and average taxonomic distinctness were the highest at undisturbed sites, whereas Bryozoa species richness was higher in sediment-impacted localities, indicating relative insensitivity of this phylum to the increased level of mineral suspension in the water column. The average taxonomic distinctness of Bryozoa did not vary between sites. The species composition of kelp-associated fauna varied between sites and depths for the whole community and the most dominant taxa (Bryozoa, Hydrozoa). The high load of inorganic suspension and sedimentation did not cause pauperization of kelp holdfast-associated fauna but instead triggered the changes in species composition and shifts between dominant taxonomic groups.

Preliminary assessment of biogeographic affinities of selected insect taxa of the state of Sonora, Mexico

Treesearch

Robert W. Jones; Alejandro Obregon-Zuniga; Sandra Guzman-Rodriguez

2013-01-01

The biogeographic affinites of butterflies (Lepidoptera: Papilionoidea and Hesperidae), damsel and dragonflies (Odonata), and ants (Hymenoptera: Formicidae) reported from the State of Sonora, Mexico were analyzed using published species lists. The combined distribution of these taxa was proportionally greater (47.4%) for those species within the Mega-Mexico3...

HEXT, a software supporting tree-based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test.

PubMed

Schneider, Kevin; Koblmüller, Stephan; Sefc, Kristina M

2015-11-11

The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the clades containing the parental taxa reduces bootstrap support in the tree. The HET is based on the expectation that excluding the hybrid taxon from the data set increases the bootstrap support for the parental clades, whereas excluding non-hybrid taxa has little effect on statistical node support. To carry out a HET, bootstrap trees are calculated with taxon-jackknife data sets, that is excluding one taxon (species, population) at a time. Excess increase in bootstrap support for certain nodes upon exclusion of a particular taxon indicates the hybrid (the excluded taxon) and its parents (the clades with increased support).We introduce a new software program, hext, which generates the taxon-jackknife data sets, runs the bootstrap tree calculations, and identifies excess bootstrap increases as outlier values in boxplot graphs. hext is written in r language and accepts binary data (0/1; e.g. AFLP) as well as co-dominant SNP and genotype data.We demonstrate the usefulness of hext in large SNP data sets containing putative hybrids and their parents. For instance, using published data of the genus Vitis (~6,000 SNP loci), hext output supports V. × champinii as a hybrid between V. rupestris and V. mustangensis .With simulated SNP and AFLP data sets, excess increases in bootstrap support were not always connected with the hybrid taxon (false positives), whereas the expected bootstrap signal failed to appear on several occasions (false negatives). Potential causes for both types of spurious results are discussed.With both empirical and simulated data sets, the taxon-jackknife output generated by hext provided additional signatures of hybrid taxa, including changes in tree topology across trees, consistent effects of exclusions of the hybrid and the parent taxa, and moderate (rather than excessive) increases in bootstrap support

Diversity, specificity, co-occurrence and hub taxa of the bacterial-fungal pollen microbiome.

PubMed

Manirajan, Binoy Ambika; Maisinger, Corinna; Ratering, Stefan; Rusch, Volker; Schwiertz, Andreas; Cardinale, Massimiliano; Schnell, Sylvia

2018-06-06

Flower pollen represents a unique microbial habitat, however the factors driving microbial assemblages and microbe-microbe interactions remain largely unexplored. Here we compared the structure and diversity of the bacterial-fungal microbiome between eight different pollen species (four wind-pollinated and four insect-pollinated) from close geographical locations, using high-throughput sequencing of a 16S the rRNA gene fragment (bacteria) and the internal transcribed spacer 2 (ITS2, fungi). Proteobacteria and Ascomycota were the most abundant bacterial and fungal phyla, respectively. Pseudomonas (bacterial) and Cladosporium (fungal) were the most abundant genera. Both bacterial and fungal microbiota were significantly influenced by plant species and pollination type, but showed a core microbiome consisting of 12 bacterial and 33 fungal genera. Co-occurrence analysis highlighted significant inter- and intra-kingdom interactions, and the interaction network was shaped by four bacterial hub taxa: Methylobacterium (two OTUs), Friedmanniella and Rosenbergiella. Rosenbergiella prevailed in insect-pollinated pollen and was negatively correlated with the other hubs, indicating habitat complementarity. Inter-kingdom co-occurrence showed a predominant effect of fungal on bacterial taxa. This study enhances our basic knowledge of pollen microbiota, and poses the basis for further inter- and intra-kingdom interaction studies in the plant reproductive organs.

Taxonomic significance of leaf micromorphology in some selected taxa of Acanthaceae (Peninsular Malaysia)

NASA Astrophysics Data System (ADS)

Nurul-Aini, C. A. C.; Noraini, T.; Latiff, A.; Amirul-Aiman, A. J.; Ruzi, A. R.; Idris, S.

2014-09-01

Comparative leaf micromorphology study was conducted in eight taxa of Acanthaceae from Peninsular Malaysia. Eight chosen taxa were Acanthus ebracteatus Vahl, A. ilicifolius L., A. volubilis Wall, A. montanus T. Anderson, Andrographis paniculata (Burm.f.) Wall. ex Nees, Asystasia gangetica subsp. micrantha (Nees) Ensermu, Chroesthes longifolia (Wight) B. Hansen and Peristrophe roxburghiana (Schult.) Bremek. The objective of this study was to identify the leaf micromorphological characteristics that can be used in species identification and also as supportive data in classification. The procedures involved such as dehydration, critical point drying, gold coated and examination under scanning electron microscope. Findings in this study have demonstrated the similarities and variations in leaf micromorphological characteristics such as in type of epicuticular waxes, cuticular ornamentations, stomata characteristics and in the presence of trichomes. Six types of epicuticular waxes and five types of trichomes were observed. Variations in cuticular ornamentations and stomata structure can be used to differentiate species. One diagnostic character was found and proven to be very useful to identify Acanthus via the presence of simple trichomes (short-conicle like). In conclusion, the results of this study have shown that leaf micromorphological characteristics have taxonomic significance that can be useful in classifications and identification especially at species level.

The wild taxa utilized as vegetables in Sicily (Italy): a traditional component of the Mediterranean diet.

PubMed

Geraci, Anna; Amato, Filippo; Di Noto, Giuseppe; Bazan, Giuseppe; Schicchi, Rosario

2018-02-14

Wild vegetables in the Mediterranean Basin are still often consumed as a part of the diet and, in particular, there is a great tradition regarding their use in Sicily. In this study, an ethnobotanical field investigation was carried out to (a) identify the wild native taxa traditionally gathered and consumed as vegetables in Sicily, comparing the collected ethnobotanical data with those of other countries that have nominated the Mediterranean diet for inclusion in the UNESCO Representative List of the Intangible Cultural Heritage of Humanity and (b) highlight new culinary uses of these plants. Interviews were carried out in 187 towns and villages in Sicily between 2005 and 2015. A total of 980 people over the age of 50 were interviewed (mainly farmers, shepherds, and experts on local traditions). Plants recorded were usually collected in collaboration with the informants to confirm the correct identification of the plants. The frequencies of citation were calculated. Two hundred fifty-three taxa (specific and intraspecific) belonging to 39 families, and 128 genera were recorded (26 were cited for the first time). The most represented families were Asteraceae, Brassicaceae, Apiaceae, Amaryllidaceae, Malvaceae, and Polygonaceae. Only 14 taxa were cited by 75% of the people interviewed. The aerial parts of wild plants, including leaves, tender shoots, and basal rosettes, are the main portions collected, while the subterranean parts are used to a lesser extent. For some vegetables, more parts are utilized. Most of the reported vegetables are consumed cooked. In addition to the widely known vegetables (Borago officinalis, Beta spp., Cichorium spp., Brassica spp., Carduus spp., etc.), the so-called ancient vegetables are included (Onopordum illyricum, Centaurea calcitrapa, Nasturtium officinale, Scolymus spp., Smyrnium rotundifolium), and some unique uses were described. Comparing the Sicilian findings to those from other countries, a very high number of vegetable taxa

Dominant plant taxa predict plant productivity responses to CO2 enrichment across precipitation and soil gradients.

PubMed

Fay, Philip A; Newingham, Beth A; Polley, H Wayne; Morgan, Jack A; LeCain, Daniel R; Nowak, Robert S; Smith, Stanley D

2015-03-30

The Earth's atmosphere will continue to be enriched with carbon dioxide (CO2) over the coming century. Carbon dioxide enrichment often reduces leaf transpiration, which in water-limited ecosystems may increase soil water content, change species abundances and increase the productivity of plant communities. The effect of increased soil water on community productivity and community change may be greater in ecosystems with lower precipitation, or on coarser-textured soils, but responses are likely absent in deserts. We tested correlations among yearly increases in soil water content, community change and community plant productivity responses to CO2 enrichment in experiments in a mesic grassland with fine- to coarse-textured soils, a semi-arid grassland and a xeric shrubland. We found no correlation between CO2-caused changes in soil water content and changes in biomass of dominant plant taxa or total community aboveground biomass in either grassland type or on any soil in the mesic grassland (P > 0.60). Instead, increases in dominant taxa biomass explained up to 85 % of the increases in total community biomass under CO2 enrichment. The effect of community change on community productivity was stronger in the semi-arid grassland than in the mesic grassland, where community biomass change on one soil was not correlated with the change in either the soil water content or the dominant taxa. No sustained increases in soil water content or community productivity and no change in dominant plant taxa occurred in the xeric shrubland. Thus, community change was a crucial driver of community productivity responses to CO2 enrichment in the grasslands, but effects of soil water change on productivity were not evident in yearly responses to CO2 enrichment. Future research is necessary to isolate and clarify the mechanisms controlling the temporal and spatial variations in the linkages among soil water, community change and plant productivity responses to CO2 enrichment. Published

Nomenclatural stability does not justify recognition of paraphyletic taxa: A response to Scherz et al. (2016).

PubMed

Peloso, Pedro L V; Raxworthy, Christopher J; Wheeler, Ward C; Frost, Darrel R

2017-06-01

Peloso et al. (2015: PELOSO) published a comprehensive phylogenetic study of the frog family Microhylidae, which resulted in the discovery that several taxa were not monophyletic. To remedy this, a series of nomenclatural changes were proposed (several generic synonymies and two new subfamilies named). A recent study published in this journal by Scherz et al. (2016: SCHERZ), provided a novel phylogeny for the Malagasy subfamily Cophylinae. SCHERZ dispute the analyses and taxonomic conclusions of PELOSO. Their study is, however, based on substantial reduction of data from the PELOSO study, limited addition of new data, and different analytical methods. In spite of the fact that their own results are consistent with the taxonomy of PELOSO, SCHERZ reject that conservative taxonomy and suggest the revalidation of Platypelis (from the synonymy of Cophyla), the revalidation of Stumpffia (from the synonymies of Rhombophryne), and the creation of at least two new genera (only one named therein). In doing so, SCHERZ accept the recognition of likely paraphyletic taxa, with Stumpffia paraphyletic in their parsimony analysis. Herein, we provide a response to several points raised in SCHERZ: (1) we discuss issues with their interpretation (and selective use) of available phylogenetic and phenotypic evidence; (2) and provide a new phylogenetic analysis of all the data in PELOSO and SCHERZ combined. In the new analysis Stumpffia is paraphyletic with respect to Rhombophryne, whereas Cophyla and Platypelis are both monophyletic and sister taxa. We provide a case for the use of the taxonomy suggested in PELOSO. Copyright © 2017 Elsevier Inc. All rights reserved.

Identifying the microbial taxa that consistently respond to soil warming across time and space.

PubMed

Oliverio, Angela M; Bradford, Mark A; Fierer, Noah

2017-05-01

Soil microbial communities are the key drivers of many terrestrial biogeochemical processes. However, we currently lack a generalizable understanding of how these soil communities will change in response to predicted increases in global temperatures and which microbial lineages will be most impacted. Here, using high-throughput marker gene sequencing of soils collected from 18 sites throughout North America included in a 100-day laboratory incubation experiment, we identified a core group of abundant and nearly ubiquitous soil microbes that shift in relative abundance with elevated soil temperatures. We then validated and narrowed our list of temperature-sensitive microbes by comparing the results from this laboratory experiment with data compiled from 210 soils representing multiple, independent global field studies sampled across spatial gradients with a wide range in mean annual temperatures. Our results reveal predictable and consistent responses to temperature for a core group of 189 ubiquitous soil bacterial and archaeal taxa, with these taxa exhibiting similar temperature responses across a broad range of soil types. These microbial 'bioindicators' are useful for understanding how soil microbial communities respond to warming and to discriminate between the direct and indirect effects of soil warming on microbial communities. Those taxa that were found to be sensitive to temperature represented a wide range of lineages and the direction of the temperature responses were not predictable from phylogeny alone, indicating that temperature responses are difficult to predict from simply describing soil microbial communities at broad taxonomic or phylogenetic levels of resolution. Together, these results lay the foundation for a more predictive understanding of how soil microbial communities respond to soil warming and how warming may ultimately lead to changes in soil biogeochemical processes. © 2016 John Wiley & Sons Ltd.

The movement of pre-adapted cool taxa in north-central Amazonia during the last glacial

NASA Astrophysics Data System (ADS)

D'Apolito, Carlos; Absy, Maria Lúcia; Latrubesse, Edgardo M.

2017-08-01

The effects of climate change on the lowland vegetation of Amazonia during the last glacial cycle are partially known for the middle and late Pleniglacial intervals (late MIS 3, 59-24 ka and MIS 2, 24-11 ka), but are still unclear for older stages of the last glacial and during the last interglacial. It is known that a more seasonal dry-wet climate caused marginal forest retraction and together with cooling rearranged forest composition to some extent. This is observed in pollen records across Amazonia depicting presence of taxa at glacial times in localities where they do not live presently. The understanding of taxa migration is hindered by the lack of continuous interglacial-glacial lowland records. We present new data from a known locality in NW Amazonia (Six Lakes Hill), showing a vegetation record that probably started during MIS 5 (130-71 ka) and lasted until the onset of the Holocene. The vegetation record unravels a novel pattern in tree taxa migration: (1) from the beginning of this cycle Podocarpus and Myrsine are recorded and (2) only later do Hedyosmum and Alnus appear. The latter group is largely restricted to montane biomes or more distant locations outside Amazonia, whereas the first is found in lowlands close to the study site on sandy soils. These findings imply that Podocarpus and Myrsine responded to environmental changes equally and this reflects their concomitant niche use in NW Amazonia. Temperature drop is not discarded as a trigger of internal forest composition change, but its effects are clearer later in the Pleniglacial rather than the Early Glacial. Therefore early climatic/environmental changes had a first order effect on vegetation that invoke alternative explanations. We claim last glacial climate-induced modifications on forest composition favoured the expansion of geomorphologic-soil related processes that initiated forest rearrangement.

Hydrolyzable tannins, the active constituents of three Greek Cytinus taxa against several tumor cell lines.

PubMed

Magiatis, P; Pratsinis, H; Kalpoutzakis, E; Konstantinidou, A; Davaris, P; Skaltsounis, A L

2001-06-01

Hydrolyzable tannins were found to be the active cytotoxic constituents of three Greek Cytinus taxa: Cytinus ruber, Cytinus hypocistis subsp. hypocistis and Cytinus hypocistis subsp. orientalis. The cytotoxic activity was evaluated against a broad spectrum of cancer cell lines. The structure of the active compounds was investigated with NMR and electrospray-MS/MS techniques.

Seed protein variations of Salicornia L. and allied taxa in Turkey.

PubMed

Yaprak, A E; Yurdakulol, E

2007-06-01

Electrophoretic seed protein patterns of a number of accessions of Salicornia europaea L. sl., S. prostrata Palas, S. fragilis P.W. Ball and Tutin, Sarcocornia fruticosa (L.) A. J. Scott, Sarcocornia perennis (Miller.) A. J. Scott, Arthrocnemum glaucum (Del.) Ung.-Sternb., Microcnemum coralloides (Loscos and Pardo) subsp. anatolicum Wagenitz and Halocnemum strobilaceum (Pall.) Bieb. were electrophoretically analysed on SDS-PAGE. In total 48 different bands were identified. The obtained data have been treated numerically using the cluster analysis method of unweighted pair group (UPGMA). Finally it was determined that all species separated according to seed protein profiles. And the cladogram obtained studied taxa have been given.

Signals of speciation: Volatile organic compounds resolve closely related sagebrush taxa, suggesting their importance in evolution

Treesearch

Deidre M. Jaeger; Justin B. Runyon; Bryce A. Richardson

2016-01-01

Volatile organic compounds (VOCs) play important roles in the environmental adaptation and fitness of plants. Comparison of the qualitative and quantitative differences in VOCs among closely related taxa and assessing the effects of environment on their emissions are important steps to deducing VOC function and evolutionary importance.

Late Quaternary refugia of Mediterranean taxa in the Portuguese Estremadura: charcoal based palaeovegetation and climatic reconstruction

NASA Astrophysics Data System (ADS)

Figueiral, I.; Terral, J.-F.

2002-02-01

The study of archaeological charcoal preserved in the sediments of Buraca Grande (Estremadura, Portugal) are used to aid the reconstruction of vegetation available to prehistoric settlements from the Upper Palaeolithic to the Neolithic. Results indicate the possible existence of three different phases. The first is mostly characterized by the presence of Pinus type sylvestris and of Buxus sempervirens. During the second phase, these taxa are replaced by more thermophilous elements dominated by Olea europaea. The decrease of Olea europaea in the last archaeological layer appears to represent the beginning of a third phase. The eco-anatomical analyses of charcoal fragments identified as Olea europaea allowed us to evaluate the palaeoclimatic conditions during this period. Two main phases are recognized; the first (Upper Pleistocene) is drier and cooler than present, while the Holocene sequence is comparable to present-day conditions. Results from both analyses are complementary and appear to show that this region was a refuge area for thermophilous taxa during the colder periods of the Pleistocene.

Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata.

PubMed

Graur, D; Gouy, M; Duret, L

1997-04-01

Contrary to morphological claims, molecular data indicate that the order Perissodactyla (e.g., horses, rhinoceroses, and tapirs) is neither part of the superordinal taxon Paenungulata (Sirenia, Proboscidea, and Hyracoidea) nor an immediate outgroup of the paenungulates. Rather, Perissodactyla is closer to Carnivora and Cetartiodactyla (Cetacea+Artiodactyla) than it is to the paenungulates. Therefore, two morphologically defined superordinal taxa, Altungulata (Proboscidea, Sirenia, Hyracoidea, and Perissodactyla) and Ungulata (Altungulata and Cetartiodactyla), are invalidated. Perissodactyla, Carnivora, and Cetartiodactyla are shown to constitute a rather tight trichotomy. However, a molecular analysis of 36 protein sequences with a total concatenated length of 7885 aligned amino acids indicates that Perissodactyla is closer to Cetartiodactyla than either taxa is to Carnivora. The relationships among Paenungulata, Primates, and the clade consisting of Perissodactyla, Carnivora, and Cetartiodactylaa could not be resolved on the basis of the available data.

Distinguishing Between Convergent Evolution and Violation of the Molecular Clock for Three Taxa.

PubMed

Mitchell, Jonathan D; Sumner, Jeremy G; Holland, Barbara R

2018-05-18

We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more similar over time. By examining the 3-taxon case in some detail we illustrate that phylogeneticists have been "spoiled" in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is tree-like. We show that there are not always good statistical reasons to prefer the usual class of tree-like models over more general convergence-divergence models. Specifically we show many 3-taxon data sets can be equally well explained by supposing violation of the molecular clock due to change in the rate of evolution along different edges, or by keeping the assumption of a constant rate of evolution but instead assuming that evolution is not a purely divergent process. Given the abundance of evidence that evolution is not strictly tree-like, our discussion is an illustration that as phylogeneticists we need to think clearly about the structural form of the models we use. For cases with four taxa we show that there will be far greater ability to distinguish models with convergence from non-clock-like tree models.

Controlling Harmful Cyanobacteria: Taxa-Specific Responses of Cyanobacteria to Grazing by Large-Bodied Daphnia in a Biomanipulation Scenario

PubMed Central

Urrutia-Cordero, Pablo; Ekvall, Mattias K.; Hansson, Lars-Anders

2016-01-01

Lake restoration practices based on reducing fish predation and promoting the dominance of large-bodied Daphnia grazers (i.e., biomanipulation) have been the focus of much debate due to inconsistent success in suppressing harmful cyanobacterial blooms. While most studies have explored effects of large-bodied Daphnia on cyanobacterial growth at the community level and/or on few dominant species, predictions of such restoration practices demand further understanding on taxa-specific responses in diverse cyanobacterial communities. In order to address these questions, we conducted three grazing experiments during summer in a eutrophic lake where the natural phytoplankton community was exposed to an increasing gradient in biomass of the large-bodied Daphnia magna. This allowed evaluating taxa-specific responses of cyanobacteria to Daphnia grazing throughout the growing season in a desired biomanipulation scenario with limited fish predation. Total cyanobacterial and phytoplankton biomasses responded negatively to Daphnia grazing both in early and late summer, regardless of different cyanobacterial densities. Large-bodied Daphnia were capable of suppressing the abundance of Aphanizomenon, Dolichospermum, Microcystis and Planktothrix bloom-forming cyanobacteria. However, the growth of the filamentous Dolichospermum crassum was positively affected by grazing during a period when this cyanobacterium dominated the community. The eutrophic lake was subjected to biomanipulation since 2005 and nineteen years of lake monitoring data (1996–2014) revealed that reducing fish predation increased the mean abundance (50%) and body-size (20%) of Daphnia, as well as suppressed the total amount of nutrients and the growth of the dominant cyanobacterial taxa, Microcystis and Planktothrix. Altogether our results suggest that lake restoration practices solely based on grazer control by large-bodied Daphnia can be effective, but may not be sufficient to control the overgrowth of all

SSR markers reveal the genetic diversity of Asian Cercis taxa at the U.S. National Arboretum

USDA-ARS?s Scientific Manuscript database

The redbud (Cercis L. species) is a popular landscape plant grown widely in the United States. There are more than twenty cultivars of eastern redbud (Cercis canadensis L.) and at least three cultivars of Asian taxa (primarily C. chinensis Bunge) in the trade. The U.S. National Arboretum (USNA) has ...

Three-dimensional geometric morphometric analysis of talar morphology in extant gorilla taxa from highland and lowland habitats.

PubMed

Knigge, Ryan P; Tocheri, Matthew W; Orr, Caley M; Mcnulty, Kieran P

2015-01-01

Western gorillas (Gorilla gorilla) are known to climb significantly more often than eastern gorillas (Gorilla beringei), a behavioral distinction attributable to major differences in their respective habitats (i.e., highland vs. lowland). Genetic evidence suggests that the lineages leading to these taxa began diverging from one another between approximately 1 and 3 million years ago. Thus, gorillas offer a special opportunity to examine the degree to which morphology of recently diverged taxa may be "fine-tuned" to differing ecological requirements. Using three-dimensional (3D) geometric morphometrics, we compared talar morphology in a sample of 87 specimens including western (lowland), mountain (highland), and grauer gorillas (lowland and highland populations). Talar shape was captured with a series of landmarks and semilandmarks superimposed by generalized Procrustes analysis. A between-group principal components analysis of overall talar shape separates gorillas by ecological habitat and by taxon. An analysis of only the trochlea and lateral malleolar facet identifies subtle variations in trochlear shape between western lowland and lowland grauer gorillas, potentially indicative of convergent evolution of arboreal adaptations in the talus. Lastly, talar shape scales differently with centroid size for highland and lowland gorillas, suggesting that ankle morphology may track body-size mediated variation in arboreal behaviors differently depending on ecological setting. Several of the observed shape differences are linked biomechanically to the facilitation of climbing in lowland gorillas and to stability and load-bearing on terrestrial substrates in the highland taxa, providing an important comparative model for studying morphological variation in groups known only from fossils (e.g., early hominins). © 2014 Wiley Periodicals, Inc.

Effect of aging on lignin content, composition and enzymatic saccharification in Corymbia hybrids and parental taxa between years 9 and 12

DOE PAGES

Healey, Adam L.; Lupoi, Jason S.; Lee, David J.; ...

2016-07-02

Corymbia (a eucalypt) is an important forestry genus and a potential lignocellulosic bioenergy feedstock. The composition of the lignocellulosic cell wall significantly impacts pretreatment efficiency and conversion to biofuel but is variable and changes with age. In this study, we estimated Klason lignin content, composition, and monosaccharide (glucose and xylose) release after enzymatic saccharification of untreated and hydrothermally pretreated biomass from Corymbia parental species Corymbia torelliana (CT), Corymbia citriodora subsp. variegata (spotted gum; CCV), and interspecific F1 hybrids (CT x CCV) at ages 9 and 12 years from planting. Analysis of lignin composition derived from syringyl/guaiacyl monolignols (S/G) found significantmore » differences among taxa, with CT S/G ratios (2.2 and 2.0) being significantly lower than CCV (2.6 and 2.3) or hybrids (2.5 and 2.3) at ages 9 and 12 respectively. In general, enzymatic saccharification yields from untreated biomass were significantly different among taxa, with CT (113 and 75 mg g -1) and hybrids (108 and 81 mg g -1) yielding significantly higher glucose from untreated biomass than CCV (82 and 56 mg g -1) at ages 9 and 12 respectively. Comparison of traits within taxa between ages 9 and 12 found S/G ratios and glucose yields from untreated biomass were significantly lower in CT, CCV and hybrid taxa. As a result, the formation of lignocellulosic cell walls is complex, influenced by genetics and age of material, requiring optimization of rotation age for biofuel production and other industrial processes.« less

Effect of aging on lignin content, composition and enzymatic saccharification in Corymbia hybrids and parental taxa between years 9 and 12

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

Healey, Adam L.; Lupoi, Jason S.; Lee, David J.

Corymbia (a eucalypt) is an important forestry genus and a potential lignocellulosic bioenergy feedstock. The composition of the lignocellulosic cell wall significantly impacts pretreatment efficiency and conversion to biofuel but is variable and changes with age. In this study, we estimated Klason lignin content, composition, and monosaccharide (glucose and xylose) release after enzymatic saccharification of untreated and hydrothermally pretreated biomass from Corymbia parental species Corymbia torelliana (CT), Corymbia citriodora subsp. variegata (spotted gum; CCV), and interspecific F1 hybrids (CT x CCV) at ages 9 and 12 years from planting. Analysis of lignin composition derived from syringyl/guaiacyl monolignols (S/G) found significantmore » differences among taxa, with CT S/G ratios (2.2 and 2.0) being significantly lower than CCV (2.6 and 2.3) or hybrids (2.5 and 2.3) at ages 9 and 12 respectively. In general, enzymatic saccharification yields from untreated biomass were significantly different among taxa, with CT (113 and 75 mg g -1) and hybrids (108 and 81 mg g -1) yielding significantly higher glucose from untreated biomass than CCV (82 and 56 mg g -1) at ages 9 and 12 respectively. Comparison of traits within taxa between ages 9 and 12 found S/G ratios and glucose yields from untreated biomass were significantly lower in CT, CCV and hybrid taxa. As a result, the formation of lignocellulosic cell walls is complex, influenced by genetics and age of material, requiring optimization of rotation age for biofuel production and other industrial processes.« less

Primary controls on species richness in higher taxa.

PubMed

Rabosky, Daniel L

2010-12-01

The disparity in species richness across the tree of life is one of the most striking and pervasive features of biological diversity. Some groups are exceptionally diverse, whereas many other groups are species poor. Differences in diversity among groups are frequently assumed to result from primary control by differential rates of net diversification. However, a major alternative explanation is that ecological and other factors exert primary control on clade diversity, such that apparent variation in net diversification rates is a secondary consequence of ecological limits on clade growth. Here, I consider a likelihood framework for distinguishing between these competing hypotheses. I incorporate hierarchical modeling to explicitly relax assumptions about the constancy of diversification rates across clades, and I propose several statistics for a posteriori evaluation of model adequacy. I apply the framework to a recent dated phylogeny of ants. My results reject the hypothesis that net diversification rates exert primary control on species richness in this group and demonstrate that clade diversity is better explained by total time-integrated speciation. These results further suggest that it may not possible to estimate meaningful speciation and extinction rates from higher-level phylogenies of extant taxa only.

Unraveling Trichoderma species in the attine ant environment: description of three new taxa.

PubMed

Montoya, Quimi Vidaurre; Meirelles, Lucas Andrade; Chaverri, Priscila; Rodrigues, Andre

2016-05-01

Fungus-growing "attine" ants forage diverse substrates to grow fungi for food. In addition to the mutualistic fungal partner, the colonies of these insects harbor a rich microbiome composed of bacteria, filamentous fungi and yeasts. Previous work reported some Trichoderma species in the fungus gardens of leafcutter ants. However, no studies systematically addressed the putative association of Trichoderma with attine ants, especially in non-leafcutter ants. Here, a total of 62 strains of Trichoderma were analyzed using three molecular markers (ITS, tef1 and rpb2). In addition, 30 out of 62 strains were also morphologically examined. The strains studied correspond to the largest sampling carried out so far for Trichoderma in the attine ant environment. Our results revealed the richness of Trichoderma in this environment, since we found 20 Trichoderma species, including three new taxa described in the present work (Trichoderma attinorum, Trichoderma texanum and Trichoderma longifialidicum spp. nov.) as well as a new phylogenetic taxon (LESF 545). Moreover, we show that all 62 strains grouped within different clades across the Trichoderma phylogeny, which are identical or closely related to strains derived from several other environments. This evidence supports the transient nature of the genus Trichoderma in the attine ant colonies. The discovery of three new species suggests that the dynamic foraging behavior of these insects might be responsible for accumulation of transient fungi into their colonies, which might hold additional fungal taxa still unknown to science.

Retention and characteristics of microplastics in natural zooplankton taxa from the East China Sea.

PubMed

Sun, Xiaoxia; Liu, Tao; Zhu, Mingliang; Liang, Junhua; Zhao, Yongfang; Zhang, Bo

2018-05-30

The ubiquitous presence and persistence of microplastics (MPs) in aquatic environments have become of particular concern in recent years. Biological interactions are among the key processes that affect the impact and fate of MPs in the oceans. Zooplankton is one of the most sensitive taxa because their prey is approximately the same size as MPs. However, the status of MPs in zooplankton within natural marine environments remains largely unknown. By focusing on zooplankton in the East China Sea, the characteristics, bioaccumulated concentration, and retention of MPs for 10 zooplankton groups were systematically studied. Three types of MPs were found in zooplankton: fibres, pellets, and fragments. The fibres (54.6%) were more common than the other two types. The average lengths of the fibres, pellets, and fragments were 295.2 ± 348.6 μm, 20.3 ± 11.0 μm, and 82.4 ± 80.5 μm, respectively. Nineteen polymers were detected in the zooplankton via the Thermo Scientific Nicolet iN10 Infrared Microscope. Polymerized oxidized organic material and polyester were dominant, accounting for 35.9% and 25.6% of the polymers, respectively. The bioaccumulated concentration of MPs in the 10 zooplankton taxa varied from 0.13 pieces/zooplankton for Copepoda to 0.35 pieces/zooplankton for Pteropoda. The bioaccumulated concentration was negatively correlated with the abundance of zooplankton, showing a significant biological dilution effect. The bioaccumulated concentration was also influenced by the feeding mode of zooplankton, showing a trend of omnivorous > carnivorous > herbivorous. High retention of MPs was found in the zooplankton community of the East China Sea, achieving 19.7 ± 22.4 pieces/m 3 . This is much higher than the MP retention in zooplankton from other reported sea areas. By revealing the characteristics and retention of MPs in the natural zooplankton taxa from the East China Sea, this research identified the influence that MPs have

Biomarker responses to environmental contamination in estuaries: A comparative multi-taxa approach.

PubMed

Duarte, Irina A; Reis-Santos, Patrick; França, Susana; Cabral, Henrique; Fonseca, Vanessa F

2017-08-01

Estuaries are highly productive ecosystems subjected to numerous anthropogenic pressures with consequent environmental quality degradation. In this study, multiple biomarker responses [superoxide dismutase (SOD), catalase (CAT), ethoxyresorufin O-deethylase (EROD) and glutathione S-transferase (GST) activities, as well as lipid peroxidation (LPO) and DNA damage (DNAd)] were determined in two fish (Dicentrarchus labrax and Pomatoschistus microps) and four macroinvertebrate species (Carcinus maenas, Crangon crangon, Hediste diversicolor and Scrobicularia plana) from the Ria de Aveiro and Tejo estuaries over distinct months. Two sites per estuarine system were selected based on anthropogenic pressures and magnitude of environmental contamination. Antioxidant enzyme activities in fish species suggested a ubiquitous response to oxidative stress, while biotransformation and effect biomarkers exhibited higher spatial and temporal variation. In invertebrate species, biotransformation enzyme activity was clearly less variable than in fish evidencing lower xenobiotic transformation capability. Overall, largest biomarker responses were found in the most contaminated sites (Tejo), yet species-specific patterns were evident. These should be factored in multi-taxa approaches, considering that the differential functional traits of species, such as habitat use, life-stage, feeding or physiology can influence exposure routes and biomarker responses. The Integrated Biomarker Response index highlighted patterns in biomarker responses which were not immediately evident when analyzing biomarkers individually. Overall, results provided insights into the complexity of species responses to contamination in naturally varying estuarine environments. Ultimately, multi-taxa and multi-biomarker approaches provide a comprehensive and complementary view of ecosystem health, encompassing diverse forms of biological integration and exposure routes, and allow the validation of results among markers

The Interacting controls of pyrolysis temperature and plant taxa on pyrogenic organic matter stability and decomposition in a Northern Michigan forest soil

NASA Astrophysics Data System (ADS)

Gibson, C. D.; Filley, T. R.; Bird, J. A.; Hatton, P. J.; Stark, R. E.; Nadelhoffer, K. J.

2017-12-01

Pyrogenic organic matter (PyOM) produced during forest fires is considered a large sink of stable soil organic matter (SOM) in boreal-temperate forest ecotones, where fire frequency and intensity is growing with changing climate. Understanding how changes in fire regime and predicted shifts in plant taxa will interact to affect PyOM dynamics in soil is imperative to assessing the impact of climate change on SOM maintenance. The stability of PyOM in soil may be co-determined by the physiochemical structure imparted on PyOM during pyrolysis and by its initial taxa-dependent wood chemistry and anatomy. To determine PyOM-C turnover rates in soil, we followed the fate of 13C-enriched wood or PyOM (200, 300, 450, or 600°C) derived from red maple (RM) or jack pine (JP) wood in soil from a recently burned forest in northern Michigan, USA. We found that pyrolysis temperature-controlled physiochemical changes influenced, with threshold dynamics, PyOM stability resulting in mean residence times of 2 (PyOM 200°C) to 450 years for both taxa, confirming that most PyOM (<600°C) turns over on the century, not millennial time scale. Water leachable C, carbohydrate and non-lignin phenol content correlated positively with early PyOM-C mineralization for both JP and RM, but the pyrolysis temperature at which this interaction was strongest differed with taxa reflecting the difference in thermal transition in which carbonization begins (300°C for JP and 450°C for RM). In contrast to previous studies, the addition of sucrose suggests that a co-metabolism mechanism of PyOM decomposition is minor in this soil. Our results show that while the first order control on PyOM stability in this soil is pyrolysis temperature, wood taxa did affect PyOM C MRT, in part due to differences in the amount of water soluble C released by PyOM during the initial decomposition dynamics in soil.

Theoretical size distribution of fossil taxa: analysis of a null model.

PubMed

Reed, William J; Hughes, Barry D

2007-03-22

This article deals with the theoretical size distribution (of number of sub-taxa) of a fossil taxon arising from a simple null model of macroevolution. New species arise through speciations occurring independently and at random at a fixed probability rate, while extinctions either occur independently and at random (background extinctions) or cataclysmically. In addition new genera are assumed to arise through speciations of a very radical nature, again assumed to occur independently and at random at a fixed probability rate. The size distributions of the pioneering genus (following a cataclysm) and of derived genera are determined. Also the distribution of the number of genera is considered along with a comparison of the probability of a monospecific genus with that of a monogeneric family.

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.

PubMed

Wurzbacher, Christian; Nilsson, R Henrik; Rautio, Milla; Peura, Sari

2017-08-01

In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.

Restingomyces, a new sequestrate genus from the Brazilian Atlantic rainforest that is phylogenetically related to early-diverging taxa in Trappeaceae (Phallales).

PubMed

Sulzbacher, Marcelo A; Grebenc, Tine; Cabral, Tiara S; Giachini, Admir J; Goto, Bruno T; Smith, Matthew E; Baseia, Iuri G

2016-09-01

Restingomyces reticulatus gen. et sp. nov. is a recently discovered false truffle species from Atlantic "restinga" rainforest in northeastern Brazil. Molecular and morphological characters separate this new sequestrate species from other described taxa in the order Phallales (Phallomycetidae, Basidiomycota). In our phylogenetic analysis based on nuc 28S rDNA and atp6, R. reticulatus forms a sister clade to Trappea darkeri and Phallobata alba, with the three taxa forming the earliest diverging lineage within Phallales. Morphological and molecular data warrant the recognition of the new genus and species, described here, and we also amend the taxonomic description for the family Trappeaceae. © 2016 by The Mycological Society of America.

Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa.

PubMed

Chen, Wei-Jen; Bonillo, Céline; Lecointre, Guillaume

2003-02-01

Although much progress has been made recently in teleostean phylogeny, relationships among the main lineages of the higher teleosts (Acanthomorpha), containing more than 60% of all fish species, remain poorly defined. This study represents the most extensive taxonomic sampling effort to date to collect new molecular characters for phylogenetic analysis of acanthomorph fishes. We compiled and analyzed three independent data sets, including: (i) mitochondrial ribosomal fragments from 12S and 16s (814bp for 97 taxa); (ii) nuclear ribosomal 28S sequences (847bp for 74 taxa); and (iii) a nuclear protein-coding gene, rhodopsin (759bp for 86 taxa). Detailed analyses were conducted on each data set separately and the principle of taxonomic congruence without consensus trees was used to assess confidence in the results as follows. Repeatability of clades from separate analyses was considered the primary criterion to establish reliability, rather than bootstrap proportions from a single combined (total evidence) data matrix. The new and reliable clades emerging from this study of the acanthomorph radiation were: Gadiformes (cods) with Zeioids (dories); Beloniformes (needlefishes) with Atheriniformes (silversides); blenioids (blennies) with Gobiesocoidei (clingfishes); Channoidei (snakeheads) with Anabantoidei (climbing gouramies); Mastacembeloidei (spiny eels) with Synbranchioidei (swamp-eels); the last two pairs of taxa grouping together, Syngnathoidei (aulostomids, macroramphosids) with Dactylopteridae (flying gurnards); Scombroidei (mackerels) plus Stromatoidei plus Chiasmodontidae; Ammodytidae (sand lances) with Cheimarrhichthyidae (torrentfish); Zoarcoidei (eelpouts) with Cottoidei; Percidae (perches) with Notothenioidei (Antarctic fishes); and a clade grouping Carangidae (jacks), Echeneidae (remoras), Sphyraenidae (barracudas), Menidae (moonfish), Polynemidae (threadfins), Centropomidae (snooks), and Pleuronectiformes (flatfishes).

Nested taxa-area curves for eastern United States floras

USGS Publications Warehouse

Bennett, J.P.

1997-01-01

The slopes of log-log species-area curves have been studied extensively and found to be influenced by the range of areas under study. Two such studies of eastern United States floras have yielded species-area curve slopes which differ by more than 100%: 0.251 and 0.113. The first slope may be too steep because the flora of the world was included, and both may be too steep because noncontiguous areas were used. These two hypotheses were tested using a set of nested floras centered in Ohio and continuing up to the flora of the world. The results suggest that this set of eastern United States floras produces a log-log species-area curve with a slope of approximately 0.20 with the flora of the world excluded, and regardless of whether or not the floras are from nested areas. Genera- and family-area curves are less steep than species-area curves and show similar patterns. Taxa ratio curves also increase with area, with the species/family ratio showing the steepest slope.

Nine-year performance of a variety of Populus taxa on an upland site in western Kentucky

Treesearch

Randall J. Rousseau; Joshua P. Adams; David W. Wilkerson

2013-01-01

A variety of hybrid poplars have been planted on upland sites throughout the Midwest and Midsouth regions of the United States. Very few of these clones have proven to be worthwhile due to susceptibility to a variety of diseases. Five different Populus taxa were planted on an upland site in western Kentucky as a means of assessing resistance to local...

Comparative analysis of essential oils of six Anthemis taxa from Serbia and Montenegro.

PubMed

Pavlović, Milica; Lakusić, Dmitar; Kovacević, Nada; Tzakou, Olga; Couladis, Maria

2010-05-01

The essential-oil composition of six Anthemis taxa from several populations in Serbia and Montenegro, Anthemis triumfetti (L.) DC., A. tinctoria L., A. austriaca Jacq., A. ruthenica Bieb., A. cotula L., and A. cretica ssp. carpatica (Willd.) Grierson were analyzed by GC and GC/MS. The main constituents have been identified as follows: camphor (13.8-15.4%), alpha-pinene (5.2-9.3%), beta-pinene (4.9-7.8%), and (E)-caryophyllene (7.3-9.8%) in three populations, and cis-chrysanthenol (27.0%) and 1,8-cineole (8.4%) in one population of A. triumfetti; 1,8-cineole (9.0-25.8%) in the oils of five populations, and borneol (16.0%) and spatulenol (16.0%) in the oil of one population of A. tinctoria; cis-chrysanthenyl acetate (17.5-22.0%), beta-pinene (8.6-13.2%), and 1,8-cineole (7.2-10.4%) in the oils of A. austriaca; germacrene D (8.3-11.3%) and terpinen-4-ol (6.3-7.3%) in A. ruthenica oils; beta-cedrene (10.3-19.0%), (E)-beta-farnesene (7.8-13.5%), and germacrene D (5.2-9.1%) in the oils of A. cotula; cis-thujone (39.0%), trans-thujone (13.5%), and yomogi alcohol (7.1%) in the oil of A. cretica ssp. carpatica. The essential oil of A. austriaca was studied for the first time. A cluster analysis based on the relative percentages of all components of the essential oils was used to determine the distances between taxa and populations.

Elucidating the substrate specificities of acyl-lipid thioesterases from diverse plant taxa.

PubMed

Kalinger, Rebecca S; Pulsifer, Ian P; Rowland, Owen

2018-06-01

Acyl-ACP thioesterase enzymes, which cleave fatty acyl thioester bonds to release free fatty acids, contribute to much of the fatty acid diversity in plants. In Arabidopsis thaliana, a family of four single hot-dog fold domain, plastid-localized acyl-lipid thioesterases (AtALT1-4) generate medium-chain (C6-C14) fatty and β-keto fatty acids as secondary metabolites. These volatile products may serve to attract insect pollinators or deter predatory insects. Homologs of AtALT1-4 are present in all plant taxa, but are nearly all uncharacterized. Despite high sequence identity, AtALT1-4 generate different lipid products, suggesting that ALT homologs in other plants also have highly varied activities. We investigated the catalytic diversity of ALT-like thioesterases by screening the substrate specificities of 15 ALT homologs from monocots, eudicots, a lycophyte, a green microalga, and the ancient gymnosperm Gingko biloba, via expression in Escherichia coli. Overall, these enzymes had highly varied substrate preferences compared to one another and to AtALT1-4, and could be classified into four catalytic groups comprising members from diverse taxa. Group 1 ALTs primarily generated 14:1 β-keto fatty acids, Group 2 ALTs produced 6-10 carbon fatty/β-keto fatty acids, Group 3 ALTs predominantly produced 12-14 carbon fatty acids, and Group 4 ALTs mainly generated 16 carbon fatty acids. Enzymes in each group differed significantly in the quantities of lipids and types of minor products they generated in E. coli. Medium-chain fatty acids are used to manufacture insecticides, pharmaceuticals, and biofuels, and ALT-like proteins are ideal candidates for metabolic engineering to produce specific fatty acids in significant quantities. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Theoretical size distribution of fossil taxa: analysis of a null model

PubMed Central

Reed, William J; Hughes, Barry D

2007-01-01

Background This article deals with the theoretical size distribution (of number of sub-taxa) of a fossil taxon arising from a simple null model of macroevolution. Model New species arise through speciations occurring independently and at random at a fixed probability rate, while extinctions either occur independently and at random (background extinctions) or cataclysmically. In addition new genera are assumed to arise through speciations of a very radical nature, again assumed to occur independently and at random at a fixed probability rate. Conclusion The size distributions of the pioneering genus (following a cataclysm) and of derived genera are determined. Also the distribution of the number of genera is considered along with a comparison of the probability of a monospecific genus with that of a monogeneric family. PMID:17376249

Coralsnake Venomics: Analyses of Venom Gland Transcriptomes and Proteomes of Six Brazilian Taxa

PubMed Central

Aird, Steven D.; da Silva, Nelson Jorge; Qiu, Lijun; Villar-Briones, Alejandro; Saddi, Vera Aparecida; Pires de Campos Telles, Mariana; Grau, Miguel L.; Mikheyev, Alexander S.

2017-01-01

Venom gland transcriptomes and proteomes of six Micrurus taxa (M. corallinus, M. lemniscatus carvalhoi, M. lemniscatus lemniscatus, M. paraensis, M. spixii spixii, and M. surinamensis) were investigated, providing the most comprehensive, quantitative data on Micrurus venom composition to date, and more than tripling the number of Micrurus venom protein sequences previously available. The six venomes differ dramatically. All are dominated by 2–6 toxin classes that account for 91–99% of the toxin transcripts. The M. s. spixii venome is compositionally the simplest. In it, three-finger toxins (3FTxs) and phospholipases A2 (PLA2s) comprise >99% of the toxin transcripts, which include only four additional toxin families at levels ≥0.1%. Micrurus l. lemniscatus venom is the most complex, with at least 17 toxin families. However, in each venome, multiple structural subclasses of 3FTXs and PLA2s are present. These almost certainly differ in pharmacology as well. All venoms also contain phospholipase B and vascular endothelial growth factors. Minor components (0.1–2.0%) are found in all venoms except that of M. s. spixii. Other toxin families are present in all six venoms at trace levels (<0.005%). Minor and trace venom components differ in each venom. Numerous novel toxin chemistries include 3FTxs with previously unknown 8- and 10-cysteine arrangements, resulting in new 3D structures and target specificities. 9-cysteine toxins raise the possibility of covalent, homodimeric 3FTxs or heterodimeric toxins with unknown pharmacologies. Probable muscarinic sequences may be reptile-specific homologs that promote hypotension via vascular mAChRs. The first complete sequences are presented for 3FTxs putatively responsible for liberating glutamate from rat brain synaptosomes. Micrurus C-type lectin-like proteins may have 6–9 cysteine residues and may be monomers, or homo- or heterodimers of unknown pharmacology. Novel KSPIs, 3× longer than any seen previously, appear to

Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

PubMed Central

Hou, Beiwei; Luo, Jing; Zhang, Yusi; Niu, Zhitao; Xue, Qingyun; Ding, Xiaoyu

2017-01-01

The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species’ diversification. Rapid radiation and genetic drift appeared to drive the evolution of D. tosaense and D. flexicaule, whereas introgression or hybridization might have been involved in the evolution of D. scoriarum and D. shixingense. The phylogeographical structure of D. officinale revealed that core natural distribution regions might have served as its glacial refuges. In recent years, human disturbances caused its artificial migration and population extinction. The five taxa may have originated from the Nanling Mountains and the Yungui Plateau and then migrated northward or eastward. After the initial iteration expansion, D. officinale populations appeared to experience the regional evolutionary patterns in different regions and follow the sequential or rapid decline in gene exchange. PMID:28262789

Microbial Community Diversities and Taxa Abundances in Soils along a Seven-Year Gradient of Potato Monoculture Using High Throughput Pyrosequencing Approach

PubMed Central

Liu, Xing; Zhang, Junlian; Gu, Tianyu; Zhang, Wenming; Shen, Qirong; Yin, Shixue; Qiu, Huizhen

2014-01-01

Background Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach. Methodology/Principal Findings Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H Shannon) and richness (S Chao1) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time. Conclusions Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait

Leonard A. Kelton, 1923-2011: Biographical sketch, list of publications, described taxa, and patronyms names in his honor

USDA-ARS?s Scientific Manuscript database

A biographical sketch of the late heteropterist, Leonard Alexander Kelton (1923-2011), a former systematist at the Canadian National Collection in Ottawa, Canada, is presented. Also provided are lists of his 71 scientific publications, the new taxa he described, and the patronyms named in his honor....

Firmicutes dominate the bacterial taxa within sugar-cane processing plants

PubMed Central

Sharmin, Farhana; Wakelin, Steve; Huygens, Flavia; Hargreaves, Megan

2013-01-01

Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial environments. The PhyloChip microarray was used to investigate bacterial diversity and community composition in three Australian sugar cane processing plants. These ecosystems were highly complex and dominated by four main Phyla, Firmicutes (the most dominant), followed by Proteobacteria, Bacteroidetes, and Chloroflexi. Significant variation (p < 0.05) in community structure occurred between samples collected from ‘floor dump sediment’, ‘cooling tower water’, and ‘bagasse leachate’. Many bacterial Classes contributed to these differences, however most were of low numerical abundance. Separation in community composition was also linked to Classes of Firmicutes, particularly Bacillales, Lactobacillales and Clostridiales, whose dominance is likely to be linked to their physiology as ‘lactic acid bacteria’, capable of fermenting the sugars present. This process may help displace other bacterial taxa, providing a competitive advantage for Firmicutes bacteria. PMID:24177592

Phylogeny of palaeotropic Derris-like taxa (Fabaceae) based on chloroplast and nuclear DNA sequences shows reorganization of (infra)generic classifications is needed.

PubMed

Sirichamorn, Yotsawate; Adema, Frits A C B; Gravendeel, Barbara; van Welzen, Peter C

2012-11-01

Palaeotropic Derris-like taxa (family Fabaceae, tribe Millettieae) comprise 6-9 genera. They are well known as important sources of rotenone toxin, which are used as organic insecticide and fish poison. However, their phylogenetic relationships and classification are still problematic due to insufficient sampling and high morphological variability. Fifty species of palaeotropic Derris-like taxa were sampled, which is more than in former studies. Three chloroplast genes (trnK-matK, trnL-F IGS, and psbA-trnH IGS) and nuclear ribosomal ITS /5.8S were analyzed using parsimony and Bayesian methods. Parsimony and Bayesian analyses of individual and combined markers show more or less similar tree topologies (only varying in terminal branches). The old-world monophyletic genera Aganope, Brachypterum, and Leptoderris are distinct from Derris s.s., and their generic status is here confirmed. Aganope may be classified into two or three subgeneric taxa. Paraderris has to be included in Derris s.s. to form a monophyletic group. The genera Philenoptera, Deguelia, and Lonchocarpus are monophyletic and distinct from each other and clearly separate from Derris s.s. Morphologically highly similar species of Derris s.s. are shown to be unrelated. Our study shows that previous infrageneric classifications of Derris are incorrect. Paraderris elliptica may contain several cryptic lineages that need further investigation. The concept of the genus Derris s.s. should be reorganized with a new generic circumscription by including Paraderris but excluding Brachypterum. Synapomorphic morphological features will be examined in future studies, and the status of the newly defined Derris and its closely related taxa will be formalized.

Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions

PubMed Central

Camanocha, Anuj; Dewhirst, Floyd E.

2014-01-01

Background and objective In addition to the well-known phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Spirochaetes, Fusobacteria, Tenericutes, and Chylamydiae, the oral microbiomes of mammals contain species from the lesser-known phyla or candidate divisions, including Synergistetes, TM7, Chlorobi, Chloroflexi, GN02, SR1, and WPS-2. The objectives of this study were to create phyla-selective 16S rDNA PCR primer pairs, create selective 16S rDNA clone libraries, identify novel oral taxa, and update canine and human oral microbiome databases. Design 16S rRNA gene sequences for members of the lesser-known phyla were downloaded from GenBank and Greengenes databases and aligned with sequences in our RNA databases. Primers with potential phylum level selectivity were designed heuristically with the goal of producing nearly full-length 16S rDNA amplicons. The specificity of primer pairs was examined by making clone libraries from PCR amplicons and determining phyla identity by BLASTN analysis. Results Phylum-selective primer pairs were identified that allowed construction of clone libraries with 96–100% specificity for each of the lesser-known phyla. From these clone libraries, seven human and two canine novel oral taxa were identified and added to their respective taxonomic databases. For each phylum, genome sequences closest to human oral taxa were identified and added to the Human Oral Microbiome Database to facilitate metagenomic, transcriptomic, and proteomic studies that involve tiling sequences to the most closely related taxon. While examining ribosomal operons in lesser-known phyla from single-cell genomes and metagenomes, we identified a novel rRNA operon order (23S-5S-16S) in three SR1 genomes and the splitting of the 23S rRNA gene by an I-CeuI-like homing endonuclease in a WPS-2 genome. Conclusions This study developed useful primer pairs for making phylum-selective 16S rRNA clone libraries. Phylum-specific libraries were shown to be useful

Incongruent genetic connectivity patterns for VME indicator taxa: implications for the management of New Zealand's vulnerable marine ecosystems

NASA Astrophysics Data System (ADS)

Clark, M. R.; Gardner, J.; Holland, L.; Zeng, C.; Hamilton, J. S.; Rowden, A. A.

2016-02-01

In the New Zealand region vulnerable marine ecosystems (VMEs) are at risk from commercial fishing activity and future seabed mining. Understanding connectivity among VMEs is important for the design of effective spatial management strategies, i.e. a network of protected areas. To date however, genetic connectivity in the New Zealand region has rarely been documented. As part of a project developing habitat suitability models and spatial management options for VMEs we used DNA sequence data and microsatellite genotyping to assess genetic connectivity for a range of VME indicator taxa, including the coral Desmophyllum dianthus, and the sponges Poecilastra laminaris and Penares palmatoclada. Overall, patterns of connectivity were inconsistent amonst taxa. Nonetheless, genetic data from each taxon were relevant to inform management at a variety of spatial scales. D. dianthus populations in the Kermadec volcanic arc and the Louisville Seamount Chain were indistinguishable, highlighting the importance of considering source-sink dynamics between populations beyond the EEZ in conservation planning. Poecilastra laminaris populations showed significant divergence across the Chatham Rise, in contrast to P. palmatoclada, which had a uniform haplotypic distribution. However, both sponge species exhibited the highest genetic diversity on the Chatham Rise, suggesting that this area is a genetic hotspot. The spatial heterogeneity of genetic patterns of structure suggest that inclusion of several taxa is necessary to facilitate understanding of regional connectivity patterns, variation in which may be attributed to alternate life history strategies, local hydrodynamic regimes, or in some cases, suboptimal sample sizes. Our findings provide important information for use by environmental managers, including summary maps of genetic diversity and barriers to gene flow, which will be used in spatial management decision-support tools.

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume.

PubMed

Kleindienst, Sara; Grim, Sharon; Sogin, Mitchell; Bracco, Annalisa; Crespo-Medina, Melitza; Joye, Samantha B

2016-02-01

The Deepwater Horizon (DWH) oil well blowout generated an enormous plume of dispersed hydrocarbons that substantially altered the Gulf of Mexico's deep-sea microbial community. A significant enrichment of distinct microbial populations was observed, yet, little is known about the abundance and richness of specific microbial ecotypes involved in gas, oil and dispersant biodegradation in the wake of oil spills. Here, we document a previously unrecognized diversity of closely related taxa affiliating with Cycloclasticus, Colwellia and Oceanospirillaceae and describe their spatio-temporal distribution in the Gulf's deepwater, in close proximity to the discharge site and at increasing distance from it, before, during and after the discharge. A highly sensitive, computational method (oligotyping) applied to a data set generated from 454-tag pyrosequencing of bacterial 16S ribosomal RNA gene V4-V6 regions, enabled the detection of population dynamics at the sub-operational taxonomic unit level (0.2% sequence similarity). The biogeochemical signature of the deep-sea samples was assessed via total cell counts, concentrations of short-chain alkanes (C1-C5), nutrients, (colored) dissolved organic and inorganic carbon, as well as methane oxidation rates. Statistical analysis elucidated environmental factors that shaped ecologically relevant dynamics of oligotypes, which likely represent distinct ecotypes. Major hydrocarbon degraders, adapted to the slow-diffusive natural hydrocarbon seepage in the Gulf of Mexico, appeared unable to cope with the conditions encountered during the DWH spill or were outcompeted. In contrast, diverse, rare taxa increased rapidly in abundance, underscoring the importance of specialized sub-populations and potential ecotypes during massive deep-sea oil discharges and perhaps other large-scale perturbations.

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume

PubMed Central

Kleindienst, Sara; Grim, Sharon; Sogin, Mitchell; Bracco, Annalisa; Crespo-Medina, Melitza; Joye, Samantha B

2016-01-01

The Deepwater Horizon (DWH) oil well blowout generated an enormous plume of dispersed hydrocarbons that substantially altered the Gulf of Mexico's deep-sea microbial community. A significant enrichment of distinct microbial populations was observed, yet, little is known about the abundance and richness of specific microbial ecotypes involved in gas, oil and dispersant biodegradation in the wake of oil spills. Here, we document a previously unrecognized diversity of closely related taxa affiliating with Cycloclasticus, Colwellia and Oceanospirillaceae and describe their spatio-temporal distribution in the Gulf's deepwater, in close proximity to the discharge site and at increasing distance from it, before, during and after the discharge. A highly sensitive, computational method (oligotyping) applied to a data set generated from 454-tag pyrosequencing of bacterial 16S ribosomal RNA gene V4–V6 regions, enabled the detection of population dynamics at the sub-operational taxonomic unit level (0.2% sequence similarity). The biogeochemical signature of the deep-sea samples was assessed via total cell counts, concentrations of short-chain alkanes (C1–C5), nutrients, (colored) dissolved organic and inorganic carbon, as well as methane oxidation rates. Statistical analysis elucidated environmental factors that shaped ecologically relevant dynamics of oligotypes, which likely represent distinct ecotypes. Major hydrocarbon degraders, adapted to the slow-diffusive natural hydrocarbon seepage in the Gulf of Mexico, appeared unable to cope with the conditions encountered during the DWH spill or were outcompeted. In contrast, diverse, rare taxa increased rapidly in abundance, underscoring the importance of specialized sub-populations and potential ecotypes during massive deep-sea oil discharges and perhaps other large-scale perturbations. PMID:26230048

Phytophthora taxa associated with cultivated Agothosmo, with emphasis on the P. citricola complex and P. capensis sp. nov.

Treesearch

C.M. Bezuidenhout; S. Deman; S.A. Kirk; W.J. Botha; L. Mostert; A. McLeod

2010-01-01

Agathosma species, which are indigenous to South Africa, are also cultivated for commercial use. Recently growers experienced severe plant loss, and symptoms shown by affected plants suggested that a soilborne disease could be the cause of death. A number of Phytophthora taxa were isolated from diseased plants, and this paper reports...

Phytophthora taxa associated with cultivated Agathosma, with emphasis on the P. citricola complex and P. capensis sp. nov.

Treesearch

C.M. Bezuidenhout; S. Denman; S.A. Kirk; W.J. Botha; L. Mostert; A. McLeod

2010-01-01

Agathosma species, which are indigenous to South Africa, are also cultivated for commercial use. Recently growers experienced severe plant loss, and symptoms shown by affected plants suggested that a soilborne disease could be the cause of death. A number of Phytophthora taxa were isolated from diseased plants, and this paper...

Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

PubMed Central

Reeder, Tod W.; Townsend, Ted M.; Mulcahy, Daniel G.; Noonan, Brice P.; Wood, Perry L.; Sites, Jack W.; Wiens, John J.

2015-01-01

Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement. PMID:25803280

Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

PubMed

Reeder, Tod W; Townsend, Ted M; Mulcahy, Daniel G; Noonan, Brice P; Wood, Perry L; Sites, Jack W; Wiens, John J

2015-01-01

Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

Possible effects of global environmental changes on Antarctic benthos: a synthesis across five major taxa

PubMed Central

Ingels, Jeroen; Vanreusel, Ann; Brandt, Angelika; Catarino, Ana I; David, Bruno; De Ridder, Chantal; Dubois, Philippe; Gooday, Andrew J; Martin, Patrick; Pasotti, Francesca; Robert, Henri

2012-01-01

Because of the unique conditions that exist around the Antarctic continent, Southern Ocean (SO) ecosystems are very susceptible to the growing impact of global climate change and other anthropogenic influences. Consequently, there is an urgent need to understand how SO marine life will cope with expected future changes in the environment. Studies of Antarctic organisms have shown that individual species and higher taxa display different degrees of sensitivity to environmental shifts, making it difficult to predict overall community or ecosystem responses. This emphasizes the need for an improved understanding of the Antarctic benthic ecosystem response to global climate change using a multitaxon approach with consideration of different levels of biological organization. Here, we provide a synthesis of the ability of five important Antarctic benthic taxa (Foraminifera, Nematoda, Amphipoda, Isopoda, and Echinoidea) to cope with changes in the environment (temperature, pH, ice cover, ice scouring, food quantity, and quality) that are linked to climatic changes. Responses from individual to the taxon-specific community level to these drivers will vary with taxon but will include local species extinctions, invasions of warmer-water species, shifts in diversity, dominance, and trophic group composition, all with likely consequences for ecosystem functioning. Limitations in our current knowledge and understanding of climate change effects on the different levels are discussed. PMID:22423336

Molecular phylogenetic analysis supports a Gondwanan origin of the Hyriidae (Mollusca: Bivalvia: Unionida) and the paraphyly of Australasian taxa.

PubMed

Graf, Daniel L; Jones, Hugh; Geneva, Anthony J; Pfeiffer, John M; Klunzinger, Michael W

2015-04-01

The freshwater mussel family Hyriidae (Mollusca: Bivalvia: Unionida) has a disjunct trans-Pacific distribution in Australasia and South America. Previous phylogenetic analyses have estimated the evolutionary relationships of the family and the major infra-familial taxa (Velesunioninae and Hyriinae: Hyridellini in Australia; Hyriinae: Hyriini, Castaliini, and Rhipidodontini in South America), but taxon and character sampling have been too incomplete to support a predictive classification or allow testing of biogeographical hypotheses. We sampled 30 freshwater mussel individuals representing the aforementioned hyriid taxa, as well as outgroup species representing the five other freshwater mussel families and their marine sister group (order Trigoniida). Our ingroup included representatives of all Australian genera. Phylogenetic relationships were estimated from three gene fragments (nuclear 28S, COI and 16S mtDNA) using maximum parsimony, maximum likelihood, and Bayesian inference, and we applied a Bayesian relaxed clock model calibrated with fossil dates to estimate node ages. Our analyses found good support for monophyly of the Hyriidae and the subfamilies and tribes, as well as the paraphyly of the Australasian taxa (Velesunioninae, (Hyridellini, (Rhipidodontini, (Castaliini, Hyriini)))). The Hyriidae was recovered as sister to a clade comprised of all other Recent freshwater mussel families. Our molecular date estimation supported Cretaceous origins of the major hyriid clades, pre-dating the Tertiary isolation of South America from Antarctica/Australia. We hypothesize that early diversification of the Hyriidae was driven by terrestrial barriers on Gondwana rather than marine barriers following disintegration of the super-continent. Copyright © 2015 Elsevier Inc. All rights reserved.

The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa.

PubMed

Wayland, Matthew T; Vainio, Jouni K; Gibson, David I; Herniou, Elisabeth A; Littlewood, D Timothy J; Väinölä, Risto

2015-01-01

The acanthocephalan genus Echinorhynchus Zoega in Müller, 1776 (sensuYamaguti 1963) is a large and widespread group of parasites of teleost fish and malacostracan crustaceans, distributed from the Arctic to the Antarctic in habitats ranging from freshwaters to the deep-sea. A total of 52 species are currently recognised based on the conventional morphological species concept; however, the true diversity in the genus is masked by cryptic speciation. The considerable diversity within Echinorhynchus is an argument for subdividing the genus if monophyletic groups with supporting morphological characters can be identified. With this objective in mind, partial sequences of two genes with different rates of evolution and patterns of inheritance (nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I) were used to infer the phylogenetic relationships among eight taxa of Echinorhynchus. These included representatives of each of three genus group taxa proposed in a controversial revision of the genus based on cement gland pattern, namely Echinorhynchus (sensu stricto), Metechinorhynchus Petrochenko, 1956 and Pseudoechinorhynchus Petrochenko, 1956. These groupings have previously been rejected by some authorities, because the diagnostic character is poorly defined; this study shows that Echinorhynchus (sensu stricto) and Metechinorhynchus are not natural, monophyletic groups. A revision of Echinorhynchus will require tandem molecular phylogenetic and morphological analyses of a larger sample of taxa, but this study has identified two morhological characters that might potentially be used to define new genera. The estimated phylogeny also provides insight into the zoogeographical history of Echinorhynchus spp. We postulate that the ancestral Echinorhynchus had a freshwater origin and the genus subsequently invaded the sea, probably several times. The freshwater taxa of the Echinorhynchusbothniensis Zdzitowiecki & Valtonen, 1987 clade may represent a reinvasion of

Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach

PubMed Central

Hua, Xiao-Mei; Liang, Li; Wen, Zhong-Ling; Du, Mei-Hang; Meng, Fan-Fan; Pang, Yan-Jun; Tang, Cheng-Yi

2018-01-01

The worldwide commercial cultivation of transgenic crops, including glyphosate-tolerant (GT) soybeans, has increased widely during the past 20 years. However, it is accompanied with a growing concern about potential effects of transgenic crops on the soil microbial communities, especially on rhizosphere bacterial communities. Our previous study found that the GT soybean line NZL06-698 (N698) significantly affected rhizosphere bacteria, including some unidentified taxa, through 16S rRNA gene (16S rDNA) V4 region amplicon deep sequencing via Illumina MiSeq. In this study, we performed 16S rDNA V5–V7 region amplicon deep sequencing via Illumina MiSeq and shotgun metagenomic approaches to identify those major taxa. Results of these processes revealed that the species richness and evenness increased in the rhizosphere bacterial communities of N698, the beta diversity of the rhizosphere bacterial communities of N698 was affected, and that certain dominant bacterial phyla and genera were related to N698 compared with its control cultivar Mengdou12. Consistent with our previous findings, this study showed that N698 affects the rhizosphere bacterial communities. In specific, N698 negatively affects Rahnella, Janthinobacterium, Stenotrophomonas, Sphingomonas and Luteibacter while positively affecting Arthrobacter, Bradyrhizobium, Ramlibacter and Nitrospira. PMID:29659545

Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

PubMed

Pei, Nancai; Erickson, David L; Chen, Bufeng; Ge, Xuejun; Mi, Xiangcheng; Swenson, Nathan G; Zhang, Jin-Long; Jones, Frank A; Huang, Chun-Lin; Ye, Wanhui; Hao, Zhanqing; Hsieh, Chang-Fu; Lum, Shawn; Bourg, Norman A; Parker, John D; Zimmerman, Jess K; McShea, William J; Lopez, Ida C; Sun, I-Fang; Davies, Stuart J; Ma, Keping; Kress, W John

2015-10-12

To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.

Chemical and biomolecular analyses to discriminate three taxa of Pistacia genus from Sardinia Island (Italy) and their antifungal activity.

PubMed

Marengo, Arianna; Piras, Alessandra; Falconieri, Danilo; Porcedda, Silvia; Caboni, Pierluigi; Cortis, Pierluigi; Foddis, Caterina; Loi, Claudia; Gonçalves, Maria José; Salgueiro, Lígia; Maxia, Andrea

2017-09-20

This work reports the results and the comparison concerning the chemical and biomolecular analyses and the antifungal activity of three wild Pistacia species (Anacardiaceae) from Sardinia. Volatile oils from leaves and twigs of Pistacia x saportae, Pistacia lentiscus and Pistacia terebinthus were characterised using GC-FID and GC-MS techniques and tested against some fungal strains. Two DNA nuclear regions (ITS and 5S-rRNA-NTS) were amplified through PCR technique and sequenced. The three **Pistacia have similar chemical profile, although there are some important quantitative differences. The analysis of ITS and 5S-rRNA-NTS regions, reveals a species-specific nucleotide variation among the three **taxa. This method could emerge as a powerful tool for the species identification, especially because the discrimination of these three **taxa appears difficult for non-expert botanists. Concerning the antifungal activity, P. lentiscus and P. x saportae show the highest activity against Cryptococcus neoformans, with a MIC value of 0.32 μL/mL.

A Multi-Proxy Investigation into the Biomineralization Pathways of Benthic Invertebrate Taxa

NASA Astrophysics Data System (ADS)

DeCorte, I. A.; Liu, Y. W.; Doss, W. C.; Ries, J. B.; Eagle, R.

2016-12-01

Ocean acidification is the result of surface ocean absorption of anthropogenic carbon dioxide emissions and endangers many marine organisms. Decreases in pH and a coupled reduction in CaCO3 saturation state have been shown to disrupt the process of biomineralization within many species of marine calcifiers. Recent studies, however, demonstrate that calcifying organisms respond in diverse ways to changes in pH and CaCO3 saturation state. We examine element ratios (including Sr/Ca, Mg/Ca, Li/Ca, and B/Ca) and boron isotope ratios (δ11B) in 7 macro-invertebrate species (blue crab, shrimp, coralline red algae, pencil urchin, purple urchin, temperate coral, and serpulid worm) and compare results to net calcification rates and experimental seawater carbonate system parameters. Correlations between seawater carbonate chemistry and the elemental compositions of biogenic calcite and aragonite vary widely and are highly taxon-specific, ranging from strongly correlated to no significant response—a finding that is consistent with mounting evidence that many marine calcifying organisms regulate the chemistry of the fluid at their site of calcification. A Rayleigh framework is used to interpret the elemental data. We then analyze δ11B of the same samples as a proxy for pH at their site of calcification. Preliminary results suggest that coralline red algae, shrimp, urchin, serpulid worm and temperate coral taxa elevate pH at the site of calcification relative to the organism's ambient seawater. We plan to utilize a multi-proxy approach to examine the biomineralization pathways that influence elemental and boron isotope fractionation during calcification and precipitation of biogenic aragonite and calcite. A better understanding of these biomineralization pathways will help us to predict the responses of benthic invertebrate taxa to ocean acidification, as well as provide insights into drivers of so-called vital effects on elemental and stable boron isotope fractionation

Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases.

PubMed

Muñoz, Marina; Ríos-Chaparro, Dora Inés; Patarroyo, Manuel Alfonso; Ramírez, Juan David

2017-03-14

Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57.7%), followed by C2 (29.1%). Regarding sequence types (STs), it was found that ST-1, belonging to C2, was the most frequent. The isolates analysed came from 17 countries, mostly from the United Kingdom (UK) (1541 STs, 87.0%). The diversity of the seven housekeeping genes in the MLST scheme was evaluated, and alleles from the profiles (STs), for identifying CD population structure. It was found that adk and atpA are conserved genes allowing a limited amount of clusters to be discriminated; however, different genes such as drx, glyA and particularly sodA showed high diversity indexes and grouped CD populations in many clusters, suggesting that these genes' contribution to CD typing should be revised. It was identified that CD STs reported to date have a mostly clonal population structure with foreseen events of recombination; however, one group of STs was not assigned to a clade being highly different containing at least nine well-supported clusters, suggesting a greater amount of clades for CD. This study shows the usefulness of CD-MLST-db as a tool for studying CD distribution and population structure, identifying the need for reviewing the usefulness of sodA as housekeeping gene within the MLST scheme and suggesting the existence of a greater amount of CD clades. The study also shows the plausible exchange of genetic material between STs, contributing towards intra-taxa genetic diversity.

Bioprospecting: evolutionary implications from a post-olmec pharmacopoeia and the relevance of widespread taxa.

PubMed

Leonti, Marco; Cabras, Stefano; Castellanos, Maria Eugenia; Challenger, Antony; Gertsch, Jürg; Casu, Laura

2013-05-02

depend on phylogeny, biogeography, ecology and ultimately allelopathy, and on culture-specific perception of organoleptic properties. The comparison of the 67 drug-productive Viridiplantae families with the ethnopharmacopoeia of the Popoluca and the APG database, shows that "traditional" pharmacopoeias and plant-derived drugs are obtained from widespread and species-rich taxa. This is not a function of family size alone. We put forward the theory that as a function of evolution, widespread taxa contain a broader range of accumulated ecological information and response encoded in their genes relative to locally occurring taxa. This information is expressed through the synthesis of allelochemicals with a wide ecological radius, showing broad-spectrum biota-specific interactions, including the targeting of proteins of mammals and primates. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Ecological characterization and molecular differentiation of Culex pipiens complex taxa and Culex torrentium in eastern Austria.

PubMed

Zittra, Carina; Flechl, Eva; Kothmayer, Michael; Vitecek, Simon; Rossiter, Heidemarie; Zechmeister, Thomas; Fuehrer, Hans-Peter

2016-04-11

Culex pipiens complex taxa differ in behaviour, ecophysiology and epidemiologic importance. Despite their epidemiologic significance, information on genetic diversity, occurrence and seasonal and spatial distribution patterns of the Cx. pipiens complex is still insufficient. Assessment of seasonal and spatial distribution patterns of Culex pipiens forms and their congener Cx. torrentium is crucial for the understanding of their vector-pathogen dynamics. Female mosquitoes were trapped from April-October 2014 twice a month for a 24-h time period with BG-sentinel traps at 24 sampling sites in eastern Austria, using carbon dioxide as attractant. Ecological forms of Cx. pipiens s.l. and their hybrids were differentiated using the CQ11 locus, and Cx. pipiens forms and their congener Cx. torrentium using the ACE-2 gene. Differential exploitation of ecological niches by Cx. pipiens forms and Cx. torrentium was analysed using likelihood ratio tests. Possible effects of environmental parameters on these taxa were tested using PERMANOVA based on distance matrices and, if significant, were modelled in nMDS ordination space to estimate non-linear relationships. For this study, 1476 Culex spp. were sampled. Culex pipiens f. pipiens representing 87.33 % of the total catch was most abundant, followed by hybrids of both forms (5.62 %), Cx. torrentium (3.79 %) and Cx. pipiens f. molestus (3.25 %). Differences in proportional abundances were found between land cover classes. Ecological parameters affecting seasonal and spatial distribution of these taxa in eastern Austria are precipitation duration, air temperature, sunlight and the interaction term of precipitation amount and the Danube water level, which can be interpreted as a proxy for breeding habitat availability. The Cx. pipiens complex of eastern Austria comprises both ecologically different forms, the mainly ornithophilic form pipiens and the mainly mammalophilic and anthropophilic form molestus. Heterogeneous agricultural

New taxa of Meconematini (Orthoptera: Tettigoniidae: Meconematinae) from Guangxi, China.

PubMed

Wang, Hanqiang; Liu, Xianwei; Li, Kai

2015-04-02

The following new taxa of Meconematini from Guangxi province were described: Sinothaumaspis damingshanicus Wang, Liu, Li gen. & sp. nov., Aphlugiolopsis punctipennis Wang, Liu, Li gen. & sp. nov., Eoxizicus (Eoxizicus) curvicercus Wang, Liu, Li sp. nov., Meconemopsis paraquadrinotata Wang, Liu, Li sp. nov., Neocrytopsis? unicolor Wang, Liu, Li sp. nov., Xiphidiopsis (Dinoxiphidiopsis) expressa Wang, Liu, Li sp. nov. Xiphidiopsis (Xiphidiopsis) fischerwaldheimi Gorochov, 1993, a synonym of Xiphidiopsis (Xiphidiopsis) jinxiuensis Xia & Liu, 1990 was described. The opposite gender of Sinocyrtaspis truncate Liu, 2000 and Abaxinicephora excellens Gorochov & Kang, 2005 were firstly described.  Xiphidiopsis (Dinoxiphidiopsis) jacobsoni Gorochov, 1993 was also firstly recorded from China. Two new combinations,  Meconemopsis quadrinotata (Bey-Bienko, 1971) Wang, Liu, Li comb. nov. and Xiphidiopsis (Dinoxiphidiopsis) fanjingshanensis (Shi & Du, 2006) Wang, Liu, Li comb. nov., as well as a synonym of the former Xizicus (Axizicus) xizangensis Jiao & Shi 2013 syn. nov. which respectively relate to M. paraquadrinotata sp. nov. and X. (D.) expressa sp. nov., were also noted.

Morphometric traits capture the climatically driven species turnover of 10 spruce taxa across China.

PubMed

Li, He; Wang, GuoHong; Zhang, Yun; Zhang, WeiKang

2016-02-01

This study explored the relative roles of climate and phylogenetic background in driving morphometric trait variation in 10 spruce taxa in China. The study further addressed the hypothesis that these variations are consistent with species turnover on climatic gradients. Nine morphometric traits of leaves, seed cones, and seeds for the 10 studied spruce taxa were measured at 504 sites. These data were analyzed in combination with species DNA sequences from NCBI GenBank. We detected the effects of phylogeny and climate through trait-variation-based K statistics and phylogenetic eigenvector regression (PVR) analyses. Multivariate analyses were performed to detect trait variation along climatic gradients with species replacement. The estimated K-values for the nine studied morphometric traits ranged from 0.19 to 0.68, and the studied environmental variables explained 39-83% of the total trait variation. Trait variation tended to be determined largely by a temperature gradient varying from wet-cool climates to dry-warm summers and, additionally, by a moisture gradient. As the climate became wetter and cooler, spruce species tended to be replaced by other spruces with smaller needle leaves and seeds but larger cones and seed scales. A regression analysis showed that spruce species tended to be successively replaced by other species, along the gradient, although the trends observed within species were not necessarily consistent with the overall trend. The climatically driven replacement of the spruces in question could be well indicated by the between-species variation in morphometric traits that carry lower phylogenetic signal. Between-species variation in these traits is driven primarily by climatic factors. These species demonstrate a narrower ecological amplitude in temperature but wider ranges on the moisture gradient.

Opening the treasure chest: A DNA-barcoding primer set for most higher taxa of Central European birds and mammals from museum collections

PubMed Central

Schäffer, Sylvia; Zachos, Frank E.

2017-01-01

DNA-barcoding is a rapidly developing method for efficiently identifying samples to species level by means of short standard DNA sequences. However, reliable species assignment requires the availability of a comprehensive DNA barcode reference library, and hence numerous initiatives aim at generating such barcode databases for particular taxa or geographic regions. Historical museum collections represent a potentially invaluable source for the DNA-barcoding of many taxa. This is particularly true for birds and mammals, for which collecting fresh (voucher) material is often very difficult to (nearly) impossible due to the special animal welfare and conservation regulations that apply to vertebrates in general, and birds and mammals in particular. Moreover, even great efforts might not guarantee sufficiently complete sampling of fresh material in a short period of time. DNA extracted from historical samples is usually degraded, such that only short fragments can be amplified, rendering the recovery of the barcoding region as a single fragment impossible. Here, we present a new set of primers that allows the efficient amplification and sequencing of the entire barcoding region in most higher taxa of Central European birds and mammals in six overlapping fragments, thus greatly increasing the value of historical museum collections for generating DNA barcode reference libraries. Applying our new primer set in recently established NGS protocols promises to further increase the efficiency of barcoding old bird and mammal specimens. PMID:28358863

Opening the treasure chest: A DNA-barcoding primer set for most higher taxa of Central European birds and mammals from museum collections.

PubMed

Schäffer, Sylvia; Zachos, Frank E; Koblmüller, Stephan

2017-01-01

DNA-barcoding is a rapidly developing method for efficiently identifying samples to species level by means of short standard DNA sequences. However, reliable species assignment requires the availability of a comprehensive DNA barcode reference library, and hence numerous initiatives aim at generating such barcode databases for particular taxa or geographic regions. Historical museum collections represent a potentially invaluable source for the DNA-barcoding of many taxa. This is particularly true for birds and mammals, for which collecting fresh (voucher) material is often very difficult to (nearly) impossible due to the special animal welfare and conservation regulations that apply to vertebrates in general, and birds and mammals in particular. Moreover, even great efforts might not guarantee sufficiently complete sampling of fresh material in a short period of time. DNA extracted from historical samples is usually degraded, such that only short fragments can be amplified, rendering the recovery of the barcoding region as a single fragment impossible. Here, we present a new set of primers that allows the efficient amplification and sequencing of the entire barcoding region in most higher taxa of Central European birds and mammals in six overlapping fragments, thus greatly increasing the value of historical museum collections for generating DNA barcode reference libraries. Applying our new primer set in recently established NGS protocols promises to further increase the efficiency of barcoding old bird and mammal specimens.

Does better taxon sampling help? A new phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha) based on 50 new taxa and the same old mitochondrial and nuclear markers.

PubMed

Zhao, Lei; Annie, Ang Shi Hui; Amrita, Srivathsan; Yi, Su Kathy Feng; Rudolf, Meier

2013-10-01

We here present a phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha), a group of schizophoran flies with ca. 320 described species that is widely used in sexual selection research. The hypothesis is based on five nuclear and five mitochondrial markers totaling 8813 bp for ca. 30% of the diversity (105 sepsid taxa) and - depending on analysis - six or nine outgroup species. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian inferences (BI) yield overall congruent, well-resolved, and supported trees that are largely unaffected by three different ways to partition the data in BI and ML analyses. However, there are also five areas of uncertainty that affect suprageneric relationships where different analyses yield alternate topologies and MP and ML trees have significant conflict according to Shimodaira-Hasegawa tests. Two of these were already affected by conflict in a previous analysis that was based on the same genes and a subset of 69 species. The remaining three involve newly added taxa or genera whose relationships were previously resolved with low support. We thus find that the denser taxon sample in the present analysis does not reduce the topological conflict that had been identified previously. The present study nevertheless presents a significant contribution to the understanding of sepsid relationships in that 50 additional taxa from 18 genera are added to the Tree-of-Life of Sepsidae and that the placement of most taxa is well supported and robust to different tree reconstruction techniques. Copyright © 2013 Elsevier Inc. All rights reserved.

Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots.

PubMed

Lewison, Rebecca L; Crowder, Larry B; Wallace, Bryan P; Moore, Jeffrey E; Cox, Tara; Zydelis, Ramunas; McDonald, Sara; DiMatteo, Andrew; Dunn, Daniel C; Kot, Connie Y; Bjorkland, Rhema; Kelez, Shaleyla; Soykan, Candan; Stewart, Kelly R; Sims, Michelle; Boustany, Andre; Read, Andrew J; Halpin, Patrick; Nichols, W J; Safina, Carl

2014-04-08

Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce--in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers--and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority.

Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots

PubMed Central

Lewison, Rebecca L.; Crowder, Larry B.; Wallace, Bryan P.; Moore, Jeffrey E.; Cox, Tara; Zydelis, Ramunas; McDonald, Sara; DiMatteo, Andrew; Dunn, Daniel C.; Kot, Connie Y.; Bjorkland, Rhema; Kelez, Shaleyla; Soykan, Candan; Stewart, Kelly R.; Sims, Michelle; Boustany, Andre; Read, Andrew J.; Halpin, Patrick; Nichols, W. J.; Safina, Carl

2014-01-01

Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce—in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers—and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority. PMID:24639512

Seed size and nutrient content variation for twenty-one invasive and native California and Oregon taxa of the tribe Cynareae (Asteraceae)

USDA-ARS?s Scientific Manuscript database

Seed characteristics are important for seed dispersal, seedling growth, and seedling survival, but there is little information on seed characteristics for several taxa of the tribe Cynareae (Family: Asteraceae). We determined seed characteristics and their variation from natural populations of twen...

Carbon concentration of standing and downed woody detritus: effects of tree taxa, decay class, position, and tissue type

Treesearch

Mark E. Harmon; Becky Fasth; Christopher W. Woodall; Jay Sexton

2013-01-01

The degree to which carbon concentration (CC) of woody detritus varies by tree taxa, stage of decay, tissue type (i.e., bark versus wood), and vertical orientation was examined in samples of 60 tree species from the Northern Hemisphere. The mean CC of 257 study samples was 49.3% with a range of 43.4-56.8%. Angiosperms had a significantly lower CC than gymnosperms, with...

Molecular phylogeny, systematics, and revision of the type species of Lobomonas, L. francei (Volvocales, Chlorophyta) and closely related taxa.

PubMed

Sausen, Nicole; Malavasi, Veronica; Melkonian, Michael

2018-04-01

In the present study, three new strains of the rare volvocalean green alga Lobomonas were isolated from field-collected samples, one from Sardinia (Italy) and two from Argentina, and comparatively studied. The Sardinian and one of the Argentinian strains were identified as Lobomonas francei, the type species of the genus, whereas the second Argentinian strain corresponded to L. panduriformis. Two additional nominal species of Lobomonas from culture collections (L. rostrata and L. sphaerica) were included in the analysis and shown to be morphologically and molecularly identical to the L. francei strains. The presence, number, and shapes of cell wall lobes, the diagnostic criterion of Lobomonas, were shown to be highly variable depending on the chemical composition of the culture medium used. The analyses by SEM gave evidence that the cell wall lobes in Lobomonas originate at the junctions of adjacent cell wall plates by extrusion of gelatinous material. The four L. francei strains had identical nrRNA gene sequences and differed by only one or two substitutions in the ITS1 + ITS2 sequences. In the phylogenetic analyses, L. francei and L. panduriformis were sister taxa; however, another nominal Lobomonas species (L. monstruosa) did not belong to this genus. Lobomonas, together with taxa designated as Vitreochlamys, Tetraspora, and Paulschulzia, formed a monophyletic group that in the combined analyses was sister to the "Chlamydomonas/Volvox-clade." Based on these results, Lobomonas was revised, the diagnosis of the type species emended, a lectotype and an epitype designated, and several taxa synonymized with the type species. © 2017 Phycological Society of America.

New taxa and notes on crickets of the subfamily Landrevinae (Orthoptera: Gryllidae) from Brunei Darussalam, Borneo.

PubMed

Tan, Ming Kai; Wahab, Rodzay Bin Haji Abdul

2017-12-19

New taxa from the subfamily Landrevinae (Orthoptera: Gryllidae) are expected despite recent work on its taxonomy. Here, two more new species from Brunei Darussalam, Borneo are described: Duolandrevus (Eulandrevus) kawataredoki sp. nov. and Endodrelanva nympha sp. nov. The male calling song of D. (E.) kawataredoki sp. nov. is also described. We report the occurrence of a Duolandrevus (Bejorama) from Brunei close to (nr.) luzonensis Otte, 1988. We also document from Brunei a case of parasitic wasp from the genus Liris (Hymenoptera: Crabronidae: Larrini) hunting a Landrevinae.

Prosopis: a global assessment of the biogeography, benefits, impacts and management of one of the world's worst woody invasive plant taxa

PubMed Central

Shackleton, Ross T.; Le Maitre, David C.; Pasiecznik, Nick M.; Richardson, David M.

2014-01-01

Invasive species cause ecological, economic and social impacts and are key drivers of global change. This is the case for the genus Prosopis (mesquite; Fabaceae) where several taxa are among the world's most damaging invasive species. Many contentious issues (‘conflicts of interest’) surround these taxa, and management interventions have not yet sustainably reduced the negative impacts. There is an urgent need to better understand the factors that drive invasions and shape management actions, and to compare the effectiveness of different management approaches. This paper presents a global review of Prosopis, focusing on its distribution, impacts, benefits and approaches to management. Prosopis was found to occur in a 129 countries globally and many more countries are climatically suitable. All areas with naturalized or invasive Prosopis species at present are suitable for more taxa and many Asian and Mediterranean countries with no records of Prosopis are bioclimatically suitable. Several Prosopis species have substantial impacts on biodiversity, ecosystem services, and local and regional economies in their native and even more so in their invasive ranges; others provide multiple benefits to local communities. Management efforts are underway in only a small part of the invaded range. Countries where more research has been done are more likely to implement formal management than those where little published research is available. Management strategies differ among countries; developed nations use mainly mechanical and chemical control whereas developing nations tend to apply control through utilization approaches. A range of countries are also using biological control. Key gaps in knowledge and promising options for management are highlighted. PMID:24899150

Implementation of artificial neural networks (ANNs) to analysis of inter-taxa communities of benthic microorganisms and macroinvertebrates in a polluted stream.

PubMed

Kim, Byunghyuk; Lee, Se-Eun; Song, Mi-Young; Choi, Jung-Hye; Ahn, Soon-Mo; Lee, Kun-Seop; Cho, Eungchun; Chon, Tae-Soo; Koh, Sung-Cheol

2008-02-01

This study was performed to gain an understanding of the structural and functional relationships between inter-taxa communities (macroinvertebrates as consumers, and microbes as decomposers or preys for the invertebrates) in a polluted stream using artificial neural networks techniques. Sediment samples, carrying microorganisms (eubacteria) and macroinvertebrates, were seasonally collected from similar habitats in streams with different levels of pollution. Microbial community taxa and densities were determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rDNA sequence analysis techniques. The identity and density of macroinvertebrates were concurrently determined. In general, differences were observed on grouping by self-organizing map (SOM) in polluted, clean and recovering sites based on the microbial densities, while the community patterns were partly dependent on the sampling period. A Spearman rank order correlation analysis revealed correlations of several eubacterial species with those of macroinvertebrates: a negative correlation was observed between Acidovorax sp. (from polluted sites) and Gammaridae (mostly from the clean site), while Herbaspirillum sp. and Janthinobacterium sp. appeared to have positive correlations with some macroinvertebrate species. The population dynamics of the tolerant texa, Tubificidae and Chironomidae, appeared to be related with changes in the densities of Acidovorax sp. This study revealed community relationships between macroinvertebrates and microorganisms, reflecting the connectivity between the two communities via the food chain. A further physio-ecological and symbiological study on the invertebrate-microorganism relationships will be required to understand the degradation and utilization of detritus in aquatic ecosystems as well as to elucidate the roles of the inter-taxa in the recovery of polluted aquatic environments.

Influence of aeration implements, phosphorus fertilizers, and soil taxa on phosphorus losses from grasslands.

PubMed

Franklin, D H; Butler, D M; Cabrera, M L; Calvert, V H; West, L T; Rema, J A

2011-01-01

Attenuation of rainfall within the solum may help to move contaminants and nutrients into the soil to be better sequestered or utilized by crops. Surface application of phosphorus (P) amendments to grasslands may lead to elevated concentrations of P in surface runoff and eutrophication of surface waters. Aeration of grasslands has been proposed as a treatment to reduce losses of applied P. Here, results from two small-plot aeration studies and two field-scale, paired-watershed studies are supplemented with previously unpublished soil P data and synthesized. The overall objective of these studies was to determine the impact of aeration on soil P, runoff volume, and runoff P losses from mixed tall fescue [Lolium arundinaceum (Schreb.) Darbysh.]-bermudagrass (Cynodon dactylon L.) grasslands fertilized with P. Small-scale rainfall simulations were conducted on two soil taxa using three types of aeration implements: spikes, disks, and cores. The-field scale study was conducted on four soil taxa with slit and knife aeration. Small-plot studies showed that core aeration reduced loads of total P and dissolved reactive P (DRP) in runoff from plots fertilized with broiler litter and that aeration was effective in reducing P export when it increased soil P in the upper 5 cm. In the field-scale study, slit aeration reduced DRP losses by 35% in fields with well-drained soils but not in poorly drained soils. Flow-weighted concentrations of DRP in aerated fields were related to water-soluble P applied in amendments and soil test P in the upper 5 cm. These studies show that the overall effectiveness of mechanical soil aeration on runoff volume and P losses is controlled by the interaction of soil characteristics such as internal drainage and compaction, soil P, type of surface-applied manure, and type of aeration implement.

Radiation of the Australian flora: what can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in present-day communities?

PubMed Central

Crisp, Mike; Cook, Lyn; Steane, Dorothy

2004-01-01

The Australian fossil record shows that from ca. 25 Myr ago, the aseasonal-wet biome (rainforest and wet heath) gave way to the unique Australian sclerophyll biomes dominated by eucalypts, acacias and casuarinas. This transition coincided with tectonic isolation of Australia, leading to cooler, drier, more seasonal climates. From 3 Myr ago, aridification caused rapid opening of the central Australian arid zone. Molecular phylogenies with dated nodes have provided new perspectives on how these events could have affected the evolution of the Australian flora. During the Mid-Cenozoic (25-10 Myr ago) period of climatic change, there were rapid radiations in sclerophyll taxa, such as Banksia, eucalypts, pea-flowered legumes and Allocasuarina. At the same time, taxa restricted to the aseasonal-wet biome (Nothofagus, Podocarpaceae and Araucariaceae) did not radiate or were depleted by extinction. During the Pliocene aridification, two Eremean biome taxa (Lepidium and Chenopodiaceae) radiated rapidly after dispersing into Australia from overseas. It is clear that the biomes have different histories. Lineages in the aseasonal-wet biome are species poor, with sister taxa that are species rich, either outside Australia or in the sclerophyll biomes. In conjunction with the fossil record, this indicates depletion of the Australian aseasonal-wet biome from the Mid-Cenozoic. In the sclerophyll biomes, there have been multiple exchanges between the southwest and southeast, rather than single large endemic radiations after a vicariance event. There is need for rigorous molecular phylogenetic studies so that additional questions can be addressed, such as how interactions between biomes may have driven the speciation process during radiations. New studies should include the hitherto neglected monsoonal tropics. PMID:15519972

Three former taxa of Cucurbitaria and considerations on Petrakia in the Melanommataceae

PubMed Central

Jaklitsch, Walter M.; Voglmayr, Hermann

2017-01-01

Based on phylogenetic analyses of an ITS-LSU-SSU-rpb2-tef1 sequence data matrix three taxa once classified in Cucurbitaria are referred to the Melanommataceae. Cucurbitaria rhododendri, also known as Melanomma rhododendri, is not congeneric with the generic type of Melanomma, M. pulvis-pyrius and thus classified in the new genus Alpinaria. Cucurbitaria piceae, known as Gemmamyces piceae, the cause of the Gemmamyces bud blight of Picea spp., belongs also to the Melanommataceae. The name Gemmamyces is conserved. For Cucurbitaria obducens, also known as Teichospora obducens, the new genus Praetumpfia is described, as it cannot be accommodated in any known genus. All species are redescribed and epitypified. Based on sequence data and morphology, Blastostroma, Mycodidymella and Xenostigmina are synonyms of Petrakia. The genus Petrakia is emended. We also provide sequences of additional markers for Beverwykella pulmonaria, Melanomma pulvis-pyrius, Petrakia echinata and Pseudotrichia mutabilis. PMID:29104325

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

PubMed

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

PubMed Central

Hettling, Hannes; Condamine, Fabien L.; Vos, Karin; Nilsson, R. Henrik; Sanderson, Michael J.; Sauquet, Hervé; Scharn, Ruud; Silvestro, Daniele; Töpel, Mats; Bacon, Christine D.; Oxelman, Bengt; Vos, Rutger A.

2017-01-01

Abstract Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable. PMID:27616324

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa

PubMed Central

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation. PMID:25978319

Comparative genomics in the Asteraceae reveals little evidence for parallel evolutionary change in invasive taxa.

PubMed

Hodgins, Kathryn A; Bock, Dan G; Hahn, Min A; Heredia, Sylvia M; Turner, Kathryn G; Rieseberg, Loren H

2015-05-01

Asteraceae, the largest family of flowering plants, has given rise to many notorious invasive species. Using publicly available transcriptome assemblies from 35 Asteraceae, including six major invasive species, we examined evidence for micro- and macro-evolutionary genomic changes associated with invasion. To detect episodes of positive selection repeated across multiple introductions, we conducted comparisons between native and introduced genotypes from six focal species and identified genes with elevated rates of amino acid change (dN/dS). We then looked for evidence of positive selection at a broader phylogenetic scale across all taxa. As invasive species may experience founder events during colonization and spread, we also looked for evidence of increased genetic load in introduced genotypes. We rarely found evidence for parallel changes in orthologous genes in the intraspecific comparisons, but in some cases we identified changes in members of the same gene family. Using among-species comparisons, we detected positive selection in 0.003-0.69% and 2.4-7.8% of the genes using site and stochastic branch-site models, respectively. These genes had diverse putative functions, including defence response, stress response and herbicide resistance, although there was no clear pattern in the GO terms. There was no indication that introduced genotypes have a higher proportion of deleterious alleles than native genotypes in the six focal species, suggesting multiple introductions and admixture mitigated the impact of drift. Our findings provide little evidence for common genomic responses in invasive taxa of the Asteraceae and hence suggest that multiple evolutionary pathways may lead to adaptation during introduction and spread in these species. © 2014 John Wiley & Sons Ltd.

Flowering Date of Taxonomic Families Predicts Phenological Sensitivity to Temperature: Implications for Forecasting the Effects of Climate Change on Unstudied Taxa

NASA Technical Reports Server (NTRS)

Mazer, Susan J.; Travers, Steven E.; Cook, Benjamin I.; Davies, T. Jonathan; Bolmgren, Kjell; Kraft, Nathan J. B.; Salamin, Nicolas; Inouye, David W.

2013-01-01

Premise of the study: Numerous long-term studies in seasonal habitats have tracked interannual variation in fi rst fl owering date (FFD) in relation to climate, documenting the effect of warming on the FFD of many species. Despite these efforts, long-term phenological observations are still lacking for many species. If we could forecast responses based on taxonomic affi nity, however, then we could leverage existing data to predict the climate-related phenological shifts of many taxa not yet studied; Methods: We examined phenological time series of 1226 species occurrences (1031 unique species in 119 families) across seven sites in North America and England to determine whether family membership (or family mean FFD) predicts the sensitivity of FFD to standardized interannual changes in temperature and precipitation during seasonal periods before fl owering and whether families differ signifi cantly in the direction of their phenological shifts; Key results: Patterns observed among species within and across sites are mirrored among family means across sites; earlyfl owering families advance their FFD in response to warming more than late-fl owering families. By contrast, we found no consistent relationships among taxa between mean FFD and sensitivity to precipitation as measured here; Conclusions: Family membership can be used to identify taxa of high and low sensitivity to temperature within the seasonal, temperate zone plant communities analyzed here. The high sensitivity of early-fl owering families (and the absence of earlyfl owering families not sensitive to temperature) may refl ect plasticity in fl owering time, which may be adaptive in environments where early-season conditions are highly variable among years.

Morphological and molecular evidence reveals recent hybridization between gorilla taxa.

PubMed

Ackermann, Rebecca Rogers; Bishop, Jacqueline M

2010-01-01

Molecular studies have demonstrated a deep lineage split between the two gorilla species, as well as divisions within these taxa; estimates place this divergence in the mid-Pleistocene, with gene flow continuing until approximately 80,000 years ago. Here, we present analyses of skeletal data indicating the presence of substantial recent gene flow among gorillas at all taxonomic levels: between populations, subspecies, and species. Complementary analyses of DNA sequence variation suggest that low-level migration occurred primarily in a westerly-to-easterly direction. In western gorillas, the locations of hybrid phenotypes map closely to expectations based on population refugia and riverine barrier hypotheses, supporting the presence of significant vicariance-driven structuring and occasional admixture within this taxon. In eastern lowland gorillas, the high frequency of hybrid phenotypes is surprising, suggesting that this region represents a zone of introgression between eastern gorillas and migrants from the west, and underscoring the conservation priority of this critically endangered group. These results highlight the complex nature of evolutionary divergence in this genus, indicate that historical gene flow has played a major role in structuring gorilla diversity, and demonstrate that our understanding of the evolutionary processes responsible for shaping biodiversity can benefit immensely from consideration of morphological and molecular data in conjunction.

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats.

PubMed

Schuelke, Taruna; Pereira, Tiago José; Hardy, Sarah M; Bik, Holly M

2018-04-01

Studies of host-associated microbes are critical for advancing our understanding of ecology and evolution across diverse taxa and ecosystems. Nematode worms are ubiquitous across most habitats on earth, yet little is known about host-associated microbial assemblages within the phylum. Free-living nematodes are globally abundant and diverse in marine sediments, with species exhibiting distinct buccal cavity (mouth) morphologies that are thought to play an important role in feeding ecology and life history strategies. Here, we investigated patterns in marine nematode microbiomes, by characterizing host-associated microbial taxa in 281 worms isolated from a range of habitat types (deep-sea, shallow water, methane seeps, Lophelia coral mounds, kelp holdfasts) across three distinct geographic regions (Arctic, Southern California and Gulf of Mexico). Microbiome profiles were generated from single worms spanning 33 distinct morphological genera, using a two-gene metabarcoding approach to amplify the V4 region of the 16S ribosomal RNA (rRNA) gene targeting bacteria/archaea and the V1-V2 region of the 18S rRNA gene targeting microbial eukaryotes. Contrary to our expectations, nematode microbiome profiles demonstrated no distinct patterns either globally (across depths and ocean basins) or locally (within site); prokaryotic and eukaryotic microbial assemblages did not correlate with nematode feeding morphology, host phylogeny or morphological identity, ocean region or marine habitat type. However, fine-scale analysis of nematode microbiomes revealed a variety of novel ecological interactions, including putative parasites and symbionts, and potential associations with bacterial/archaeal taxa involved in nitrogen and methane cycling. Our results suggest that in marine habitats, free-living nematodes may utilize diverse and generalist foraging strategies that are not correlated with host genotype or feeding morphology. Furthermore, some abiotic factors such as geographic region

Characterization of Two New Records of Zygomycete Species Belonging to Undiscovered Taxa in Korea.

PubMed

Nguyen, Thi Thuong Thuong; Lee, Seo Hee; Bae, Sarah; Jeon, Sun Jeong; Mun, Hye Yeon; Lee, Hyang Burm

2016-03-01

During a biodiversity survey of undiscovered taxa in Korea, two zygomycetous fungal strains were isolated. The first strain, EML-FSDY6-1 was isolated from a soil sample collected at Dokdo Island in the East Sea of Korea in 2013, and the second strain, EML-DG-NH3-1 was isolated from a rat dung sample collected at Chonnam National University garden, Gwangju, Korea in 2014. Based on the morphological characteristics and phylogenetic analysis of the internal transcribed spacer, 18S and 28S rDNA, actin and translation elongation factor-1α genes. EML-FSDY6-1 and EML-DG-NH3-1 isolates were confirmed as zygomycete species, Absidia pseudocylindrospora and Absidia glauca, respectively. Neither species has previously been described in Korea.

Characterization of Two New Records of Zygomycete Species Belonging to Undiscovered Taxa in Korea

PubMed Central

Nguyen, Thi Thuong Thuong; Lee, Seo Hee; Bae, Sarah; Jeon, Sun Jeong; Mun, Hye Yeon

2016-01-01

During a biodiversity survey of undiscovered taxa in Korea, two zygomycetous fungal strains were isolated. The first strain, EML-FSDY6-1 was isolated from a soil sample collected at Dokdo Island in the East Sea of Korea in 2013, and the second strain, EML-DG-NH3-1 was isolated from a rat dung sample collected at Chonnam National University garden, Gwangju, Korea in 2014. Based on the morphological characteristics and phylogenetic analysis of the internal transcribed spacer, 18S and 28S rDNA, actin and translation elongation factor-1α genes. EML-FSDY6-1 and EML-DG-NH3-1 isolates were confirmed as zygomycete species, Absidia pseudocylindrospora and Absidia glauca, respectively. Neither species has previously been described in Korea. PMID:27103852

Atlas of relations between climatic parameters and distributions of important trees and shrubs in North America: Revisions for all taxa from the United States and Canada and new taxa from the western United States

USGS Publications Warehouse

Thompson, Robert S.; Anderson, Katherine H.; Pelltier, Richard T.; Strickland, Laura E.; Shafer, Sarah L.; Bartlein, Patrick J.; McFadden, Andrew K.

2015-01-01

This volume of the atlas provides numerous changes, updates, and enhancements from previous volumes. Its geographic coverage is now restricted to Canada and the continental United States, and the source and time period of the climatic data have changed. New variables were added, including monthly values for temperature and precipitation, and measures of interannual variability. The distribution maps for all previously published species were redigitized, some distribution maps were revised, and 148 new species were added from the arid and semiarid western United States. The graphical displays were expanded to illustrate the new climatic variables, and the data tables were modified to provide more detail on the population distributions of plant taxa relative to climatic variables.

Seasonality and Paleoecology of the Late Cretaceous Multi-Taxa Vertebrate Assemblage of “Lo Hueco” (Central Eastern Spain)

PubMed Central

Domingo, Laura; Barroso-Barcenilla, Fernando; Cambra-Moo, Oscar

2015-01-01

Isotopic studies of multi-taxa terrestrial vertebrate assemblages allow determination of paleoclimatic and paleoecological aspects on account of the different information supplied by each taxon. The late Campanian-early Maastrichtian “Lo Hueco” Fossil-Lagerstätte (central eastern Spain), located at a subtropical paleolatitude of ~31°N, constitutes an ideal setting to carry out this task due to its abundant and diverse vertebrate assemblage. Local δ18OPO4 values estimated from δ18OPO4 values of theropods, sauropods, crocodyliforms, and turtles are close to δ18OH2O values observed at modern subtropical latitudes. Theropod δ18OH2O values are lower than those shown by crocodyliforms and turtles, indicating that terrestrial endothermic taxa record δ18OH2O values throughout the year, whereas semiaquatic ectothermic taxa δ18OH2O values represent local meteoric waters over a shorter time period when conditions are favorable for bioapatite synthesis (warm season). Temperatures calculated by combining theropod, crocodyliform, and turtle δ18OH2O values and gar δ18OPO4 have enabled us to estimate seasonal variability as the difference between mean annual temperature (MAT, yielded by theropods) and temperature of the warmest months (TWMs, provided by crocodyliforms and turtles). ΔTWMs-MAT value does not point to a significantly different seasonal thermal variability when compared to modern coastal subtropical meteorological stations and Late Cretaceous rudists from eastern Tethys. Bioapatite and bulk organic matter δ13C values point to a C3 environment in the “Lo Hueco” area. The estimated fractionation between sauropod enamel and diet is ~15‰. While waiting for paleoecological information yielded by the ongoing morphological study of the “Lo Hueco” crocodyliforms, δ13C and δ18OCO3 results point to incorporation of food items with brackish influence, but preferential ingestion of freshwater. “Lo Hueco” turtles showed the lowest δ13C and δ18OCO3

A shift in nuclear state as the result of natural interspecific hybridization between two North American taxa of the basidiomycete complex Heterobasidion

Treesearch

Matteo Garbelotto; Paolo Gonthier; Rachel Linzer; Giovanni Nicolotti; William Otrosina

2004-01-01

A natural first generation hybrid fungus shows interspecific heterozygosity. The nuclear condition of a rare natural hybrid between two taxa of the Heterobasidion complex is investigated. Heterobasidion species are known to be either homokaryotic (haploid) or heterokaryotic (n + n), but heterokaryons are made up of both...

Divergence of brain and retinal anatomy and histology in pelagic antarctic notothenioid fishes of the sister taxa Dissostichus and Pleuragramma.

PubMed

Eastman, Joseph T; Lannoo, Michael J

2011-04-01

The neutrally buoyant Antarctic fishes of the sister taxa Dissostichus (D. eleginoides and D. mawsoni) and Pleuragramma antarcticum diverged early in the notothenioid radiation and filled different niches in the pelagic realm of the developing Southern Ocean. To assess the influence of phylogenetic and ecological factors in shaping neural morphology in these taxa, we studied the anatomy and histology of the brains and retinae, and determined the proportional weights of brain regions. With the brain of the non-Antarctic sister taxon Eleginops maclovinus as plesiomorphic, statistically significant departures in the brains of the two Antarctic taxa include reduction of the corpus cerebelli and expansion of the mesencephalon and medulla. Compared to Eleginops, both species also have a relatively smaller telencephalon, although this is significant only in Dissostichus. There are a number of apomorphic features in the brain of Pleuragramma including reduced olfactory nerves and bulbs, an extremely small corpus cerebelli and an expanded mesencephalon. Although there is not a significant difference in the relative weights of the medulla in the two taxa, the prominence of the eminentia granularis and bulging cap-like appearance of the crista cerebellaris are distinctive in Pleuragramma. Brain histology of Dissostichus and Pleuragramma reflects typical perciform patterns and the two species of Dissostichus are histologically identical. Lateral compression in Pleuragramma and notable lobation in Dissostichus also contribute to differences between the taxa. Compression in Pleuragramma is attributable to convergence on an anchovy/herring body shape and to the relatively large brain in this small fish. The less prominent pattern of lobation of the telencephalon, inferior lobes and corpus cerebelli in Pleuragramma probably reflects underlying histology, specifically a reduction in cellularity of the neuropil in the nuclei and lobes. The retinal histology of Dissostichus and

Regional Differences in Seasonal Timing of Rainfall Discriminate between Genetically Distinct East African Giraffe Taxa

PubMed Central

Thomassen, Henri A.; Freedman, Adam H.; Brown, David M.; Buermann, Wolfgang; Jacobs, David K.

2013-01-01

Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated

Regional differences in seasonal timing of rainfall discriminate between genetically distinct East African giraffe taxa.

PubMed

Thomassen, Henri A; Freedman, Adam H; Brown, David M; Buermann, Wolfgang; Jacobs, David K

2013-01-01

Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated

Community level patterns in diverse systems: A case study of litter fauna in a Mexican pine-oak forest using higher taxa surrogates and re-sampling methods

NASA Astrophysics Data System (ADS)

Moreno, Claudia E.; Guevara, Roger; Sánchez-Rojas, Gerardo; Téllez, Dianeis; Verdú, José R.

2008-01-01

Environmental assessment at the community level in highly diverse ecosystems is limited by taxonomic constraints and statistical methods requiring true replicates. Our objective was to show how diverse systems can be studied at the community level using higher taxa as biodiversity surrogates, and re-sampling methods to allow comparisons. To illustrate this we compared the abundance, richness, evenness and diversity of the litter fauna in a pine-oak forest in central Mexico among seasons, sites and collecting methods. We also assessed changes in the abundance of trophic guilds and evaluated the relationships between community parameters and litter attributes. With the direct search method we observed differences in the rate of taxa accumulation between sites. Bootstrap analysis showed that abundance varied significantly between seasons and sampling methods, but not between sites. In contrast, diversity and evenness were significantly higher at the managed than at the non-managed site. Tree regression models show that abundance varied mainly between seasons, whereas taxa richness was affected by litter attributes (composition and moisture content). The abundance of trophic guilds varied among methods and seasons, but overall we found that parasitoids, predators and detrivores decreased under management. Therefore, although our results suggest that management has positive effects on the richness and diversity of litter fauna, the analysis of trophic guilds revealed a contrasting story. Our results indicate that functional groups and re-sampling methods may be used as tools for describing community patterns in highly diverse systems. Also, the higher taxa surrogacy could be seen as a preliminary approach when it is not possible to identify the specimens at a low taxonomic level in a reasonable period of time and in a context of limited financial resources, but further studies are needed to test whether the results are specific to a system or whether they are general

A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa

PubMed Central

Raupach, Michael J.; Hannig, Karsten; Morinière, Jérome; Hendrich, Lars

2016-01-01

Abstract As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well. PMID:27408547

How many taxa can be recognized within the complex Tillandsia capillaris (Bromeliaceae, Tillandsioideae)? Analysis of the available classifications using a multivariate approach.

PubMed

Castello, Lucía V; Galetto, Leonardo

2013-01-01

Tillandsia capillaris Ruiz & Pav., which belongs to the subgenus Diaphoranthema is distributed in Ecuador, Peru, Bolivia, northern and central Argentina, and Chile, and includes forms that are difficult to circumscribe, thus considered to form a complex. The entities of this complex are predominantly small-sized epiphytes, adapted to xeric environments. The most widely used classification defines 5 forms for this complex based on few morphological reproductive traits: Tillandsia capillaris Ruiz & Pav. f. capillaris, Tillandsia capillaris f. incana (Mez) L.B. Sm., Tillandsia capillaris f. cordobensis (Hieron.) L.B. Sm., Tillandsia capillaris f. hieronymi (Mez) L.B. Sm. and Tillandsia capillaris f. virescens (Ruiz & Pav.) L.B. Sm. In this study, 35 floral and vegetative characters were analyzed with a multivariate approach in order to assess and discuss different proposals for classification of the Tillandsia capillaris complex, which presents morphotypes that co-occur in central and northern Argentina. To accomplish this, data of quantitative and categorical morphological characters of flowers and leaves were collected from herbarium specimens and field collections and were analyzed with statistical multivariate techniques. The results suggest that the last classification for the complex seems more comprehensive and three taxa were delimited: Tillandsia capillaris (=Tillandsia capillaris f. incana-hieronymi), Tillandsia virescens s. str. (=Tillandsia capillaris f. cordobensis) and Tillandsia virescens s. l. (=Tillandsia capillaris f. virescens). While Tillandsia capillaris and Tillandsia virescens s. str. co-occur, Tillandsia virescens s. l. is restricted to altitudes above 2000 m in Argentina. Characters previously used for taxa delimitation showed continuous variation and therefore were not useful. New diagnostic characters are proposed and a key is provided for delimiting these three taxa within the complex.

How many taxa can be recognized within the complex Tillandsia capillaris (Bromeliaceae, Tillandsioideae)? Analysis of the available classifications using a multivariate approach

PubMed Central

Castello, Lucía V.; Galetto, Leonardo

2013-01-01

Abstract Tillandsia capillaris Ruiz & Pav., which belongs to the subgenus Diaphoranthema is distributed in Ecuador, Peru, Bolivia, northern and central Argentina, and Chile, and includes forms that are difficult to circumscribe, thus considered to form a complex. The entities of this complex are predominantly small-sized epiphytes, adapted to xeric environments. The most widely used classification defines 5 forms for this complex based on few morphological reproductive traits: Tillandsia capillaris Ruiz & Pav. f. capillaris, Tillandsia capillaris f. incana (Mez) L.B. Sm., Tillandsia capillaris f. cordobensis (Hieron.) L.B. Sm., Tillandsia capillaris f. hieronymi (Mez) L.B. Sm. and Tillandsia capillaris f. virescens (Ruiz & Pav.) L.B. Sm. In this study, 35 floral and vegetative characters were analyzed with a multivariate approach in order to assess and discuss different proposals for classification of the Tillandsia capillaris complex, which presents morphotypes that co-occur in central and northern Argentina. To accomplish this, data of quantitative and categorical morphological characters of flowers and leaves were collected from herbarium specimens and field collections and were analyzed with statistical multivariate techniques. The results suggest that the last classification for the complex seems more comprehensive and three taxa were delimited: Tillandsia capillaris (=Tillandsia capillaris f. incana-hieronymi), Tillandsia virescens s. str. (=Tillandsia capillaris f. cordobensis) and Tillandsia virescens s. l. (=Tillandsia capillaris f. virescens). While Tillandsia capillaris and Tillandsia virescens s. str. co-occur, Tillandsia virescens s. l. is restricted to altitudes above 2000 m in Argentina. Characters previously used for taxa delimitation showed continuous variation and therefore were not useful. New diagnostic characters are proposed and a key is provided for delimiting these three taxa within the complex. PMID:23805053

Comparative anatomy of the female genitalia of generic-level taxa in tribe Aedini (Diptera: Culicidae). Part XXXII. Genus Jarnellius Reinert, Harbach and Kitching

USDA-ARS?s Scientific Manuscript database

A comparative, morphological analysis of the female genitalia of species included in genus Jarnellius Reinert, Harbach and Kitching was conducted. The female genitalia of the genus are characterized and a comparison with other taxa is provided. The type species of the genus, Ja. varipalpus (Coquil...

Rifaximin is associated with modest, transient decreases in multiple taxa in the gut microbiota of patients with diarrhoea-predominant irritable bowel syndrome.

PubMed

Fodor, Anthony A; Pimentel, Mark; Chey, William D; Lembo, Anthony; Golden, Pamela L; Israel, Robert J; Carroll, Ian M

2018-04-30

Rifaximin, a non-systemic antibiotic, is efficacious for the treatment of diarrhoea-predominant irritable bowel syndrome (IBS-D). Given the emerging association between the gut microbiota and IBS, this study examined potential effects of rifaximin on the gastrointestinal microbial community in patients with IBS-D. TARGET 3 was a randomised, double-blind, placebo-controlled, phase 3 study. Patients with IBS-D initially received open-label rifaximin 550 mg 3 times daily (TID) for 2 weeks. Patients who responded to the initial treatment and then relapsed were randomised to receive 2 repeat courses of rifaximin 550 mg TID or placebo for 2 weeks, with each course separated by 10 weeks. Stool samples were collected at the beginning and end of open-label treatment, at the beginning and end of the first double-blind treatment, and at the end of the study. As a secondary analysis to the TARGET 3 trial, the composition and diversity of the gut microbiota were assessed, from a random subset of patients, using variable 4 hypervariable region 16S ribosomal RNA gene sequencing. Samples from 103 patients were included. After open-label rifaximin treatment for 2 weeks, 7 taxa (e.g. Peptostreptococcaceae, Verrucomicrobiaceae, Enterobacteriaceae) had significantly lower relative abundance at a 10% false discovery rate threshold. The effects of rifaximin were generally short-term, as there was little evidence of significantly different changes in taxa relative abundance at the end of the study (up to 46 weeks) versus baseline. The results suggest that rifaximin has a modest, largely transient effect across a broad range of stool microbes. Future research may determine whether the taxa affected by rifaximin are causally linked to IBS-D. ClinicalTrials.gov identifier number: NCT01543178.

Natural abundance (δ¹⁵N) indicates shifts in nitrogen relations of woody taxa along a savanna-woodland continental rainfall gradient.

PubMed

Soper, Fiona M; Richards, Anna E; Siddique, Ilyas; Aidar, Marcos P M; Cook, Garry D; Hutley, Lindsay B; Robinson, Nicole; Schmidt, Susanne

2015-05-01

Water and nitrogen (N) interact to influence soil N cycling and plant N acquisition. We studied indices of soil N availability and acquisition by woody plant taxa with distinct nutritional specialisations along a north Australian rainfall gradient from monsoonal savanna (1,600-1,300 mm annual rainfall) to semi-arid woodland (600-250 mm). Aridity resulted in increased 'openness' of N cycling, indicated by increasing δ(15)N(soil) and nitrate:ammonium ratios, as plant communities transitioned from N to water limitation. In this context, we tested the hypothesis that δ(15)N(root) xylem sap provides a more direct measure of plant N acquisition than δ(15)N(foliage). We found highly variable offsets between δ(15)N(foliage) and δ(15)N(root) xylem sap, both between taxa at a single site (1.3-3.4 ‰) and within taxa across sites (0.8-3.4 ‰). As a result, δ(15)N(foliage) overlapped between N-fixing Acacia and non-fixing Eucalyptus/Corymbia and could not be used to reliably identify biological N fixation (BNF). However, Acacia δ(15)N(root) xylem sap indicated a decline in BNF with aridity corroborated by absence of root nodules and increasing xylem sap nitrate concentrations and consistent with shifting resource limitation. Acacia dominance at arid sites may be attributed to flexibility in N acquisition rather than BNF capacity. δ(15)N(root) xylem sap showed no evidence of shifting N acquisition in non-mycorrhizal Hakea/Grevillea and indicated only minor shifts in Eucalyptus/Corymbia consistent with enrichment of δ(15)N(soil) and/or decreasing mycorrhizal colonisation with aridity. We propose that δ(15)N(root) xylem sap is a more direct indicator of N source than δ(15)N(foliage), with calibration required before it could be applied to quantify BNF.

Adaptations and Predispositions of Different Middle European Arthropod Taxa (Collembola, Araneae, Chilopoda, Diplopoda) to Flooding and Drought Conditions

PubMed Central

Marx, Michael Thomas; Guhmann, Patrick; Decker, Peter

2012-01-01

Simple Summary This review summarizes adaptations and predispositions of different arthropod taxa (springtails, web spiders, millipedes and centipedes) to flood and drought conditions. The main focus sis directed to arthropod species, which are living in Middle European floodplain forests and wetlands, because of the fast change of flood and drought conditions in these habitats. Furthermore the effects of the predicted regional climate change like increasing aperiodic summer flooding and decreasing winter and spring floods are also discussed. Abstract Floodplain forests and wetlands are amongst the most diverse and species rich habitats on earth. Arthropods are a key group for the high diversity pattern of these landscapes, due to the fact that the change between flooding and drought causes in different life cycles and in a variety of adaptations in the different taxa. The floodplain forests and wetlands of Central Amazonia are well investigated and over the last 50 years many adaptations of several hexapod, myriapod and arachnid orders were described. In contrast to Amazonia the Middle European floodplains were less investigated concerning the adaptations of arthropods to flood and drought conditions. This review summarizes the adaptations and predispositions of springtails, web spiders, millipedes and centipedes to the changeable flood and drought conditions of Middle European floodplain forests and wetlands. Furthermore the impact of regional climate change predictions like increasing aperiodic summer floods and the decrease of typical winter and spring floods are discussed in this article. PMID:26487164

Cross-species evaluation of molecular target sequence and structural conservation as a line of evidence for identification of susceptible taxa to inform toxicity testing

EPA Science Inventory

The 1985 U.S. Environmental Protection Agency Guidelines for Deriving Aquatic Life Criteria require acute and chronic toxicity testing with a fixed list of taxa that cover a broad spectrum of aquatic organisms from vertebrate, invertebrate, and plant families. In considering revi...

Revision of the status of some genus-level water mite taxa in the families Pionidae Thor, 1900, Aturidae Thor, 1900, and Nudomideopsidae Smith, 1990 (Acari: Hydrachnidiae).

PubMed

Smith, Ian M; Cook, David R; Gerecke, Reinhard

2015-02-16

A number of changes to the status of genus group names in water mites are proposed to foster a more consistent and phylogenetically defensible approach to the ranking of taxa at this level of the classification. The water mite taxa Acercopsis Viets, 1926 (Pionidae: Tiphyinae), Madawaska Habeeb, 1954 (Pionidae: Foreliinae), Brachypodopsis Piersig, 1903, Cubanaxonopsis Orghidan & Gruia, 1981, Hexaxonopsis Viets, 1926, Paraxonopsis Motaş & Tanasachi, 1947, Vicinaxonopsis Cook, 1974, Parabrachypoda Viets, 1929, and Ocybrachypoda Cook, 1974 (Aturidae: Axonopsinae), Ameribrachypoda Smith, 1991 (Aturidae: Aturinae), and Allomideopsis Smith, 1990 (Nudomideopsidae) are elevated in rank from subgenera to full genera to reflect current knowledge of their species diversity, morphological distinctness, relationships and apparent age. In light of the above changes in the subfamily Axonopsinae, the subgenera Kalobrachypoda Viets, 1929 and Navinaxonopsis Cook, 1967 are transferred from the genus Axonopsis to the genus Brachypodopsis, the subgenus Plesiobrachypoda Viets, 1942 is transferred from the genus Axonopsis to the genus Hexaxonopsis, and the species formerly placed in the subgenus Hemibrachypoda Viets, 1937 are transferred from the genus Brachypoda to the genus Parabrachypoda Viets, 1929, and Hemibrachypoda is placed in synonymy with Parabrachypoda. The family group taxa to which all of these genera belong are reviewed to provide context for the proposed changes.

A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations.

PubMed

Laroche, Olivier; Wood, Susanna A; Tremblay, Louis A; Ellis, Joanne I; Lear, Gavin; Pochon, Xavier

2018-02-01

Standardized ecosystem-based monitoring surveys are critical for providing information on marine ecosystem health. Environmental DNA/RNA (eDNA/eRNA) metabarcoding may facilitate such surveys by quickly and effectively characterizing multi-trophic levels. In this study, we assessed the suitability of eDNA/eRNA metabarcoding to evaluate changes in benthic assemblages of bacteria, Foraminifera and other eukaryotes along transects at three offshore oil and gas (O&G) drilling and production sites, and compared these to morphologically characterized macro-faunal assemblages. Bacterial communities were the most responsive to O&G activities, followed by Foraminifera, and macro-fauna (the latter assessed by morphology). The molecular approach enabled detection of hydrocarbon degrading taxa such as the bacteria Alcanivorax and Microbulbifer at petroleum impacted stations. Most identified indicator taxa, notably among macro-fauna, were highly specific to site conditions. Based on our results we suggest that eDNA/eRNA metabarcoding can be used as a stand-alone method for biodiversity assessment or as a complement to morphology-based monitoring approaches. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

PubMed Central

Garzón-Martínez, Gina A.; Osorio-Guarín, Jaime A.; Delgadillo-Durán, Paola; Mayorga, Franklin; Enciso-Rodríguez, Felix E.; Landsman, David

2015-01-01

The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation FST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies. PMID:26550601

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers.

PubMed

Garzón-Martínez, Gina A; Osorio-Guarín, Jaime A; Delgadillo-Durán, Paola; Mayorga, Franklin; Enciso-Rodríguez, Felix E; Landsman, David; Mariño-Ramírez, Leonardo; Barrero, Luz Stella

2015-12-01

The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation F ST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies.

[Fatty acids in the species of several zygomycete taxa].

PubMed

Konova, I V; Galanina, L A; Kochkina, G A; Pan'kina, O I

2002-01-01

The composition of fatty acids synthesized de novo by thirty strains of zygomycetes from various taxa was studied. The qualitative fatty acid compositions of the fungal lipids were found to be virtually identical, but there were significant differences in the contents of individual acids. Highly active producers of essential C18 fatty acids, with their content exceeding 30-40% of total fatty acids, were discovered among the fungi of the families Mucoraceae, Pilobolaceae, and Radiomycetaceae. Linoleic acid was found to predominate in the fungi of the genera Radiomyces, Mycotypha, and Circinella, and linolenic acid (identified as its gamma-isomer by gas-liquid chromatography), in the fungi of the genera Absidia, Circinella, Pilaira, and Hesseltinella. The total yield (mg/l) of bioactive acids (C18:3, C18:2, C18:1) varied from 761.4 in Pilaira anomala to 3477.9 in Syncephalastrum racemosum; the total yield of essential acids, from 520.7 in Pilaira anomala to 1154.5 in Hesseltinella vesiculosa; of linoleic acid, from 279.7 in Pilaira anomala to 836.3 in Mycotypha indica; and of linolenic acid, from 120.8 in Mycotypha indica to 708.0 in Hesseltinella vesiculosa. The data on the efficient synthesis of these acids make the actively producing strains promising for biotechnological synthesis of commercially valuable lipids. Linderina pennispora VKM F-1219, a zygomycete of the family Kickxellaceae, which was earlier singled out into the order Kickxellales [12], was shown to differ from zygomycetes of the order Mucorales in having a high content of cis-9-hexadecenoic (palmitoleic) acid, reaching 37.0% of the fatty acid total.

New mescaline concentrations from 14 taxa/cultivars of Echinopsis spp. (Cactaceae) ("San Pedro") and their relevance to shamanic practice.

PubMed

Ogunbodede, Olabode; McCombs, Douglas; Trout, Keeper; Daley, Paul; Terry, Martin

2010-09-15

The aim of the present study is to determine in a procedurally uniform manner the mescaline concentrations in stem tissue of 14 taxa/cultivars of the subgenus Trichocereus of the genus Echinopsis (Cactaceae) and to evaluate the relationship (if any) between mescaline concentration and actual shamanic use of these plants. Columnar cacti of the genus Echinopsis, some of which are used for diagnostic and therapeutic purposes by South American shamans in traditional medicine, were selected for analysis because they were vegetative clones of plants of documented geographic origin and/or because they were known to be used by practitioners of shamanism. Mescaline content of the cortical stem chlorenchyma of each cactus was determined by Soxhlet extraction with methanol, followed by acid-base extraction with water and dichloromethane, and high-pressure liquid chromatography (HPLC). By virtue of the consistent analytical procedures used, comparable alkaloid concentrations were obtained that facilitated the ranking of the various selected species and cultivars of Echinopsis, all of which exhibited positive mescaline contents. The range of mescaline concentrations across the 14 taxa/cultivars spanned two orders of magnitude, from 0.053% to 4.7% by dry weight. The mescaline concentrations reported here largely support the hypothesis that plants with the highest mescaline concentrations - particularly E. pachanoi from Peru - are most associated with documented shamanic use. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

Revision of the genus-group Hystricella R. T. Lowe, 1855 from Porto Santo (Madeira Archipelago), with descriptions of new recent and fossil taxa (Gastropoda, Helicoidea, Geomitridae)

PubMed Central

Mattia, Willy De; Neiber, Marco T.; Groh, Klaus

2018-01-01

Abstract The genus-group Hystricella R. T. Lowe, 1855 is revised on the basis of conchological, anatomical and genetic characteristics. A new genus Wollastonia gen. n., two recent species, W. jessicae sp. n. and W. klausgrohi sp. n., and one recent subspecies, W. jessicae monticola ssp. n. are described as new to science, as well as five fossil taxa, H. microcarinata sp. n., W. beckmanni sp. n., W. falknerorum sp. n., W. ripkeni sp. n., and W. inexpectata sp. n. For Helix vermetiformis R. T. Lowe, 1855, H. leacockiana Wollaston, 1878, H. oxytropis R. T. Lowe, 1831, H. duplicata R. T. Lowe, 1831 and H. oxytropis var. ß subcarinulata Wollaston, 1878 lectotypes are designated. For the taxa Helix bicarinata G. B. Sowerby I, 1824, Helix bicarinata var. ß aucta Wollaston, 1878 and Discula bulverii W. Wood, 1828 neotypes are selected. The taxa aucta and subcarinulata are elevated to specific rank. For the hitherto monospecific (sub-) genus Callina R. T. Lowe, 1855 it is shown that it is not closely related to the genus Discula but to the Hystricella-group and its generic rank is confirmed. The taxon D. bulverii W. Wood, 1828 is transferred from the genus Discula s. str. to the genus Callina. A further fossil taxon C. waldeni sp. n. is described as new to science. PMID:29416404

Habitat structure and body size distributions: Cross-ecosystem comparison for taxa with determinate and indeterminate growth

USGS Publications Warehouse

Nash, Kirsty L.; Allen, Craig R.; Barichievy, Chris; Nystrom, Magnus; Sundstrom, Shana M.; Graham, Nicholas A.J.

2014-01-01

Habitat structure across multiple spatial and temporal scales has been proposed as a key driver of body size distributions for associated communities. Thus, understanding the relationship between habitat and body size is fundamental to developing predictions regarding the influence of habitat change on animal communities. Much of the work assessing the relationship between habitat structure and body size distributions has focused on terrestrial taxa with determinate growth, and has primarily analysed discontinuities (gaps) in the distribution of species mean sizes (species size relationships or SSRs). The suitability of this approach for taxa with indeterminate growth has yet to be determined. We provide a cross-ecosystem comparison of bird (determinate growth) and fish (indeterminate growth) body mass distributions using four independent data sets. We evaluate three size distribution indices: SSRs, species size–density relationships (SSDRs) and individual size–density relationships (ISDRs), and two types of analysis: looking for either discontinuities or abundance patterns and multi-modality in the distributions. To assess the respective suitability of these three indices and two analytical approaches for understanding habitat–size relationships in different ecosystems, we compare their ability to differentiate bird or fish communities found within contrasting habitat conditions. All three indices of body size distribution are useful for examining the relationship between cross-scale patterns of habitat structure and size for species with determinate growth, such as birds. In contrast, for species with indeterminate growth such as fish, the relationship between habitat structure and body size may be masked when using mean summary metrics, and thus individual-level data (ISDRs) are more useful. Furthermore, ISDRs, which have traditionally been used to study aquatic systems, present a potentially useful common currency for comparing body size distributions

Systematics of the family Plectopylidae in Vietnam with additional information on Chinese taxa (Gastropoda, Pulmonata, Stylommatophora)

PubMed Central

Páll-Gergely, Barna; Hunyadi, András; Ablett, Jonathan; Lương, Hào Văn; Fred Naggs; Asami, Takahiro

2015-01-01

Abstract Vietnamese species from the family Plectopylidae are revised based on the type specimens of all known taxa, more than 600 historical non-type museum lots, and almost 200 newly-collected samples. Altogether more than 7000 specimens were investigated. The revision has revealed that species diversity of the Vietnamese Plectopylidae was previously overestimated. Overall, thirteen species names (anterides Gude, 1909, bavayi Gude, 1901, congesta Gude, 1898, fallax Gude, 1909, gouldingi Gude, 1909, hirsuta Möllendorff, 1901, jovia Mabille, 1887, moellendorffi Gude, 1901, persimilis Gude, 1901, pilsbryana Gude, 1901, soror Gude, 1908, tenuis Gude, 1901, verecunda Gude, 1909) were synonymised with other species. In addition to these, Gudeodiscus hemmeni sp. n. and Gudeodiscus messageri raheemi ssp. n. are described from north-western Vietnam. Sixteen species and two subspecies are recognized from Vietnam. The reproductive anatomy of eight taxa is described. Based on anatomical information, Halongella gen. n. is erected to include Plectopylis schlumbergeri and Plectopylis fruhstorferi. Additionally, the genus Gudeodiscus is subdivided into two subgenera (Gudeodiscus and Veludiscus subgen. n.) on the basis of the morphology of the reproductive anatomy and the radula. The Chinese Gudeodiscus phlyarius werneri Páll-Gergely, 2013 is moved to synonymy of Gudeodiscus phlyarius. A spermatophore was found in the organ situated next to the gametolytic sac in one specimen. This suggests that this organ in the Plectopylidae is a diverticulum. Statistically significant evidence is presented for the presence of calcareous hook-like granules inside the penis being associated with the absence of embryos in the uterus in four genera. This suggests that these probably play a role in mating periods before disappearing when embryos develop. Sicradiscus mansuyi is reported from China for the first time. PMID:25632253

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments.

PubMed

Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

2016-11-25

Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

PubMed Central

Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

2016-01-01

Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies. PMID:27886221

TaxaGloss - A Glossary and Translation Tool for Biodiversity Studies.

PubMed

Collin, Rachel; Fredericq, Suzanne; Freshwater, D Wilson; Gilbert, Edward; Madrid, Maycol; Maslakova, Svetlana; Miglietta, Maria Pia; Rocha, Rosana M; Rodríguez, Estefanía; Thacker, Robert W

2016-01-01

Correctly identifying organisms is key to most biological research, and is especially critical in areas of biodiversity and conservation. Yet it remains one of the greatest challenges when studying all but the few well-established model systems. The challenge is in part due to the fact that most species have yet to be described, vanishing taxonomic expertise and the relative inaccessibility of taxonomic information. Furthermore, identification keys and other taxonomic resources are based on complex, taxon-specific vocabularies used to describe important morphological characters. Using these resources is made difficult by the fact that taxonomic documentation of the world's biodiversity is an international endeavour, and keys and field guides are not always available in the practitioner's native language. To address this challenge, we have developed a publicly available on-line illustrated multilingual glossary and translation tool for technical taxonomic terms using the Symbiota Software Project biodiversity platform. Illustrations, photographs and translations have been sourced from the global community of taxonomists working with marine invertebrates and seaweeds. These can be used as single-language illustrated glossaries or to make customized translation tables. The glossary has been launched with terms and illustrations of seaweeds, tunicates, sponges, hydrozoans, sea anemones, and nemerteans, and already includes translations into seven languages for some groups. Additional translations and development of terms for more taxa are underway, but the ultimate utility of this tool depends on active participation of the international taxonomic community.

Comparing mechanisms of host manipulation across host and parasite taxa

USGS Publications Warehouse

Lafferty, Kevin D.; Shaw, Jenny C.

2013-01-01

Parasites affect host behavior in several ways. They can alter activity, microhabitats or both. For trophically transmitted parasites (the focus of our study), decreased activity might impair the ability of hosts to respond to final-host predators, and increased activity and altered microhabitat choice might increase contact rates between hosts and final-host predators. In an analysis of trophically transmitted parasites, more parasite groups altered activity than altered microhabitat choice. Parasites that infected vertebrates were more likely to impair the host’s reaction to predators, whereas parasites that infected invertebrates were more likely to increase the host’s contact with predators. The site of infection might affect how parasites manipulate their hosts. For instance, parasites in the central nervous system seem particularly suited to manipulating host behavior. Manipulative parasites commonly occupy the body cavity, muscles and central nervous systems of their hosts. Acanthocephalans in the data set differed from other taxa in that they occurred exclusively in the body cavity of invertebrates. In addition, they were more likely to alter microhabitat choice than activity. Parasites in the body cavity (across parasite types) were more likely to be associated with increased host contact with predators. Parasites can manipulate the host through energetic drain, but most parasites use more sophisticated means. For instance, parasites target four physiological systems that shape behavior in both invertebrates and vertebrates: neural, endocrine, neuromodulatory and immunomodulatory. The interconnections between these systems make it difficult to isolate specific mechanisms of host behavioral manipulation.

Towards a phylogenetic generic classification of Thelypteridaceae: Additional sampling suggests alterations of neotropical taxa and further study of paleotropical genera.

PubMed

Almeida, Thaís Elias; Hennequin, Sabine; Schneider, Harald; Smith, Alan R; Batista, João Aguiar Nogueira; Ramalho, Aline Joseph; Proite, Karina; Salino, Alexandre

2016-01-01

Thelypteridaceae is one of the largest fern families, having about 950 species and a cosmopolitan distribution but with most species occurring in tropical and subtropical regions. Its generic classification remains controversial, with different authors recognizing from one up to 32 genera. Phylogenetic relationships within the family have not been exhaustively studied, but previous studies have confirmed the monophyly of the lineage. Thus far, sampling has been inadequate for establishing a robust hypothesis of infrafamilial relationships within the family. In order to understand phylogenetic relationships within Thelypteridaceae and thus to improve generic reclassification, we expand the molecular sampling, including new samples of Old World taxa and, especially, many additional neotropical representatives. We also explore the monophyly of exclusively or mostly neotropical genera Amauropelta, Goniopteris, Meniscium, and Steiropteris. Our sampling includes 68 taxa and 134 newly generated sequences from two plastid genomic regions (rps4-trnS and trnL-trnF), plus 73 rps4 and 72 trnL-trnF sequences from GenBank. These data resulted in a concatenated matrix of 1980 molecular characters for 149 taxa. The combined data set was analyzed using maximum parsimony and bayesian inference of phylogeny. Our results are consistent with the general topological structure found in previous studies, including two main lineages within the family: phegopteroid and thelypteroid. The thelypteroid lineage comprises two clades; one of these included the segregates Metathelypteris, Coryphopteris, and Amauropelta (including part of Parathelypteris), whereas the other comprises all segregates of Cyclosorus s.l., such as Goniopteris, Meniscium, and Steiropteris (including Thelypteris polypodioides, previously incertae sedis). The three mainly neotropical segregates were found to be monophyletic but nested in a broadly defined Cyclosorus. The fourth mainly neotropical segregate, Amauropelta

Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America.

PubMed

Ramey, Andrew M; Goraichuk, Iryna V; Hicks, Joseph T; Dimitrov, Kiril M; Poulson, Rebecca L; Stallknecht, David E; Bahl, Justin; Afonso, Claudio L

2017-03-03

Avian paramyxovirus serotype 1 (APMV-1) viruses are globally distributed, infect wild, peridomestic, and domestic birds, and sometimes lead to outbreaks of disease. Thus, the maintenance, evolution, and spread of APMV-1 viruses are relevant to avian health. In this study we sequenced the fusion gene from 58 APMV-1 isolates recovered from thirteen species of wild birds sampled throughout the USA during 2007-2014. We analyzed sequence information with previously reported data in order to assess contemporary genetic diversity and inter-taxa/inter-region exchange of APMV-1 in wild birds sampled in North America. Our results suggest that wild birds maintain previously undescribed genetic diversity of APMV-1; however, such diversity is unlikely to be pathogenic to domestic poultry. Phylogenetic analyses revealed that APMV-1 diversity detected in wild birds of North America has been found in birds belonging to numerous taxonomic host orders and within hosts inhabiting multiple geographic regions suggesting some level of viral exchange. However, our results also provide statistical support for associations between phylogenetic tree topology and host taxonomic order/region of sample origin which supports restricted exchange among taxa and geographical regions of North America for some APMV-1 sub-genotypes. We identify previously unrecognized genetic diversity of APMV-1 in wild birds in North America which is likely a function of continued viral evolution in reservoir hosts. We did not, however, find support for the emergence or maintenance of APMV-1 strains predicted to be pathogenic to poultry in wild birds of North America outside of the order Suliformes (i.e., cormorants). Furthermore, genetic evidence suggests that ecological drivers or other mechanisms may restrict viral exchange among taxa and regions of North America. Additional and more systematic sampling for APMV-1 in North America would likely provide further inference on viral dynamics for this infectious agent

Origins of domestication and polyploidy in oca (Oxalis tuberosa; Oxalidaceae). 3. AFLP data of oca and four wild, tuber-bearing taxa.

PubMed

Emshwiller, Eve; Theim, Terra; Grau, Alfredo; Nina, Victor; Terrazas, Franz

2009-10-01

Many crops are polyploids, and it can be challenging to untangle the often complicated history of their origins of domestication and origins of polyploidy. To complement other studies of the origins of polyploidy of the octoploid tuber crop oca (Oxalis tuberosa) that used DNA sequence data and phylogenetic methods, we here compared AFLP data for oca with four wild, tuber-bearing Oxalis taxa found in different regions of the central Andes. Results confirmed the divergence of two use-categories of cultivated oca that indigenous farmers use for different purposes, suggesting the possibility that they might have had separate origins of domestication. Despite previous results with nuclear-encoded, chloroplast-expressed glutamine synthetase suggesting that O. picchensis might be a progenitor of oca, AFLP data of this species, as well as different populations of wild, tuber-bearing Oxalis found in Lima Department, Peru, were relatively divergent from O. tuberosa. Results from all analytical methods suggested that the unnamed wild, tuber-bearing Oxalis found in Bolivia and O. chicligastensis in NW Argentina are the best candidates as the genome donors for polyploid O. tuberosa, but the results were somewhat equivocal about which of these two taxa is the more strongly supported as oca's progenitor.

Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments.

PubMed

Díaz-Muñoz, Samuel L

2017-01-01

Infection of more than one virus in a host, coinfection, is common across taxa and environments. Viral coinfection can enable genetic exchange, alter the dynamics of infections, and change the course of viral evolution. Yet, a systematic test of the factors explaining variation in viral coinfection across different taxa and environments awaits completion. Here I employ three microbial data sets of virus-host interactions covering cross-infectivity, culture coinfection, and single-cell coinfection (total: 6,564 microbial hosts, 13,103 viruses) to provide a broad, comprehensive picture of the ecological and biological factors shaping viral coinfection. I found evidence that ecology and virus-virus interactions are recurrent factors shaping coinfection patterns. Host ecology was a consistent and strong predictor of coinfection across all three data sets: cross-infectivity, culture coinfection, and single-cell coinfection. Host phylogeny or taxonomy was a less consistent predictor, being weak or absent in the cross-infectivity and single-cell coinfection models, yet it was the strongest predictor in the culture coinfection model. Virus-virus interactions strongly affected coinfection. In the largest test of superinfection exclusion to date, prophage sequences reduced culture coinfection by other prophages, with a weaker effect on extrachromosomal virus coinfection. At the single-cell level, prophage sequences eliminated coinfection. Virus-virus interactions also increased culture coinfection with ssDNA-dsDNA coinfections >2× more likely than ssDNA-only coinfections. The presence of CRISPR spacers was associated with a ∼50% reduction in single-cell coinfection in a marine bacteria, despite the absence of exact spacer matches in any active infection. Collectively, these results suggest the environment bacteria inhabit and the interactions among surrounding viruses are two factors consistently shaping viral coinfection patterns. These findings highlight the role of

DNA barcode data accurately assign higher spider taxa

PubMed Central

Coddington, Jonathan A.; Agnarsson, Ingi; Cheng, Ren-Chung; Čandek, Klemen; Driskell, Amy; Frick, Holger; Gregorič, Matjaž; Kostanjšek, Rok; Kropf, Christian; Kweskin, Matthew; Lokovšek, Tjaša; Pipan, Miha; Vidergar, Nina

2016-01-01

The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of

Unique method of tooth replacement in durophagous placodont marine reptiles, with new data on the dentition of Chinese taxa

PubMed Central

Neenan, James M; Li, Chun; Rieppel, Olivier; Bernardini, Federico; Tuniz, Claudio; Muscio, Giuseppe; Scheyer, Torsten M

2014-01-01

The placodonts of the Triassic period (˜252–201 mya) represent one of the earliest and most extreme specialisations to a durophagous diet of any known reptile group. Exceptionally enlarged crushing tooth plates on the maxilla, dentary and palatine cooperated to form functional crushing areas in the buccal cavity. However, the extreme size of these teeth, combined with the unusual way they occluded, constrained how replacement occurred. Using an extensive micro-computed tomographic dataset of 11 specimens that span all geographic regions and placodont morphotypes, tooth replacement patterns were investigated. In addition, the previously undescribed dental morphologies and formulae of Chinese taxa are described for the first time and incorporated into the analysis. Placodonts have a unique tooth replacement pattern and results follow a phylogenetic trend. The plesiomorphic Placodus species show many replacement teeth at various stages of growth, with little or no discernible pattern. On the other hand, the more derived cyamodontoids tend to have fewer replacement teeth growing at any one time, replacing teeth unilaterally and/or in functional units, thus maintaining at least one functional crushing area at all times. The highly derived placochelyids have fewer teeth and, as a result, only have one or two replacement teeth in the upper jaw. This supports previous suggestions that these taxa had an alternative diet to other placodonts. Importantly, all specimens show at least one replacement tooth growing at the most posterior palatine tooth plates, indicating increased wear at this point and thus the most efficient functional crushing area. PMID:24517163

Cross-species evaluation of molecular target sequence and structural conservation as a line of evidence for identification of susceptible taxa to inform derivation of aquatic life criteria

EPA Science Inventory

The 1985 U.S. Environmental Protection Agency (EPA) Guidelines for Deriving Aquatic Life Criteria (ALC) require acute and chronic toxicity testing with a fixed list of taxa that cover aquatic organisms from vertebrates, invertebrates, and plants. In considering Guideline revision...

AMS Radiocarbon Dating Individual Taxa and Individual Specimens: Implications for Small Mammal Paleoecology.

NASA Astrophysics Data System (ADS)

Graham, Russell; Stafford, Thomas, Jr.; Semken, Holmes, Jr.

2010-05-01

Advances in AMS physics and organic geochemistry have revolutionized our ability to establish absolute chronologies on vertebrate fossils. Highly purified collagen, which provides extremely accurate 14C ages, can be extracted from single bones and teeth as small as 50 mg. Combined with measurement precisions of ±15 to 25 years for ages of < 20,000 yr, the direct AMS 14C technique enables fossil deposits to be chronologically dissected at the level of single animals. Analysis of data from a variety of sites in the United States indicates that most excavation levels (analysis units) as small as 10 cm can be time averaged by several thousand years at a minimum, even with the greatest care in excavation and processing of sediments. Time averaging of this magnitude has important implications for fine-scale paleoecological analysis of faunas, especially when compared to high-resolution climate records like those derived from speleothems, ice cores, or marine cores. To this end, we propose saturation dating of indicative taxa and plotting dates of individual specimens against high-resolution climate records rather than analysis of complete faunas or faunules. This technique provides even higher resolution of paleoenvironments than pollen spectra.

Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America

USGS Publications Warehouse

Ramey, Andy M.; Goraichuk, Iryna V.; Hicks, Joseph T.; Dimitrov, Kiril M.; Poulson, Rebecca L.; Stallknecht, David E.; Bahl, Justin; Afonso, Claudio L.

2017-01-01

BackgroundAvian paramyxovirus serotype 1 (APMV-1) viruses are globally distributed, infect wild, peridomestic, and domestic birds, and sometimes lead to outbreaks of disease. Thus, the maintenance, evolution, and spread of APMV-1 viruses are relevant to avian health.MethodsIn this study we sequenced the fusion gene from 58 APMV-1 isolates recovered from thirteen species of wild birds sampled throughout the USA during 2007–2014. We analyzed sequence information with previously reported data in order to assess contemporary genetic diversity and inter-taxa/inter-region exchange of APMV-1 in wild birds sampled in North America.ResultsOur results suggest that wild birds maintain previously undescribed genetic diversity of APMV-1; however, such diversity is unlikely to be pathogenic to domestic poultry. Phylogenetic analyses revealed that APMV-1 diversity detected in wild birds of North America has been found in birds belonging to numerous taxonomic host orders and within hosts inhabiting multiple geographic regions suggesting some level of viral exchange. However, our results also provide statistical support for associations between phylogenetic tree topology and host taxonomic order/region of sample origin which supports restricted exchange among taxa and geographical regions of North America for some APMV-1 sub-genotypes.ConclusionsWe identify previously unrecognized genetic diversity of APMV-1 in wild birds in North America which is likely a function of continued viral evolution in reservoir hosts. We did not, however, find support for the emergence or maintenance of APMV-1 strains predicted to be pathogenic to poultry in wild birds of North America outside of the order Suliformes (i.e., cormorants). Furthermore, genetic evidence suggests that ecological drivers or other mechanisms may restrict viral exchange among taxa and regions of North America. Additional and more systematic sampling for APMV-1 in North America would likely provide further inference on viral

I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation

PubMed Central

Mooers, Arne Ø.; Caccone, Adalgisa; Russello, Michael A.

2016-01-01

In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization. PMID:27635324

I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation.

PubMed

Jensen, Evelyn L; Mooers, Arne Ø; Caccone, Adalgisa; Russello, Michael A

2016-01-01

In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization.

Sustaining salmonid populations: A caring understanding of naturalness of taxa

USGS Publications Warehouse

Nielsen, Jennifer L.; Regier, Henry A.; Knudsen, E. Eric

2004-01-01

Species of the family of Salmonidae occur naturally in Northern Hemisphere waters that remain clear and cool to cold in summer. For purposes of reproduction, salmonids generally behaviorally respond to the currents of streams and lakes in recently glaciated areas. For feeding and maturation, many larger species migrate into existing systems of large lakes, seas, and oceans. The subfamilies include Salmoninae, Coregoninae, and Thymallinae. In many locales and regions of the hemisphere, numerous species of these subfamilies evolved and self-organized into species flocks or taxocenes of bewildering complexity. For example, any individual species may play different or unique ecological roles in different taxocenes. The northern Pacific and Atlantic Ocean ecosystems, with their seas and tributaries, each contained a metacomplex of such taxocenes that, in their natural state some centuries ago, resembled each other but differed in many ways. Humans have valued all species of this family for subsistence, ceremonial, naturalist, gustatory, angling, and commercial reasons for centuries. Modern progressive humans (MPHs), whose industrial and commercial enterprises have gradually spread over this hemisphere in recent time, now affect aquatic ecosystems at all scales from local to global. These human effects mingle in complex ways that together induce uniquely natural salmonid taxocenes to disintegrate with the loss of species, including those groups least tolerant to human manipulations, but extending more recently to those taxa more adapted to anthropogenic change. As we leave the modern era, dominated by MPHs, will we find ways to live sustainably with salmonid taxocenes that still exhibit self-organizational integrity, or will only individual, isolated populations of salmonid species, derived from those most tolerant of MPHs, survive? To achieve future sustainability of salmonids, we suggest implementation of a search for intuitive knowledge based on faith in the wisdom of

Are Cranial Biomechanical Simulation Data Linked to Known Diets in Extant Taxa? A Method for Applying Diet-Biomechanics Linkage Models to Infer Feeding Capability of Extinct Species

PubMed Central

Tseng, Zhijie Jack; Flynn, John J.

2015-01-01

Performance of the masticatory system directly influences feeding and survival, so adaptive hypotheses often are proposed to explain craniodental evolution via functional morphology changes. However, the prevalence of “many-to-one” association of cranial forms and functions in vertebrates suggests a complex interplay of ecological and evolutionary histories, resulting in redundant morphology-diet linkages. Here we examine the link between cranial biomechanical properties for taxa with different dietary preferences in crown clade Carnivora, the most diverse clade of carnivorous mammals. We test whether hypercarnivores and generalists can be distinguished based on cranial mechanical simulation models, and how such diet-biomechanics linkages relate to morphology. Comparative finite element and geometric morphometrics analyses document that predicted bite force is positively allometric relative to skull strain energy; this is achieved in part by increased stiffness in larger skull models and shape changes that resist deformation and displacement. Size-standardized strain energy levels do not reflect feeding preferences; instead, caniform models have higher strain energy than feliform models. This caniform-feliform split is reinforced by a sensitivity analysis using published models for six additional taxa. Nevertheless, combined bite force-strain energy curves distinguish hypercarnivorous versus generalist feeders. These findings indicate that the link between cranial biomechanical properties and carnivoran feeding preference can be clearly defined and characterized, despite phylogenetic and allometric effects. Application of this diet-biomechanics linkage model to an analysis of an extinct stem carnivoramorphan and an outgroup creodont species provides biomechanical evidence for the evolution of taxa into distinct hypercarnivorous and generalist feeding styles prior to the appearance of crown carnivoran clades with similar feeding preferences. PMID:25923776

Intraspecific Signals Inducing Aggregation in Periplaneta americana (Insecta: Dictyoptera).

PubMed

Imen, Saïd; Christian, Malosse; Virginie, Durier; Colette, Rivault

2015-06-01

Chemical communication is necessary to induce aggregation and to maintain the cohesion of aggregates in Periplaneta americana (L.) cockroaches. We aimed to identify the chemical message inducing aggregation in this species. Two types of bioassays were used-binary choice tests in Petri dishes and tests in Y-olfactometer. Papers conditioned by direct contact of conspecifics induce aggregation when proposed in binary choice tests and were attractive in a Y-olfactometer. The identification of the molecules present on these conditioned papers indicated that dichloromethane extracts contained mainly cuticular hydrocarbons whereas methanol extracts contained more volatile molecules. Only a mixture of extracts in both solvents induced aggregation. High concentrations of cuticular hydrocarbons are necessary to induce aggregation when presented alone. When presented with volatile molecules present in methanol extracts, low concentrations of cuticular hydrocarbons are sufficient to induce aggregation if they are presented in contact. Among volatile molecules collected on filter paper, a mixture of three compounds-hexadecanoic acid, pentadecanoic acid, and pentaethylene glycol-induced aggregation. Our results provide evidence that aggregation processes in P. americana relies on a dual mechanism: attraction over long distances by three volatile molecules and maintenance on site by contact with cuticular hydrocarbons. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Contribution to a Taxonomic Revision of the Sicilian Helichrysum Taxa by PCA Analysis of Their Essential-Oil Compositions.

PubMed

Maggio, Antonella; Bruno, Maurizio; Guarino, Riccardo; Senatore, Felice; Ilardi, Vincenzo

2016-02-01

The chemical profile of the essential oils in ten populations of the genus Helichrysum Mill. (Asteraceae), collected in the loci classici of the nomenclatural types of the taxa endemic to Sicily, were analyzed. Our results confirm that the analysis of secondary metabolites can be used to fingerprint wild populations of Helichrysum, the chemical profiles being coherent with the systematic arrangement of the investigated populations in three main clusters, referring to the aggregates of H. stoechas, H. rupestre, and H. italicum, all belonging to the section Stoechadina. The correct nomenclatural designation of the investigated populations is discussed and the following two new combinations are proposed: Helichrysum preslianum subsp. compactum (Guss.) Maggio, Bruno, Guarino, Senatore & Ilardi and Helichrysum panormitanum subsp. latifolium Maggio, Bruno, Guarino, Senatore & Ilardi. Copyright © 2016 Verlag Helvetica Chimica Acta AG, Zürich.

Supporting biodiversity by prescribed burning in grasslands - A multi-taxa approach.

PubMed

Valkó, Orsolya; Deák, Balázs; Magura, Tibor; Török, Péter; Kelemen, András; Tóth, Katalin; Horváth, Roland; Nagy, Dávid D; Debnár, Zsuzsanna; Zsigrai, György; Kapocsi, István; Tóthmérész, Béla

2016-12-01

There are contrasting opinions on the use of prescribed burning management in European grasslands. On the one hand, prescribed burning can be effectively used for the management of open landscapes, controlling dominant species, reducing accumulated litter or decreasing wildfire risk. On the other hand burning can have a detrimental impact on grassland biodiversity by supporting competitor grasses and by threatening several rare and endangered species, especially arthropods. We studied the effects of prescribed burning in alkaline grasslands of high conservation interest. Our aim was to test whether dormant-season prescribed burning can be an alternative conservation measure in these grasslands. We selected six sites in East-Hungary: in three sites, a prescribed fire was applied in November 2011, while three sites remained unburnt. We studied the effects of burning on soil characteristics, plant biomass and on the composition of vegetation and arthropod assemblages (isopods, spiders, ground beetles and rove beetles). Soil pH, organic matter, potassium and phosphorous did not change, but soluble salt content increased significantly in the burnt sites. Prescribed burning had several positive effects from the nature conservation viewpoint. Shannon diversity and the number of flowering shoots were higher, and the cover of the dominant grass Festuca pseudovina was lower in the burnt sites. Graminoid biomass was lower, while total, green and forb biomass were higher in the burnt plots compared to the control. The key finding of our study was that prescribed burning did not decrease the abundance and diversity of arthropod taxa. Species-level analyses showed that out of the most abundant invertebrate species, 10 were not affected, 1 was negatively and 1 was positively affected by burning. Moreover, our results suggest that prescribed burning leaving unburnt patches can be a viable management tool in open landscapes, because it supports plant diversity and does not threaten

How territoriality and host-tree taxa determine the structure of ant mosaics.

PubMed

Dejean, Alain; Ryder, Suzanne; Bolton, Barry; Compin, Arthur; Leponce, Maurice; Azémar, Frédéric; Céréghino, Régis; Orivel, Jérôme; Corbara, Bruno

2015-06-01

Very large colonies of territorially dominant arboreal ants (TDAAs), whose territories are distributed in a mosaic pattern in the canopies of many tropical rainforests and tree crop plantations, have a generally positive impact on their host trees. We studied the canopy of an old Gabonese rainforest (ca 4.25 ha sampled, corresponding to 206 "large" trees) at a stage just preceding forest maturity (the Caesalpinioideae dominated; the Burseraceae were abundant). The tree crowns sheltered colonies from 13 TDAAs plus a co-dominant species out of the 25 ant species recorded. By mapping the TDAAs' territories and using a null model co-occurrence analysis, we confirmed the existence of an ant mosaic. Thanks to a large sampling set and the use of the self-organizing map algorithm (SOM), we show that the distribution of the trees influences the structure of the ant mosaic, suggesting that each tree taxon attracts certain TDAA species rather than others. The SOM also improved our knowledge of the TDAAs' ecological niches, showing that these ant species are ecologically distinct from each other based on their relationships with their supporting trees. Therefore, TDAAs should not systematically be placed in the same functional group even when they belong to the same genus. We conclude by reiterating that, in addition to the role played by TDAAs' territorial competition, host trees contribute to structuring ant mosaics through multiple factors, including host-plant selection by TDAAs, the age of the trees, the presence of extrafloral nectaries, and the taxa of the associated hemipterans.

How territoriality and host-tree taxa determine the structure of ant mosaics

NASA Astrophysics Data System (ADS)

Dejean, Alain; Ryder, Suzanne; Bolton, Barry; Compin, Arthur; Leponce, Maurice; Azémar, Frédéric; Céréghino, Régis; Orivel, Jérôme; Corbara, Bruno

2015-06-01

Very large colonies of territorially dominant arboreal ants (TDAAs), whose territories are distributed in a mosaic pattern in the canopies of many tropical rainforests and tree crop plantations, have a generally positive impact on their host trees. We studied the canopy of an old Gabonese rainforest (ca 4.25 ha sampled, corresponding to 206 "large" trees) at a stage just preceding forest maturity (the Caesalpinioideae dominated; the Burseraceae were abundant). The tree crowns sheltered colonies from 13 TDAAs plus a co-dominant species out of the 25 ant species recorded. By mapping the TDAAs' territories and using a null model co-occurrence analysis, we confirmed the existence of an ant mosaic. Thanks to a large sampling set and the use of the self-organizing map algorithm (SOM), we show that the distribution of the trees influences the structure of the ant mosaic, suggesting that each tree taxon attracts certain TDAA species rather than others. The SOM also improved our knowledge of the TDAAs' ecological niches, showing that these ant species are ecologically distinct from each other based on their relationships with their supporting trees. Therefore, TDAAs should not systematically be placed in the same functional group even when they belong to the same genus. We conclude by reiterating that, in addition to the role played by TDAAs' territorial competition, host trees contribute to structuring ant mosaics through multiple factors, including host-plant selection by TDAAs, the age of the trees, the presence of extrafloral nectaries, and the taxa of the associated hemipterans.

When decisions on homologous structures cause ambiguous taxa relationships: the Neomorphinae (Aves, Cuculidae) example.

PubMed

Posso, S R; Donatelli, R J

2010-02-01

The anatomy of Neomorphinae is poorly understood and the systematics of this sub-family is also the most controversial of the cuckoo taxa, mainly with regard to the systematic position of Tapera and Dromococcyx. In this study, morphological similarities of the Neomorphinae are discussed after a comprehensive description of the cranial osteology was conducted in seven species, embracing all the Neomorphinae genera. This description is followed by comparisons with other cuckoos in order to contribute to the anatomy and systematics of this sub-family. In this way, we provide illustrations that enable the osteological descriptions and the proposed primary homologies to be visualised and compared. Even though Neomorphinae species share many cranial osteological characteristics, there are some anatomical divergences that allowed us to divide them into two distinct groups: (Dromococcyx/Tapera) and (Morococcyx(Neomorphus/Geococcyx)). After comparisons among all cuckoos this study suggests that Neomorphinae are more similar to Crotophaginae and Couinae than to other sub-families of cuckoos. Our results contrast with a recent phylogenetic study based on morphological features, mainly because alternative interpretations to the primary osteological homologies in this study grouped Tapera and Dromococcyx with Cuculinae. Although morphological studies can be used in phylogenetic analysis, we demonstrated here that decisions in the interpretation of the homologies can provide ambiguous results.

Seabirds drive plant species turnover on small Mediterranean islands at the expense of native taxa.

PubMed

Vidal, E; Médail, F; Tatoni, T; Bonnet, V

2000-02-01

The analysis of long-term floristic changes was conducted on nine west-Mediterranean limestone islands (size range: 2-95 ha) which have recently undergone a severe demographic explosion in their yellow-legged gull Larus cachinnans colonies. A comparison of past and present plant inventories was used to quantify extinction-colonization events, both from a classical biogeographical perspective (per island approach) and a metapopulational perspective (per species approach). In the first approach, floristic turnover intensity was negatively related to island area and positively to gull nesting density, but was independent of island isolation. In the second, species turnover rate was compared with a set of plant species life history traits (dispersal mode, Grime CSR strategy, growth form, biogeographical type). Plants which exhibited the highest turnover rate were primarily ruderal, annual, wind-dispersed species with a wide geographic range. The severe disturbance induced by seabird activities has tended to select and favour some adapted plant species groups at the expense of indigenous island taxa. The relationships between specific turnover intensity and plant life history traits justify using the metapopulation approach and point to the importance of interspecific variations in extinction-colonization patterns.

Do neighboring lakes share common taxa of bacterioplankton? Comparison of 16S rDNA fingerprints and sequences from three geographic regions.

PubMed

Lindström, E S; Leskinen, E

2002-07-01

Bacterioplankton community composition was studied in 12 lakes in three different geographic regions in Scandinavia using denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rDNA. Area-specific abundant taxa were found in the lakes in two of the regions. In the region of Uppland the lakes had an alpha-proteobacterium, belonging to the subgroup Alpha V in common. The Alpha V bacteria appeared to be favored by neutral or higher pH values. The lakes in Lappland were found to harbor Actinobacteria, which appeared to be favored in bog lakes. No abundant taxon was found to be in common for the lakes in Svalbard, the third region studied.

Temporal and Spatial Variations in Transcriptional Patterns among Closely Related Marine Microbial Taxa

NASA Astrophysics Data System (ADS)

Shilova, I. N.; Robidart, J.; DeLong, E.; Zehr, J. P.

2016-02-01

Marine microbial communities are complex, and even closely related marine microbial populations are genetically and physiologically diverse. Despite such great diversity, conserved and highly synchronized rhythmic transcriptional patterns have been observed in microbial communities worldwide. The current widely used approaches analyzing high-throughput sequence data from microbiomes are not designed to differentiate transcription at strain or ecotype level. We used a novel MicroArray-inspired Gene-Centric (MAGC) bioinformatics approach to discern daily transcription by individual strains in previously analyzed metatranscriptomes from two oceanic regions, California Current System and central North Pacific. The results demonstrated that marine microbial taxa (within cyanobacteria Prochlorococcus and Synechococcus, Alphaproteobacterium Pelagibacter and picoeukaryote Ostreococcus) have unique transcription patterns and respond differentially to variability in space and time in the ocean. For example, the timing of maximum transcription for the photosynthesis and pigments genes varied among Synechococcus strains in the California Current study, likely for optimizing light utilization based on their differences in genetics and physiology. While several Prochlorococcus genotypes were present in the North Pacific study, transcription of the phosphate transporter gene, pstS, in specific genotypes was negatively correlated with phosphate concentrations. These individual transcriptional patterns underlie whole microbial community responses and may be sensitive indicators of environmental conditions, including those associated with long-term environmental change. The MAGC applied here to ocean ecosystems is a promising complementary approach that can enhance the ability to analyze metatranscriptomic data from a variety of environmental microbiomes.

Biological diversity of Salix taxa in Cu, Pb and Zn phytoextraction from soil.

PubMed

Mleczek, Mirosław; Rutkowski, Paweł; Goliński, Piotr; Kaczmarek, Zygmunt; Szentner, Kinga; Waliszewska, Bogusława; Stolarski, Mariusz; Szczukowski, Stefan

2017-02-01

The aim of the study was to estimate the efficiency of copper (Cu), lead (Pb) and zinc (Zn) phytoextraction by 145 Salix taxa cultivated in an area affected by industrial activity. Survivability and biomass of plants were also analyzed. The highest Cu, Pb and Zn content in shoots was 33.38 ± 2.91 (S. purpurea × viminalis 8), 24.64 ± 1.97 (S. fragilis 1) and 58.99 ± 4.30 (S. eriocephala 7) mg kg -1 dry weight, respectively. In the case of unwashed leaves, the highest content of these metals was 135.06 ± 8.14 (S. purpurea 26), 67.98 ± 5.27 (S. purpurea 45) and 142.56 ± 12.69 (S. alba × triandra 2) mg kg -1 dw, while in washed leaves it was 106.02 ± 11.12 (S. purpurea 45), 55.06 ± 5.75 (S. purpurea 45) and 122.87 ± 12.33 (S. alba × triandra 2) mg kg -1 dw, respectively. The differences between the highest and lowest values for Cu, Pb and Zn were 545%, 20500% and 535% in shoots; 2692%, 2560% and 7500% in unwashed leaves; and 3286%, 2221% and 6950% in washed leaves, respectively. S. acutifolia was able to effectively accumulate all three metals jointly, producing shoots that were well developed in both length and diameter when compared with the other tested willows-an ability that would suggest its high suitability for practical application.

Consistency of effects of tropical-forest disturbance on species composition and richness relative to use of indicator taxa.

PubMed

Stork, N E; Srivastava, D S; Eggleton, P; Hodda, M; Lawson, G; Leakey, R R B; Watt, A D

2017-08-01

Lawton et al. (1998) found, in a highly cited study, that the species richness of 8 taxa each responds differently to anthropogenic disturbance in Cameroon forests. Recent developments in conservation science suggest that net number of species is an insensitive measure of change and that understanding which species are affected by disturbance is more important. It is also recognized that all disturbance types are not equal in their effect on species and that grouping species according to function rather than taxonomy is more informative of responses of biodiversity to change. In a reanalysis of most of the original Cameroon data set (canopy and ground ants, termites, canopy beetles, nematodes, and butterflies), we focused on changes in species and functional composition rather than richness and used a more inclusive measure of forest disturbance based on 4 component drivers of change: years since disturbance, tree cover, soil compaction, and degree of tree removal. Effects of disturbance on compositional change were largely concordant between taxa. Contrary to Lawton et al.'s findings, species richness for most groups did not decline with disturbance level, providing support for the view that trends in species richness at local scales do not reflect the resilience of ecosystems to disturbance. Disturbance affected species composition more strongly than species richness for butterflies, canopy beetles, and litter ants. For these groups, disturbance caused species replacements rather than just species loss. Only termites showed effects of disturbance on species richness but not composition, indicating species loss without replacement. Although disturbance generally caused changes in composition, the strength of this relationship depended on the disturbance driver. Butterflies, litter ants, and nematodes were correlated with amount of tree cover, canopy beetles were most strongly correlated with time since disturbance, and termites were most strongly correlated with

Aerobiological study in east-central Iberian Peninsula: pollen diversity and dynamics for major taxa.

PubMed

Pérez-Badia, Rosa; Rapp, Ana; Vaquero, Consolación; Fernández-González, Federico

2011-01-01

A study was made of airborne pollen counts in Cuenca (east-central Iberian Peninsula, Spain), using data obtained over a 3-year period (2008-2010). This is the first such study carried out in the World Heritage city of Cuenca, situated in the large region of Castilla-La Mancha. Air monitoring was performed using the sampling and analysis procedures recommended by the Spanish Aerobiology Network. Sampling commenced in mid- 2007, and provided the first recorded pollen-spectrum for the area. The greatest pollen-type diversity was recorded in spring, whilst the highest pollen counts (over 80 percent of the annual total) were observed between February and June. The lowest counts were found in September, November and December. The 10 leading taxa, in order of abundance, were: Cupressaceae, Quercus, Urticaceae, Pinus, Olea, Poaceae, Populus, Platanus, Chenopodiaceae-Amaranthaceae and Plantago. The pollen calendar was thus typically Mediterrean, and comprised the 27 pollen types reaching 10-day mean counts of over 1 grain/m(3) of air. Maximum concentration values during the day were recorded between 12:00-20:00, coinciding with the highest temperatures and lowest humidity levels. The pollen types responsible for most allergies in the city of Cuenca, ordered by the number of days on which risk levels were reached, were: Poaceae, Urticaceae, Cupressaceae, Olea, Platanus and Chenopodiaceae-Amaranthaceae.

Eucalyptus microfungi known from culture. 1. Cladoriella and Fulvoflamma genera nova, with notes on some other poorly known taxa

PubMed Central

Crous, Pedro W.; Verkley, Gerard J.M.; Groenewald, Johannes Z.

2006-01-01

A study of microfungi associated with living Eucalyptus leaves and leaf litter revealed several novel and interesting taxa. Cladoriella eucalypti gen. et sp. nov. is described as a Cladosporium-like genus associated with litter collected in South Africa, while Fulvoflamma eucalypti gen. et. sp. nov. is newly described from leaf litter collected in Spain. Beta-conidia are newly reported for species of Pestalotiopsis, namely Pestalotiopsis disseminata in New Zealand, and a Pestalotiopsis sp. from Colombia. Satchmopsis brasiliensis is reported from litter in Colombia and Indonesia, while Torrendiella eucalypti is reported from leaf litter in Indonesia, and shown to have a Sporothrix-like anamorph. Leptospora rubella is reported from living Eucalyptus leaves in Colombia, where it is associated with leaf spots of Mycosphaerella longibasalis, while Macrohilum eucalypti is reported from leaf spots of Eucalyptus in New Zealand. PMID:18490971

The Blattodea s.s. (Insecta, Dictyoptera) of the Guiana Shield

PubMed Central

Evangelista, Dominic A.; Chan, Kimberly; Kaplan, Kayla L.; Wilson, Megan M.; Ware, Jessica L.

2015-01-01

Abstract Here we provide a checklist of cockroach species known from areas within the Guiana Shield based on literature records and new field collection. We give records of sixteen species collected in Guyana, eight of which are new records for Guyana and one of which is a new generic record for the entire Guiana Shield. We also provide a description for a geographically disparate species of Calhypnorna Stal, and the new species Xestoblatta berenbaumae. The complete checklist contains 234 species of Blattodea s.s. currently known in the shield. This checklist shows particularly low richness in Guianan Venezuela, Roraima and Amapa Brazil, but this is likely an artifact due to under–sampling. Indeed, based on previously published data and current fieldwork, we believe that most regions of the Guiana Shield are under–sampled for cockroaches. Despite this, French Guiana (151 spp.) and Suriname (136 spp.) rank as the second and sixth most species dense faunas of cockroaches in the neotropics. PMID:25684997

DNA Barcoding for the Identification of Phyllanthus Taxa Used Medicinally in Brazil.

PubMed

Inglis, Peter W; Mata, Lorena R; da Silva, Marcos José; Vieira, Roberto F; Alves, Rosa de B N; Silva, Dijalma B; Azevedo, Vânia C R

2018-06-21

Plants of the genus Phyllanthus, principally Phyllanthus amarus, Phyllanthus urinaria, Phyllanthus niruri , and Phyllanthus tenellus, are used in Brazilian folk medicine to treat kidney stones as well as other ailments, where the latter two species are listed in the Brazilian Pharmacopeia as quebra-pedra ( stone-breaker ). However, only P. niruri has been shown to be effective in a clinical setting. Nuclear ribosomal internal transcribed spacer (ITS1 - 5.8S rRNA-ITS2), internal transcribed spacer 2, and chloroplasts rbc L, mat K, psb A- trn H, trn L, and trn L- trn F were screened for their potential as DNA barcodes for the identification of 48 Phyllanthus taxa in Brazilian medicinal plant germplasm banks and in "living pharmacies". The markers were also tested for their ability to validate four commercial herbal teas labelled as quebra-pedra . Using the criterion of high clade posterior probability in Bayesian phylogenetic analysis, the internal transcribed spacer, internal transcribed spacer 2, and chloroplast mat K, psb A- trn H, trn L, and trn L- trn F markers all reliably differentiated the four Phyllanthus species, with the internal transcribed spacer and mat K possessing the additional advantage that the genus is well represented for these markers in the Genbank database. However, in the case of rbc L, posterior probability for some clades was low and while P. amarus and P. tenellus formed monophyletic groups, P. niruri and P. urinaria accessions could not be reliably distinguished with this marker. Packaged dried quebra-pedra herb from three Brazilian commercial suppliers comprised P. tenellus , but one sample was also found to be mixed with alfalfa ( Medicago sativa ). An herb marketed as quebra-pedra from a fourth supplier was found to be composed of a mixture of Desmodium barbatum and P. niruri . Georg Thieme Verlag KG Stuttgart · New York.

A Metagenomic Assembly-Based Approach to Decoding Taxa in the Dead Zone

NASA Astrophysics Data System (ADS)

Thrash, C.; Baker, B.; Seitz, K.; Gillies, L.; Temperton, B.; Rabalais, N. N.; Mason, O. U.

2016-02-01

Coastal regions of eutrophication-driven oxygen depletion are widespread and increasing in number. Also known as dead zones, these regions take their name from the deleterious effects of hypoxia (dissolved oxygen less than 2 mg/L) on shrimp, demersal fish, and other animal life. Dead zones result from nutrient enrichment of primary production, concomitant consumption by chemoorganotrophic aerobic microorganisms, and strong stratification that prevents ventilation of bottom water. One of the largest dead zones in the world occurs seasonally in the northern Gulf of Mexico (nGOM), where hypoxia can reach up to 22,000 square kilometers. To explore the underlying genomic variation and metabolic potential of microorganisms in hypoxia, we performed metagenomic and metatranscriptomic sequencing on six samples from the 2013 nGOM dead zone from both hypoxic and oxic bottom waters. Over 217 Mb of sequence was assembled into contigs of at least 3 kb with IDBA-UD, with 72 greater than 100 kb, and the largest 495 kb in length. Annotation by IMG recovered over 224 thousand genes in these contigs. Binning with tetra-ESOM and quality filtering based on relative coverage of sample-specific reads led to the recovery of 83 partial to near complete (31 over 70%) high-quality genomes. These metagenomes represent key microbial taxa previously determined to be numerically abundant from 16S rRNA data, such as Thaumarcheaota, Marine Group II Euryarchaeota, SAR406, Synechococcus spp., Actinobacteria, and Planctomycetes. Ongoing work includes the recruitment of metatranscriptomic data to binned contigs for evaluation of relative gene expression, metabolic reconstruction, and comparative genomics with related organisms elsewhere in the global oceans. These data will provide us with detailed information regarding the metabolic potential and activity of many of the key players in the nGOM dead zone.

Physiological typing of Pseudallescheria and Scedosporium strains using Taxa Profile, a semi-automated, 384-well microtitre system.

PubMed

Horré, R; Schaal, K P; Marklein, G; de Hoog, G S; Reiffert, S-M

2011-10-01

During the last few decades, Pseudallescheria and Scedosporium infections in humans are noted with increasing frequency. Multi-drug resistance commonly occurring in this species complex interferes with adequate therapy. Rapid and correct identification of clinical isolates is of paramount significance for optimal treatment in the early stages of infection, while strain typing is necessary for epidemiological purposes. In view of the development of physiological diagnostic parameters, 570 physiological reactions were evaluated using the Taxa Profile Micronaut system, a semi-automatic, computer-assisted, 384-well microtitre platform. Thirty two strains of the Pseudallescheria and Scedosporium complex were analysed after molecular verification of correct species attribution. Of the compounds tested, 254 proved to be polymorphic. Cluster analysis was performed with the Micronaut profile software, which is linked to the ntsypc® program. The systemic opportunist S. prolificans was unambiguously separated from the remaining species. Within the P. boydii/P. apiosperma complex differentiation was noted at the level of individual strains, but no unambiguous parameters for species recognition were revealed. © 2011 Blackwell Verlag GmbH.

Functional characterization of IgA-targeted bacterial taxa from malnourished Malawian children that produce diet-dependent enteropathy

PubMed Central

Kau, Andrew L.; Planer, Joseph D.; Liu, Jie; Rao, Sindhuja; Yatsunenko, Tanya; Trehan, Indi; Manary, Mark J.; Liu, Ta-Chiang; Stappenbeck, Thaddeus S.; Maleta, Kenneth M.; Ashorn, Per; Dewey, Kathryn G.; Houpt, Eric R.; Hsieh, Chyi-Song; Gordon, Jeffrey I.

2015-01-01

To gain insights into the interrelationships among childhood undernutrition, the gut microbiota, and gut mucosal immune/barrier function, we purified bacterial strains targeted by IgA from the fecal microbiota of two cohorts of Malawian infants and children. IgA responses to several bacterial taxa, including Enterobacteriaceae, correlated with anthropometric measurements of nutritional status in longitudinal studies. The relationship between IgA responses and growth was further explained by enteropathogen burden. Gnotobiotic mouse recipients of an IgA+-bacterial consortium purified from the gut microbiota of undernourished children exhibited a diet-dependent enteropathy characterized by rapid disruption of the small intestinal and colonic epithelial barrier, weight loss and sepsis that could be prevented by administering two IgA-targeted bacterial species from a healthy microbiota. Dissection of a culture collection of 11 IgA-targeted strains from an undernourished donor, sufficient to transmit these phenotypes, disclosed that Enterobacteriaceae interacted with other consortium members to produce enteropathy. These findings indicate that bacterial targets of IgA responses have etiologic, diagnostic, and therapeutic implications for childhood undernutrition. PMID:25717097

Does Size Matter? Atmospheric CO2 May Be a Stronger Driver of Stomatal Closing Rate Than Stomatal Size in Taxa That Diversified under Low CO2.

PubMed

Elliott-Kingston, Caroline; Haworth, Matthew; Yearsley, Jon M; Batke, Sven P; Lawson, Tracy; McElwain, Jennifer C

2016-01-01

One strategy for plants to optimize stomatal function is to open and close their stomata quickly in response to environmental signals. It is generally assumed that small stomata can alter aperture faster than large stomata. We tested the hypothesis that species with small stomata close faster than species with larger stomata in response to darkness by comparing rate of stomatal closure across an evolutionary range of species including ferns, cycads, conifers, and angiosperms under controlled ambient conditions (380 ppm CO2; 20.9% O2). The two species with fastest half-closure time and the two species with slowest half-closure time had large stomata while the remaining three species had small stomata, implying that closing rate was not correlated with stomatal size in these species. Neither was response time correlated with stomatal density, phylogeny, functional group, or life strategy. Our results suggest that past atmospheric CO2 concentration during time of taxa diversification may influence stomatal response time. We show that species which last diversified under low or declining atmospheric CO2 concentration close stomata faster than species that last diversified in a high CO2 world. Low atmospheric [CO2] during taxa diversification may have placed a selection pressure on plants to accelerate stomatal closing to maintain adequate internal CO2 and optimize water use efficiency.

Does Size Matter? Atmospheric CO2 May Be a Stronger Driver of Stomatal Closing Rate Than Stomatal Size in Taxa That Diversified under Low CO2

PubMed Central

Elliott-Kingston, Caroline; Haworth, Matthew; Yearsley, Jon M.; Batke, Sven P.; Lawson, Tracy; McElwain, Jennifer C.

2016-01-01

One strategy for plants to optimize stomatal function is to open and close their stomata quickly in response to environmental signals. It is generally assumed that small stomata can alter aperture faster than large stomata. We tested the hypothesis that species with small stomata close faster than species with larger stomata in response to darkness by comparing rate of stomatal closure across an evolutionary range of species including ferns, cycads, conifers, and angiosperms under controlled ambient conditions (380 ppm CO2; 20.9% O2). The two species with fastest half-closure time and the two species with slowest half-closure time had large stomata while the remaining three species had small stomata, implying that closing rate was not correlated with stomatal size in these species. Neither was response time correlated with stomatal density, phylogeny, functional group, or life strategy. Our results suggest that past atmospheric CO2 concentration during time of taxa diversification may influence stomatal response time. We show that species which last diversified under low or declining atmospheric CO2 concentration close stomata faster than species that last diversified in a high CO2 world. Low atmospheric [CO2] during taxa diversification may have placed a selection pressure on plants to accelerate stomatal closing to maintain adequate internal CO2 and optimize water use efficiency. PMID:27605929

Contrasting Taxonomic and Phylogenetic Diversity Responses to Forest Modifications: Comparisons of Taxa and Successive Plant Life Stages in South African Scarp Forest

PubMed Central

Grass, Ingo; Brandl, Roland; Botzat, Alexandra; Neuschulz, Eike Lena; Farwig, Nina

2015-01-01

The degradation of natural forests to modified forests threatens subtropical and tropical biodiversity worldwide. Yet, species responses to forest modification vary considerably. Furthermore, effects of forest modification can differ, whether with respect to diversity components (taxonomic or phylogenetic) or to local (α-diversity) and regional (β-diversity) spatial scales. This real-world complexity has so far hampered our understanding of subtropical and tropical biodiversity patterns in human-modified forest landscapes. In a subtropical South African forest landscape, we studied the responses of three successive plant life stages (adult trees, saplings, seedlings) and of birds to five different types of forest modification distinguished by the degree of within-forest disturbance and forest loss. Responses of the two taxa differed markedly. Thus, the taxonomic α-diversity of birds was negatively correlated with the diversity of all plant life stages and, contrary to plant diversity, increased with forest disturbance. Conversely, forest disturbance reduced the phylogenetic α-diversity of all plant life stages but not that of birds. Forest loss neither affected taxonomic nor phylogenetic diversity of any taxon. On the regional scale, taxonomic but not phylogenetic β-diversity of both taxa was well predicted by variation in forest disturbance and forest loss. In contrast to adult trees, the phylogenetic diversity of saplings and seedlings showed signs of contemporary environmental filtering. In conclusion, forest modification in this subtropical landscape strongly shaped both local and regional biodiversity but with contrasting outcomes. Phylogenetic diversity of plants may be more threatened than that of mobile species such as birds. The reduced phylogenetic diversity of saplings and seedlings suggests losses in biodiversity that are not visible in adult trees, potentially indicating time-lags and contemporary shifts in forest regeneration. The different

Controlling cyanobacterial blooms in hypertrophic Lake Taihu, China: will nitrogen reductions cause replacement of non-N2 fixing by N2 fixing taxa?

PubMed

Paerl, Hans W; Xu, Hai; Hall, Nathan S; Zhu, Guangwei; Qin, Boqiang; Wu, Yali; Rossignol, Karen L; Dong, Linghan; McCarthy, Mark J; Joyner, Alan R

2014-01-01

Excessive anthropogenic nitrogen (N) and phosphorus (P) inputs have caused an alarming increase in harmful cyanobacterial blooms, threatening sustainability of lakes and reservoirs worldwide. Hypertrophic Lake Taihu, China's third largest freshwater lake, typifies this predicament, with toxic blooms of the non-N2 fixing cyanobacteria Microcystis spp. dominating from spring through fall. Previous studies indicate N and P reductions are needed to reduce bloom magnitude and duration. However, N reductions may encourage replacement of non-N2 fixing with N2 fixing cyanobacteria. This potentially counterproductive scenario was evaluated using replicate, large (1000 L), in-lake mesocosms during summer bloom periods. N+P additions led to maximum phytoplankton production. Phosphorus enrichment, which promoted N limitation, resulted in increases in N2 fixing taxa (Anabaena spp.), but it did not lead to significant replacement of non-N2 fixing with N2 fixing cyanobacteria, and N2 fixation rates remained ecologically insignificant. Furthermore, P enrichment failed to increase phytoplankton production relative to controls, indicating that N was the most limiting nutrient throughout this period. We propose that Microcystis spp. and other non-N2 fixing genera can maintain dominance in this shallow, highly turbid, nutrient-enriched lake by outcompeting N2 fixing taxa for existing sources of N and P stored and cycled in the lake. To bring Taihu and other hypertrophic systems below the bloom threshold, both N and P reductions will be needed until the legacy of high N and P loading and sediment nutrient storage in these systems is depleted. At that point, a more exclusive focus on P reductions may be feasible.

Controlling Cyanobacterial Blooms in Hypertrophic Lake Taihu, China: Will Nitrogen Reductions Cause Replacement of Non-N2 Fixing by N2 Fixing Taxa?

PubMed Central

Paerl, Hans W.; Xu, Hai; Hall, Nathan S.; Zhu, Guangwei; Qin, Boqiang; Wu, Yali; Rossignol, Karen L.; Dong, Linghan; McCarthy, Mark J.; Joyner, Alan R.

2014-01-01

Excessive anthropogenic nitrogen (N) and phosphorus (P) inputs have caused an alarming increase in harmful cyanobacterial blooms, threatening sustainability of lakes and reservoirs worldwide. Hypertrophic Lake Taihu, China’s third largest freshwater lake, typifies this predicament, with toxic blooms of the non-N2 fixing cyanobacteria Microcystis spp. dominating from spring through fall. Previous studies indicate N and P reductions are needed to reduce bloom magnitude and duration. However, N reductions may encourage replacement of non-N2 fixing with N2 fixing cyanobacteria. This potentially counterproductive scenario was evaluated using replicate, large (1000 L), in-lake mesocosms during summer bloom periods. N+P additions led to maximum phytoplankton production. Phosphorus enrichment, which promoted N limitation, resulted in increases in N2 fixing taxa (Anabaena spp.), but it did not lead to significant replacement of non-N2 fixing with N2 fixing cyanobacteria, and N2 fixation rates remained ecologically insignificant. Furthermore, P enrichment failed to increase phytoplankton production relative to controls, indicating that N was the most limiting nutrient throughout this period. We propose that Microcystis spp. and other non-N2 fixing genera can maintain dominance in this shallow, highly turbid, nutrient-enriched lake by outcompeting N2 fixing taxa for existing sources of N and P stored and cycled in the lake. To bring Taihu and other hypertrophic systems below the bloom threshold, both N and P reductions will be needed until the legacy of high N and P loading and sediment nutrient storage in these systems is depleted. At that point, a more exclusive focus on P reductions may be feasible. PMID:25405474

A pest is a pest is a pest? The dilemma of neotropical leaf-cutting ants: Keystone taxa of natural ecosystems

NASA Astrophysics Data System (ADS)

Fowler, Harold G.; Pagani, Maria Inez; da Silva, Osvaldo Aulino; Forti, Luis Carlos; da Silva, Virgilio Pereira; de Vasconcelos, Heraldo Luis

1989-11-01

Leaf-cutting ants of the genera Acromyrmex and Atta are considered the principal polyphagous pests of the Neotropics Although some members of these genera are of economic importance, have a broad geographic distribution, and are extremely good colonizers, others are endemic and closely interact with native ecosystems. Control is generally practiced against any colony, irrespective of its taxonomic status. Indiscriminate control coupled with habitat destruction threatens endemic species with extinction, and, through habitat simplification, favors other pest species. As nests of Atta are large, having several square meters of nest surface, the endemic taxa can be easily used as environmental indicators for natural ecosystems Likewise, the pest species can be used to detect environmental disturbance As these ants are keystone species and easily identified by nonspecialists, efforts should be made to integrate these into viable conservation programs

The Evolution of Diapsid Reproductive Strategy with Inferences about Extinct Taxa.

PubMed

Moore, Jason R; Varricchio, David J

2016-01-01

Diapsids show an extremely wide range of reproductive strategies. Offspring may receive no parental care, care from only one sex, care from both parents, or care under more complex regimes. Young may vary from independent, super-precocial hatchlings to altricial neonates needing much care before leaving the nest. Parents can invest heavily in a few young, or less so in a larger number. Here we examine the evolution of these traits across a composite phylogeny spanning the extant diapsids and including the limited number of extinct taxa for which reproductive strategies can be well constrained. Generalized estimating equation(GEE)-based phylogenetic comparative methods demonstrate the influences of body mass, parental care strategy and hatchling maturity on clutch volume across the diapsids. The influence of polygamous reproduction is not important despite a large sample size. Applying the results of these models to the dinosaurs supports the hypothesis of paternal care (male only) in derived non-avian theropods, previously suggested based on simpler analyses. These data also suggest that sauropodomorphs did not care for their young. The evolution of parental-care occurs in an almost linear series of transitions. Paternal care rarely gives rise to other care strategies. Where hatchling condition changes, diapsids show an almost unidirectional tendency of evolution towards increased altriciality. Transitions to social monogamy from the ancestral state in diapsids, where both sexes are polygamous, are common. In contrast, once evolved, polygyny and polyandry are very evolutionarily stable. Polygyny and maternal care correlate, as do polyandry and paternal care. Ancestral-character estimation (ACE) of these care strategies with the character transition likelihoods estimated from the original data gives good confidence at most important nodes. These analyses suggest that the basalmost diapsids had no parental care. Crocodilians independently evolved maternal care

The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa.

PubMed

Viver, Tomeu; Orellana, Luis H; Hatt, Janet K; Urdiain, Mercedes; Díaz, Sara; Richter, Michael; Antón, Josefa; Avian, Massimo; Amann, Rudolf; Konstantinidis, Konstantinos T; Rosselló-Móra, Ramon

2017-08-01

Cotylorhiza tuberculata is an important scyphozoan jellyfish producing population blooms in the Mediterranean probably due to pelagic ecosystem's decay. Its gastric cavity can serve as a simple model of microbial-animal digestive associations, yet poorly characterized. Using state-of-the-art metagenomic population binning and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), we show that only four novel clonal phylotypes were consistently associated with multiple jellyfish adults. Two affiliated close to Spiroplasma and Mycoplasma genera, one to chlamydial 'Candidatus Syngnamydia', and one to bacteroidetal Tenacibaculum, and were at least one order of magnitude more abundant than any other bacteria detected. Metabolic modelling predicted an aerobic heterotrophic lifestyle for the chlamydia, which were found intracellularly in Onychodromopsis-like ciliates. The Spiroplasma-like organism was predicted to be an anaerobic fermenter associated to some jellyfish cells, whereas the Tenacibaculum-like as free-living aerobic heterotroph, densely colonizing the mesogleal axis inside the gastric filaments. The association between the jellyfish and its reduced microbiome was close and temporally stable, and possibly related to food digestion and protection from pathogens. Based on the genomic and microscopic data, we propose three candidate taxa: 'Candidatus Syngnamydia medusae', 'Candidatus Medusoplasma mediterranei' and 'Candidatus Tenacibaculum medusae'. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Stable nitrogen and carbon isotope (δ 15N and δ 13C) variability in shallow tropical Pacific soft coral and black coral taxa and implications for paleoceanographic reconstructions

NASA Astrophysics Data System (ADS)

Williams, Branwen; Grottoli, Andréa G.

2010-09-01

Soft corals and black corals are useful proxy tools for paleoceanographic reconstructions. However, most work has focused on deep-water taxa and few studies have used these corals as proxy organisms in shallow water (<200 m). To facilitate the use of stable nitrogen and carbon isotope (δ 15N and δ 13C) records from shallow-water soft coral and black coral taxa for paleoceanographic reconstructions, quantification of the inherent variability in skeletal isotope values between sites, across depth, and among taxa is needed. Here, skeletal δ 15N and δ 13C values were measured in multiple colonies from eleven genera of soft corals and two genera of black corals from across a depth transect (5-105 m) at two sites in Palau located in the tropical western Pacific Ocean. Overall, no difference in skeletal δ 15N and δ 13C values between sites was present. Skeletal δ 15N values significantly increased and δ 13C values decreased with depth. This is consistent with changes in isotope values of suspended particulate organic matter (POM) across the photic zone, suggesting that the primary food source to these corals is suspended POM and that the stable isotopic composition of POM controls the skeletal isotopic composition of these corals. Thus, to compare the isotope records of corals collected across a depth range in the photic zone, first order depth corrections of -0.013‰ m -1 and +0.023‰ m -1 are recommended for δ 15N and δ 13C, respectively. Average depth-corrected δ 15N values were similar between black corals and soft corals, indicating that corals in these orders feed at a similar trophic level. In contrast, average depth-corrected δ 13C values of black corals were significantly lower than that of soft corals, potentially resulting from metabolic processes associated with differing skeletal compositions among the orders (i.e., gorgonin vs. chitin based). Thus, a correction of +1.0‰ is recommended for black corals when comparing their δ 13C-based proxy

A comparative study on the antinociceptive and anti-inflammatory activities of five Juniperus taxa.

PubMed

Akkol, Esra Küpeli; Güvenç, Ayşegül; Yesilada, Erdem

2009-09-07

Juniperus L. (Cupressaceae) species have been used to various inflammatory and infectious diseases such as bronchitis, colds, cough, fungal infections, hemorrhoids, gynecological diseases, and wounds in Turkish folk medicine. To evaluate this traditional information, anti-inflammatory and antinociceptive activities of the methanolic and aqueous extracts prepared from different parts (stem, fruit and leaves) of the five Turkish taxa under Juniperus section of the gender; J. drupacea, J. communis var. communis, J. communis var. saxatilis, J. oxycedrus subsp. oxycedrus, and J. oxycedrus subsp. macrocarpa growing were investigated. For the anti-inflammatory activity, carrageenan-induced and PGE(2)-induced hind paw edema models, and for the antinociceptive activity p-benzoquinone-induced writhing and hot plate tests in mice were employed. The methanolic extracts of fruit and leaves from J. oxycedrus subsp. oxycedrus and J. communis var. saxatilis exhibited notable inhibition in carrageenan-induced edema model at a dose of 100mg/kg. The same extracts also displayed significant activity against PGE(2)-induced edema model. While, the remaining extracts were found inactive against these edema models. A similar activity pattern was observed against p-benzoquinone-induced abdominal constriction test without inducing any gastric damage or apparent acute toxicity, whereas all extracts were inactive in hot plate test. The experimental data demonstrated that J. oxycedrus subsp. oxycedrus and J. communis var. saxatilis displayed remarkable anti-inflammatory and antinociceptive activities; however, further studies are warranted to define and isolate the active anti-inflammatory and antinociceptive components from these active species which may yield safe and effective agents to be used in the treatment of inflammatory disorders.

Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy.

PubMed

Kau, Andrew L; Planer, Joseph D; Liu, Jie; Rao, Sindhuja; Yatsunenko, Tanya; Trehan, Indi; Manary, Mark J; Liu, Ta-Chiang; Stappenbeck, Thaddeus S; Maleta, Kenneth M; Ashorn, Per; Dewey, Kathryn G; Houpt, Eric R; Hsieh, Chyi-Song; Gordon, Jeffrey I

2015-02-25

To gain insights into the interrelationships among childhood undernutrition, the gut microbiota, and gut mucosal immune/barrier function, we purified bacterial strains targeted by immunoglobulin A (IgA) from the fecal microbiota of two cohorts of Malawian infants and children. IgA responses to several bacterial taxa, including Enterobacteriaceae, correlated with anthropometric measurements of nutritional status in longitudinal studies. The relationship between IgA responses and growth was further explained by enteropathogen burden. Gnotobiotic mouse recipients of an IgA(+) bacterial consortium purified from the gut microbiota of undernourished children exhibited a diet-dependent enteropathy characterized by rapid disruption of the small intestinal and colonic epithelial barrier, weight loss, and sepsis that could be prevented by administering two IgA-targeted bacterial species from a healthy microbiota. Dissection of a culture collection of 11 IgA-targeted strains from an undernourished donor, sufficient to transmit these phenotypes, disclosed that Enterobacteriaceae interacted with other consortium members to produce enteropathy. These findings indicate that bacterial targets of IgA responses have etiologic, diagnostic, and therapeutic implications for childhood undernutrition. Copyright © 2015, American Association for the Advancement of Science.

Alt a 1 allergen homologs from Alternaria and related taxa: analysis of phylogenetic content and secondary structure.

PubMed

Hong, Soon Gyu; Cramer, Robert A; Lawrence, Christopher B; Pryor, Barry M

2005-02-01

A gene for the Alternaria major allergen, Alt a 1, was amplified from 52 species of Alternaria and related genera, and sequence information was used for phylogenetic study. Alt a 1 gene sequences evolved 3.8 times faster and contained 3.5 times more parsimony-informative sites than glyceraldehyde-3-phosphate dehydrogenase (gpd) sequences. Analyses of Alt a 1 gene and gpd exon sequences strongly supported grouping of Alternaria spp. and related taxa into several species-groups described in previous studies, especially the infectoria, alternata, porri, brassicicola, and radicina species-groups and the Embellisia group. The sonchi species-group was newly suggested in this study. Monophyly of the Nimbya group was moderately supported, and monophyly of the Ulocladium group was weakly supported. Relationships among species-groups and among closely related species of the same species-group were not fully resolved. However, higher resolution could be obtained using Alt a 1 sequences or a combined dataset than using gpd sequences alone. Despite high levels of variation in amino acid sequences, results of in silico prediction of protein secondary structure for Alt a 1 demonstrated a high degree of structural similarity for most of the species suggesting a conservation of function.

[Ants’ higher taxa as surrogates of species richness in a chronosequence of fallows, old-grown forests and agroforestry systems in the Eastern Amazon, Brazil].

PubMed

Muñoz Gutiérrez, Jhonatan Andrés; Roussea, Guillaume Xavier; Andrade-Silva, Joudellys; Delabie, Jacques Hubert Charles

2017-03-01

Deforestation in Amazon forests is one of the main causes for biodiversity loss worldwide. Ants are key into the ecosystem because act like engineers; hence, the loss of ants’ biodiversity may be a guide to measure the loss of essential functions into the ecosystems. The aim of this study was to evaluate soil ant’s richness and to estimate whether higher taxa levels (Subfamily and Genus) can be used as surrogates of species richness in different vegetation types (fallows, old-growth forests and agroforestry systems) in Eastern Amazon. The samples were taken in 65 areas in the Maranhão and Pará States in the period 2011-2014. The sampling scheme followed the procedure of Tropical Soil Biology and Fertility (TSBF). Initially, the vegetation types were characterized according to their age and estimated species richness. Linear and exponential functions were applied to evaluate if higher taxa can be used as surrogates and correlated with the Pearson coefficient. In total, 180 species distributed in 60 genera were identified. The results showed that ant species richness was higher in intermediate fallows (88) and old secondary forest (76), and was lower in agroforestry systems (38) and mature riparian forest (35). The genus level was the best surrogate to estimate the ant’s species richness across the different vegetation types, and explained 72-97 % (P < 0.001) of the total species variability. The results confirmed that the genus level is an excellent surrogate to estimate the ant’s species richness in the region and that both fallows and agroforestry systems may contribute in the conservation of Eastern Amazon ant community.

A modern plant-climate research dataset for modelling eastern North American plant taxa.

NASA Astrophysics Data System (ADS)

Gonzales, L. M.; Grimm, E. C.; Williams, J. W.; Nordheim, E. V.

2008-12-01

Continental-scale modern pollen-climate data repositories are a primary data source for paleoclimate reconstructions. However, these repositories can contain artifacts, such as records from different depositional environment and replicate records, that can influence the observed pollen-climate relationships as well as the paleoclimate reconstructions derived from these relationships. In this paper, we address the issues related to these artifacts as we define the methods used to create a research dataset from the North American Modern Pollen Database (Whitmore et al., 2005). Additionally, we define the methods used to select the environmental variables that are best for modeling regional pollen-climate relationships from the research dataset. Because the depositional environment determines the relative strengths of the local and regional pollen signals, combining data from different depositional environments results in pollen abundances that can be influenced by the local pollen signal. Replicate records in pollen-climate datasets can skew pollen-climate relationships by causing an over- or under- representation of pollen abundances in climate space. When these two artifacts are combined, the errors introduced into pollen-climate relationship modeling are compounded. The research dataset we present consists of 2,613 records in eastern North America, of which 70.9% are lacustrine sites. We demonstrate that this new research database improves upon the modeling of regional pollen-climate relationships for eastern North American taxa. The research dataset encompasses the majority of the temperature and mean summer precipitation ranges of the NAMPD's climatic range and 40% of its mean winter precipitation range. NAMPD sites with higher winter precipitation are located along the northwestern coast of North America where a rainshadow effect produces abundant winter precipitation. We present our analysis of the research dataset for use in paleoclimate reconstructions, and

Large-scale gene flow in the barnacle Jehlius cirratus and contrasts with other broadly-distributed taxa along the Chilean coast

PubMed Central

Guo, Baoying

2017-01-01

We evaluate the population genetic structure of the intertidal barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from over 3,000 km of the linear range of this species, there is only slight regional structure indicated, with overall Φ CT of 0.036 (p < 0.001) yet no support for isolation by distance. While these results suggest greater structure than previous studies of J. cirratus had indicated, the pattern of diversity is still far more subtle than in other similarly-distributed species with similar larval and life history traits. We compare these data and results with recent findings in four other intertidal species that have planktotrophic larvae. There are no clear patterns among these taxa that can be associated with intertidal depth or other known life history traits. PMID:28194316

Hierarchical multi-taxa models inform riparian vs. hydrologic restoration of urban streams in a permeable landscape.

PubMed

Gwinn, Daniel C; Middleton, Jen A; Beesley, Leah; Close, Paul; Quinton, Belinda; Storer, Tim; Davies, Peter M

2018-03-01

The degradation of streams caused by urbanization tends to follow predictable patterns; however, there is a growing appreciation for heterogeneity in stream response to urbanization due to the local geoclimatic context. Furthermore, there is building evidence that streams in mildly sloped, permeable landscapes respond uncharacteristically to urban stress calling for a more nuanced approach to restoration. We evaluated the relative influence of local-scale riparian characteristics and catchment-scale imperviousness on the macroinvertebrate assemblages of streams in the flat, permeable urban landscape of Perth, Western Australia. Using a hierarchical multi-taxa model, we predicted the outcomes of stylized stream restoration strategies to increase the riparian integrity at the local scale or decrease the influences of imperviousness at the catchment scale. In the urban streams of Perth, we show that local-scale riparian restoration can influence the structure of macroinvertebrate assemblages to a greater degree than managing the influences of catchment-scale imperviousness. We also observed an interaction between the effect of riparian integrity and imperviousness such that the effect of increased riparian integrity was enhanced at lower levels of catchment imperviousness. This study represents one of few conducted in flat, permeable landscapes and the first aimed at informing urban stream restoration in Perth, adding to the growing appreciation for heterogeneity of the Urban Stream Syndrome and its importance for urban stream restoration. © 2017 by the Ecological Society of America.

Influence of taxa, trophic level, and location on bioaccumulation of toxic metals in bird's feathers: a preliminary biomonitoring study using multiple bird species from Pakistan.

PubMed

Abbasi, Naeem Akhtar; Jaspers, Veerle Leontina Bernard; Chaudhry, Muhammad Jamshed Iqbal; Ali, Sakhawat; Malik, Riffat Naseem

2015-02-01

Increasing concentrations of heavy metals in the environment and their effects on ecosystems and biota is still an imminent threat, particularly in developing parts of the globe. The aim of the present study was to screen the heavy metal concentrations in multiple bird species across Pakistan and to preliminary evaluate the influence of taxa, trophic level, and geographical location on heavy metal accumulation in various bird species. For this purpose, we measured the concentration of 9 heavy metals (Pb, Cd, Cr, Ni, Co, Cu, Fe, Zn and Mn) in feathers of 48 bird species from different localities in Pakistan. Species exhibited heterogeneous levels of heavy metals in feathers with marked inter and intra specific variations. Mean concentrations of studied metals in feathers followed the trend Fe>Zn>Cu>Pb>Mn>Cr>Ni>Co>Cd. Species belonging to closely related taxa (families) showed comparable metal concentrations in their feathers, inferring potential phylogenetic similarities in metal exposure or accumulation. In general, concentrations of metals were greatest in carnivorous species followed by omnivorous and insectivorous birds, and granivores showing minimal levels (p<0.000). Furthermore, concentrations of metals varied significantly between locations (p<0.000) exhibiting highest concentrations in Punjab province and Baluchistan, probably due to higher industrial and agricultural activity and runoff, respectively. With certain limitation, influence of trophic level, taxonomic affiliation and sampling location of birds on toxic metal accumulation was also statistically corroborated through principal component analysis (PCA). This study highlights that despite restricted emissions, heavy metals persist in the local environment and may pose elevated risks for the studied bird species in Pakistan. Copyright © 2014 Elsevier Ltd. All rights reserved.

Shared Epizoic Taxa and Differences in Diatom Community Structure Between Green Turtles (Chelonia mydas) from Distant Habitats.

PubMed

Majewska, Roksana; de Vijver, Bart Van; Nasrolahi, Ali; Ehsanpour, Maryam; Afkhami, Majid; Bolaños, Federico; Iamunno, Franco; Santoro, Mario; De Stefano, Mario

2017-11-01

The first reports of diatoms growing on marine mammals date back to the early 1900s. However, only recently has direct evidence been provided for similar associations between diatoms and sea turtles. We present a comparison of diatom communities inhabiting carapaces of green turtles Chelonia mydas sampled at two remote sites located within the Indian (Iran) and Atlantic (Costa Rica) Ocean basins. Diatom observations and counts were carried out using scanning electron microscopy. Techniques involving critical point drying enabled observations of diatoms and other microepibionts still attached to sea turtle carapace and revealed specific aspects of the epizoic community structure. Species-poor, well-developed diatom communities were found on all examined sea turtles. Significant differences between the two host sea turtle populations were observed in terms of diatom abundance and their community structure (including growth form structure). A total of 12 and 22 diatom taxa were found from sea turtles in Iran and Costa Rica, respectively, and eight of these species belonging to Amphora, Chelonicola, Cocconeis, Navicula, Nitzschia and Poulinea genera were observed in samples from both locations. Potential mechanisms of diatom dispersal and the influence of the external environment, sea turtle behaviour, its life stage, and foraging and breeding habitats, as well as epibiotic bacterial flora on epizoic communities, are discussed.

[Effect of sampling effort on taxa richness of aquatic macroinvertebrates and the BMWP/Atitlán index].

PubMed

Reyes-Morales, Fátima; Springer, Monika

2014-04-01

Aquatic macroinvertebrates are the group of organisms most commonly used to determine ecosystem health in water quality studies and freshwater biomonitoring. Nevertheless, the methods and collecting time of biomonitoring have not yet been sufficiently adapted and tested in tropical aquatic environments. Twelve rivers in the Lago de Atitlán watershed in Guatemala were assessed with different collecting times, during the dry season. The method involved the collection of organic and inorganic material including benthic organisms, from different microhabitats, for a pre-established time period (5, 10, 15 min) with a D-frame net. Samples were preserved with 95% ethanol in the field, and sorted in the laboratory. As expected, the analysis showed that the abundance and taxonomic richness was higher with increasing sampling effort. The water quality categories obtained from the newly proposed BMWP/Atitlán index varied among sampling times. However, the Kruskal-Wallis test showed no significant differences between the categories obtained with the index and the number of taxa collected at 10 and 15 min. Therefore, we recommend a reduction of sample time, but maintaining the tree subsamples in order to include most variety of microhabitats and assure a representative sample of the aquatic macroinvertebrates.

Evolutionary history of freshwater sculpins, genus Cottus (Teleostei; Cottidae) and related taxa, as inferred from mitochondrial DNA phylogeny.

PubMed

Yokoyama, Ryota; Goto, Akira

2005-09-01

The freshwater sculpins, genus Cottus (Teleostei; Cottidae), comprise bottom-dwelling fishes that exhibit various life-history styles, having radiated throughout Northern Hemisphere freshwater habitats. The phylogenetic relationships among Cottus and related taxa were estimated from mitochondrial DNA 12S rRNA and control region (CR) sequences, the freshwater sculpins examined falling into five lineages (A-E). Lineage A consisted of Trachidermus fasciatus and C. kazika, both having a catadromous life-history. The remaining species (lineages B-E) spawn in freshwater habitats regardless of life-history (amphidromous, lacustrine or fluvial), suggesting that the various life-history types post-dated a common ancestor of lineages B-E. Molecular clock estimates suggested a Pliocene-Pleistocene radiation (or Miocene-Pliocene from the alternative clock) of lineages B-E. In eastern Eurasia, speciation with life-history changes to amphidromous or fluvial styles has apparently occurred independently in some lineages, as a general pattern. Mitochondrial DNA CR phylogeny showed the monophyletic Baikalian cottoids (Cottoidei) to be nested within Cottus and Trachidermus, suggesting that the former ecologically and morphologically divergent cottoids may have originated from a single lineage which invaded the ancient lake.

Identification of evolutionary hotspots based on genetic data from multiple terrestrial and aquatic taxa and gap analysis of hotspots in protected lands encompassed by the South Atlantic Landscape Conservation Cooperative.

USGS Publications Warehouse

Robinson, J.; Snider, M.; Duke, J.; Moyer, G.R.

2014-01-01

 The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction . Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands w h ere an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa , many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest (displaying varying levels of genetic divergence and greater than average levels of genetic diversity) and a large portion of the coastal regions of North and South Carolina

Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: a case study with the lizard Anolis roosevelti.

PubMed

Revell, Liam J; Mahler, D Luke; Reynolds, R Graham; Slater, Graham J

2015-04-01

In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from tissue collections, or are unavailable for molecular analysis for other reasons such as restrictive biological sample export laws. Other species went extinct recently and are only available in formalin museum preparations or perhaps even as subfossils. In this brief communication we present a new method for placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny of extant taxa using continuous character data. This method is based on a relatively simple modification of an established maximum likelihood (ML) method for phylogeny inference from continuous traits. We show that the method works well on simulated trees and data. We then apply it to the case of placing the Culebra Island Giant Anole (Anolis roosevelti) into a phylogeny of Caribbean anoles. Anolis roosevelti is a "crown-giant" ecomorph anole hypothesized to have once been found throughout the Spanish, United States, and British Virgin Islands, but that has not been encountered or collected since the 1930s. Although this species is widely thought to be closely related to the Puerto Rican giant anole, A. cuvieri, our ML method actually places A. roosevelti in a different part of the tree and closely related to a clade of morphologically similar species. We are unable, however, to reject a phylogenetic position for A. roosevelti that places it as sister taxon to A. cuvieri; although close relationship with the remainder of Puerto Rican anole species is strongly rejected by our method. �

Evaluating green infrastructure in urban environments using a multi-taxa and functional diversity approach.

PubMed

Pinho, Pedro; Correia, Otília; Lecoq, Miguel; Munzi, Silvana; Vasconcelos, Sasha; Gonçalves, Paula; Rebelo, Rui; Antunes, Cristina; Silva, Patrícia; Freitas, Catarina; Lopes, Nuno; Santos-Reis, Margarida; Branquinho, Cristina

2016-05-01

Forested areas within cities host a large number of species, responsible for many ecosystem services in urban areas. The biodiversity in these areas is influenced by human disturbances such as atmospheric pollution and urban heat island effect. To ameliorate the effects of these factors, an increase in urban green areas is often considered sufficient. However, this approach assumes that all types of green cover have the same importance for species. Our aim was to show that not all forested green areas are equal in importance for species, but that based on a multi-taxa and functional diversity approach it is possible to value green infrastructure in urban environments. After evaluating the diversity of lichens, butterflies and other-arthropods, birds and mammals in 31 Mediterranean urban forests in south-west Europe (Almada, Portugal), bird and lichen functional groups responsive to urbanization were found. A community shift (tolerant species replacing sensitive ones) along the urbanization gradient was found, and this must be considered when using these groups as indicators of the effect of urbanization. Bird and lichen functional groups were then analyzed together with the characteristics of the forests and their surroundings. Our results showed that, contrary to previous assumptions, vegetation density and more importantly the amount of urban areas around the forest (matrix), are more important for biodiversity than forest quantity alone. This indicated that not all types of forested green areas have the same importance for biodiversity. An index of forest functional diversity was then calculated for all sampled forests of the area. This could help decision-makers to improve the management of urban green infrastructures with the goal of increasing functionality and ultimately ecosystem services in urban areas. Copyright © 2016 Elsevier Inc. All rights reserved.

Impacts of invasive plants on resident animals across ecosystems, taxa, and feeding types: a global assessment.

PubMed

Schirmel, Jens; Bundschuh, Mirco; Entling, Martin H; Kowarik, Ingo; Buchholz, Sascha

2016-02-01

As drivers of global change, biological invasions have fundamental ecological consequences. However, it remains unclear how invasive plant effects on resident animals vary across ecosystems, animal classes, and functional groups. We performed a comprehensive meta-analysis covering 198 field and laboratory studies reporting a total of 3624 observations of invasive plant effects on animals. Invasive plants had reducing (56%) or neutral (44%) effects on animal abundance, diversity, fitness, and ecosystem function across different ecosystems, animal classes, and feeding types while we could not find any increasing effect. Most importantly, we found that invasive plants reduced overall animal abundance, diversity and fitness. However, this significant overall effect was contingent on ecosystems, taxa, and feeding types of animals. Decreasing effects of invasive plants were most evident in riparian ecosystems, possibly because frequent disturbance facilitates more intense plant invasions compared to other ecosystem types. In accordance with their immediate reliance on plants for food, invasive plant effects were strongest on herbivores. Regarding taxonomic groups, birds and insects were most strongly affected. In insects, this may be explained by their high frequency of herbivory, while birds demonstrate that invasive plant effects can also cascade up to secondary consumers. Since data on impacts of invasive plants are rather limited for many animal groups in most ecosystems, we argue for overcoming gaps in knowledge and for a more differentiated discussion on effects of invasive plant on native fauna. © 2015 John Wiley & Sons Ltd.

Ciliate diversity, community structure, and novel taxa in lakes of the McMurdo Dry Valleys, Antarctica.

PubMed

Xu, Yuan; Vick-Majors, Trista; Morgan-Kiss, Rachael; Priscu, John C; Amaral-Zettler, Linda

2014-10-01

We report an in-depth survey of next-generation DNA sequencing of ciliate diversity and community structure in two permanently ice-covered McMurdo Dry Valley lakes during the austral summer and autumn (November 2007 and March 2008). We tested hypotheses on the relationship between species richness and environmental conditions including environmental extremes, nutrient status, and day length. On the basis of the unique environment that exists in these high-latitude lakes, we expected that novel taxa would be present. Alpha diversity analyses showed that extreme conditions-that is, high salinity, low oxygen, and extreme changes in day length-did not impact ciliate richness; however, ciliate richness was 30% higher in samples with higher dissolved organic matter. Beta diversity analyses revealed that ciliate communities clustered by dissolved oxygen, depth, and salinity, but not by season (i.e., day length). The permutational analysis of variance test indicated that depth, dissolved oxygen, and salinity had significant influences on the ciliate community for the abundance matrices of resampled data, while lake and season were not significant. This result suggests that the vertical trends in dissolved oxygen concentration and salinity may play a critical role in structuring ciliate communities. A PCR-based strategy capitalizing on divergent eukaryotic V9 hypervariable region ribosomal RNA gene targets unveiled two new genera in these lakes. A novel taxon belonging to an unknown class most closely related to Cryptocaryon irritans was also inferred from separate gene phylogenies. © 2014 Marine Biological Laboratory.

Algal Attributes: An Autecological Classification of Algal Taxa Collected by the National Water-Quality Assessment Program

USGS Publications Warehouse

Porter, Stephen D.

2008-01-01

Algae are excellent indicators of water-quality conditions, notably nutrient and organic enrichment, and also are indicators of major ion, dissolved oxygen, and pH concentrations and stream microhabitat conditions. The autecology, or physiological optima and tolerance, of algal species for various water-quality contaminants and conditions is relatively well understood for certain groups of freshwater algae, notably diatoms. However, applications of autecological information for water-quality assessments have been limited because of challenges associated with compiling autecological literature from disparate sources, tracking name changes for a large number of algal species, and creating an autecological data base from which algal-indicator metrics can be calculated. A comprehensive summary of algal autecological attributes for North American streams and rivers does not exist. This report describes a large, digital data file containing 28,182 records for 5,939 algal taxa, generally species or variety, collected by the U.S. Geological Survey?s National Water-Quality Assessment (NAWQA) Program. The data file includes 37 algal attributes classified by over 100 algal-indicator codes or metrics that can be calculated easily with readily available software. Algal attributes include qualitative classifications based on European and North American autecological literature, and semi-quantitative, weighted-average regression approaches for estimating optima using regional and national NAWQA data. Applications of algal metrics in water-quality assessments are discussed and national quartile distributions of metric scores are shown for selected indicator metrics.

A systematic analysis of Heliotropium, Tournefortia, and allied taxa of the Heliotropiaceae (Boraginales) based on ITS1 sequences and morphological data.

PubMed

Diane, Nadja; Förther, Harald; Hilger, Hartmut H

2002-02-01

The relationships of Heliotropium, Tournefortia, Schleidenia, Ixorhea, and Ceballosia of the Heliotropiaceae (Boraginaceae in the traditional sense, Boraginales) are investigated using molecular data (ITS1). These genera form a monophyletic group. Five clades can be distinguished on the basis of molecular data, morphological traits, and distribution. In their current circumscription, Tournefortia is polyphyletic and Heliotropium is paraphyletic. Tournefortia section Cyphocyema is the sister group to all other ingroup taxa. Heliotropium section Orthostachys including Schleidenia sensu lato is the well supported sister group of a clade comprising the other species of Heliotropium sensu stricto (s.s.), Tournefortia section Tournefortia, and Ceballosia. Heliotropium s.s. forms two clades: one clade includes all species of the Old World and represents the only monophylum of Heliotropium s.s. The other clade consists of all Heliotropium s.s. species of the New World but also includes Tournefortia section Tournefortia and Ceballosia. The results suggest that taxonomic changes are inevitable.

Is evolutionary biology becoming too politically correct? A reflection on the scala naturae, phylogenetically basal clades, anatomically plesiomorphic taxa, and 'lower' animals.

PubMed

Diogo, Rui; Ziermann, Janine M; Linde-Medina, Marta

2015-05-01

The notion of scala naturae dates back to thinkers such as Aristotle, who placed plants below animals and ranked the latter along a graded scale of complexity from 'lower' to 'higher' animals, such as humans. In the last decades, evolutionary biologists have tended to move from one extreme (i.e. the idea of scala naturae or the existence of a general evolutionary trend in complexity from 'lower' to "higher" taxa, with Homo sapiens as the end stage) to the other, opposite, extreme (i.e. to avoid using terms such as 'phylogenetically basal' and 'anatomically plesiomorphic' taxa, which are seen as the undesired vestige of old teleological theories). The latter view tries to avoid any possible connotations with the original anthropocentric idea of a scala naturae crowned by man and, in that sense, it can be regarded as a more politically correct view. In the past years and months there has been renewed interest in these topics, which have been discussed in various papers and monographs that tend to subscribe, in general, to the points defended in the more politically correct view. Importantly, most evolutionary and phylogenetic studies of tetrapods and other vertebrates, and therefore most discussions on the scala naturae and related issues have been based on hard tissue and, more recently, on molecular data. Here we provide the first discussion of these topics based on a comparative myological study of all the major vertebrate clades and of myological cladistic and Bayesian phylogenetic analyses of bony fish and tetrapods, including Primates. We specifically (i) contradict the notions of a scala naturae or evolutionary progressive trends leading to more complexity in 'higher' animals and culminating in Homo sapiens, and (ii) stress that the refutation of these old notions does not necessarily mean that one should not keep using the terms 'phylogenetically basal' and particularly 'anatomically plesiomorphic' to refer to groups such as the urodeles within the Tetrapoda

Coupling between populations of copepod taxa within an estuarine ecosystem and the adjacent offshore regions

NASA Astrophysics Data System (ADS)

McGinty, N.; Johnson, M. P.; Power, A. M.

2012-07-01

Population dynamics in open systems are complicated by the interactions of local demography and local environmental forcing with processes occurring at larger scales. A local system such as an estuary or bay may contain a zooplankton population that effectively becomes independent of regional dynamics or the local dynamics may be closely coupled to a broader scale pattern. As an alternative, the details of migration and advection may mean that dynamics in a local system are coupled to other specific areas rather than tracking the overall dynamics at a larger scale. We used a reconstructed time series (1973-1987) for copepod taxa to examine the extent to which zooplankton dynamics in Galway Bay reflect processes in broader areas of the NE Atlantic. Continuous Plankton Recorder (CPR) counts were used to establish time series for nine offshore ecoregions, with the regions themselves defined using underlying patterns of chlorophyll variability. The open nature of Galway Bay was reflected in strong associations between bay zooplankton counts and offshore CPR data in a majority of cases (7/10). For each zooplankton taxon, there were large differences among regions in the degree of association with Galway Bay time series. Akaike weights indicated that one ecoregion tended to be the dominant link for each taxon. This indicates that the zooplankton of the Bay reflect more than the local modification of a regional signal and that different zooplankton in the bay may have separate source regions. The data from Galway Bay also fall within a 'sampling shadow' of the CPR. Later years of the time series showed evidence for changes in phenology, with spring zooplankton peaks generally occurring earlier in the year for smaller species.

The applicability of ordinary least squares to consistently short distances between taxa in phylogenetic tree construction and the normal distribution test consequences.

PubMed

Roux, C Z

2009-05-01

Short phylogenetic distances between taxa occur, for example, in studies on ribosomal RNA-genes with slow substitution rates. For consistently short distances, it is proved that in the completely singular limit of the covariance matrix ordinary least squares (OLS) estimates are minimum variance or best linear unbiased (BLU) estimates of phylogenetic tree branch lengths. Although OLS estimates are in this situation equal to generalized least squares (GLS) estimates, the GLS chi-square likelihood ratio test will be inapplicable as it is associated with zero degrees of freedom. Consequently, an OLS normal distribution test or an analogous bootstrap approach will provide optimal branch length tests of significance for consistently short phylogenetic distances. As the asymptotic covariances between branch lengths will be equal to zero, it follows that the product rule can be used in tree evaluation to calculate an approximate simultaneous confidence probability that all interior branches are positive.

In Vitro Lethal Activity of the Nematophagous Fungus Clonostachys rosea (Ascomycota: Hypocreales) against Nematodes of Five Different Taxa.

PubMed

Rodríguez-Martínez, Rosalia; Mendoza-de-Gives, Pedro; Aguilar-Marcelino, Liliana; López-Arellano, María Eugenia; Gamboa-Angulo, Marcela; Hanako Rosas-Saito, Greta; Reyes-Estébanez, Manuela; Guadalupe García-Rubio, Virginia

2018-01-01

This study was aimed to evaluate the in vitro lethal activity of the nematophagous fungi Clonostachys rosea against 5 nematodes species belonging to different taxa. Two groups of 35 Petri dishes (PD) each were divided into 5 series of 7 (PD). Group 1 (series 1, 2, 3, 4, and 5) contained only water agar; meanwhile group 2 plates (series 6, 7, 8, 9, and 10) contained C. rosea cultures growth on water agar. Every plate from the two groups was added with 500 nematodes corresponding to the following genera/specie: Haemonchus contortus , Caenorhabditis elegans, Rhabditis sp., Panagrellus redivivus , and Butlerius sp. After 5-day incubation at room temperature, free (nontrapped) larvae were recovered from plates using the Baermann funnel technique. Recovered nematodes were counted and compared with their proper controls. Results shown an important reduction percentage of the nematode population attributed to the fungal lethal activity as follows: H. contortus (L 3 ) 87.7%; C. elegans 94.7%; Rhabditis sp. 71.9%; P. redivivus 92.7%; and Butlerius sp. 100% ( p ≤ 0.05). The activity showed by C. rosea against the H. contortus can be crucial for further studies focused to the biological control of sheep haemonchosis, although the environmental impact against beneficial nematodes should be evaluated.

Taxonomic review of the plant bug subfamily Isometopinae for Taiwan and Japanese Southwest Islands, with descriptions of new taxa (Hemiptera: Heteroptera: Miridae: Isometopinae).

PubMed

Yasunaga, Tomohide; Yamada, Kazutaka; Tsai, Jing-Fu

2017-12-19

The fauna of plant bug subfamily Isometopinae in Taiwan and Japanese Southwest (Nansei) Islands is reviewed. Twenty-five species are recognized, including two new species of Myiomma Puton, M. austroccidens sp. nov. and M. kentingense sp. nov., which are herein diagnosed and described. In addition, Isometopus yehi Lin, 2004 is synonymized with I. bipunctatus Lin; Isometopidea yangi Lin is transferred to Kohnometopus; and a substitute name, Alcecoris linyangorum, is proposed for A. formosanus (Lin Yang) (= a junior secondary homonym of Alcecoris formosanus Lin). An annotated checklist, with updated distributional record and biological information, is provided for all treated taxa. A new tribe Sophianini is proposed for two genera, Alcecoris and Sophianus, characterized principally by the conspicuously modified antennal structures. An additional new species, Alcecoris cochlearatus sp. nov., found during examination of related Oriental specimens, is described from the Malay Peninsula.

Near-future ocean acidification causes differences in microbial associations within diverse coral reef taxa.

PubMed

Webster, N S; Negri, A P; Flores, F; Humphrey, C; Soo, R; Botté, E S; Vogel, N; Uthicke, S

2013-04-01

Microorganisms form symbiotic partnerships with a diverse range of marine organisms and can be critical to the health and survival of their hosts. Despite the importance of these relationships, the sensitivity of symbiotic microbes to ocean acidification (OA) is largely unknown and this needs to be redressed to adequately predict marine ecosystem resilience in a changing climate. We adopted a profiling approach to explore the sensitivity of microbes associated with coral reef biofilms and representatives of three ecologically important calcifying invertebrate phyla [corals, foraminifera and crustose coralline algae (CCA)] to OA. The experimental design for this study comprised four pHs consistent with current IPCC predictions for the next few centuries (pHNIST 8.1, 7.9, 7.7, 7.5); these pH/pCO₂ conditions were produced in flow-through aquaria using CO₂ bubbling. All reduced pH/increased pCO₂ treatments caused clear differences in the microbial communities associated with coral, foraminifera, CCA and reef biofilms over 6 weeks, while no visible signs of host stress were detected over this period. The microbial communities of coral, foraminifera, CCA and biofilms were significantly different between pH 8.1 (pCO₂ = 464 μatm) and pH 7.9 (pCO₂ = 822 μatm), a concentration likely to be exceeded by the end of the present century. This trend continued at lower pHs/higher pCO₂. 16S rRNA gene sequencing revealed variable and species-specific changes in the microbial communities with no microbial taxa consistently present or absent from specific pH treatments. The high sensitivity of coral, foraminifera, CCA and biofilm microbes to OA conditions projected to occur by 2100 is a concern for reef ecosystems and highlights the need for urgent research to assess the implications of microbial shifts for host health and coral reef processes. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders.

PubMed

Wood, Hannah Marie; Matzke, Nicholas J; Gillespie, Rosemary G; Griswold, Charles E

2013-03-01

Incorporation of fossils into biogeographic studies can have a profound effect on the conclusions that result, particularly when fossil ranges are nonoverlapping with extant ranges. This is the case in archaeid spiders, where there are known fossils from the Northern Hemisphere, yet all living members are restricted to the Southern Hemisphere. To better understand the biogeographic patterns of archaeid spiders and their palpimanoid relatives, we estimate a dated phylogeny using a relaxed clock on a combined molecular and morphological data set. Dating information is compared with treating the archaeid fossil taxa as both node calibrations and as noncontemporaneous terminal tips, both with and without additional calibration points. Estimation of ancestral biogeographic ranges is then performed, using likelihood and Bayesian methods to take into account uncertainty in phylogeny and in dating. We find that treating the fossils as terminal tips within a Bayesian framework, as opposed to dating the phylogeny based only on molecular data with the dates coming from node calibrations, removes the subjectivity involved in assigning priors, which has not been possible with previous methods. Our analyses suggest that the diversification of the northern and southern archaeid lineages was congruent with the breakup of Pangaea into Laurasia and Gondwanaland. This analysis provides a rare example, and perhaps the most strongly supported, where a dated phylogeny confirms a biogeographical hypothesis based on vicariance due to the breakup of the ancient continental plates.

Import and export fluxes of macrozooplankton are taxa- and season-dependent at Jiuduansha marsh, Yangtze River estuary

NASA Astrophysics Data System (ADS)

Qin, Haiming; Sheng, Qiang; Chu, Tianjiang; Wang, Sikai; Wu, Jihua

2015-09-01

Macrozooplankton may play important roles in influencing nutrient exchange between salt marsh and nearby estuarine ecosystems through predator-prey interactions and their transport by tidal flows. In this study, macrozooplankton transport through year-round monthly sampling was investigated in a salt marsh creek of the Yangtze River estuary. Twenty-one orders of macrozooplankton were captured. Calanoida and Decapoda were dominant and numerically comprised 59.59% and 37.59% respectively of the total captured macrozooplankton throughout the year. Decapoda mainly occurred in April, May and June. In other months, the Calanoida contributed over 90% of the total individuals. The annual Ferrari index (I) for total individual number of macrozooplankton was 0.27, which generally supports the viewpoint that salt marshes are sources of zooplankton. The salt marsh was mainly a source for decapods and mysids, possibly because of larval release in their breeding seasons. The marsh was also a source for amphipods, probably because some benthic forms became transient planktonic forms during tidal water flushing. Copepods and fish larvae exhibited net import into the salt marsh, which may result from predation from salt marsh settlers or retention in the salt marsh. Monthly Ferrari index (I) estimations revealed that the role of the salt marsh as a sink or source of macrozooplankton was time-dependent, which is related to the life history of animals. This study showed that whether the salt marsh zooplankton act as energy importers or exporters is group/taxa-dependent and time-dependent.

A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

NASA Astrophysics Data System (ADS)

Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic; Olsen, Jesper; Andersen, Kenneth; Holm, Jakob; Funder, Svend; Willerslev, Eske; Kjær, Kurt H.

2013-09-01

We use 2nd generation sequencing technology on sedimentary ancient DNA (sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the results with those previously obtained from pollen and macrofossils in the same lake. Thirty-eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g-h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (Scrophulariaceae and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650 cal yr BP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less detailed than pollen and macrofossil analyses can be a complementary tool for establishing the composition of both terrestrial and aquatic local plant communities and a method for identifying additional taxa.

Larvicidal Activity of Essential Oils of Five Apiaceae Taxa and Some of Their Main Constituents Against Culex quinquefasciatus.

PubMed

Pavela, Roman; Maggi, Filippo; Cianfaglione, Kevin; Bruno, Maurizio; Benelli, Giovanni

2018-01-01

Apiaceae are aromatic herbs producing essential oils which are used on an industrial scale for various purposes. Notably, Apiaceae essential oils may replace synthetic insecticides keeping most of their efficacy and avoiding environmental pollution and human poisoning. In the present work, we explored the insecticidal potential of the essential oils from five Apiaceae taxa, namely Sison amomum, Echinophora spinosa, Heracleum sphondylium subsp. sphondylium, Heracleum sphondylium subsp. ternatum, and Trachyspemum ammi, as well as their major constituents (sabinene, p-cymene, terpinolene, myristicin, and thymol), against the filariasis vector Culex quinquefasciatus. For the purpose, the essential oils were obtained by hydrodistillation and their composition was achieved by gas chromatography/mass spectrometry (GC/MS). Their acute toxicity on third instar larvae of C. quinquefasciatus was determined. The two most active essential oils were those from T. ammi fruits and E. spinosa roots, showing LC 50 below 20 μl/l and LD 90 below 50 μl/l. These oils were dominated by the monoterpene phenol thymol and the phenylpropanoid myristicin, respectively, which showed the strongest larvicidal activity (LC 50 of 15.1 and 16.3 μl/l, respectively) among the pure compounds tested. These results showed that Apiaceae may be useful as source of larvicidal compounds to be used for the development of cheap, effective and eco-friendly insecticidal formulations. © 2018 Wiley-VHCA AG, Zurich, Switzerland.

Linking autotrophic activity in environmental samples with specific bacterial taxa by detection of 13C-labelled fatty acids.

PubMed

Knief, Claudia; Altendorf, Karlheinz; Lipski, André

2003-11-01

A method for the detection of physiologically active autotrophic bacteria in complex microbial communities was developed based on labelling with the stable isotope 13C. Labelling of autotrophic nitrifying, sulphur-oxidizing and iron-oxidizing populations was performed in situ by incubation with NaH[13C]O3. Incorporated label into fatty acid methyl esters (FAMEs) was detected and quantified using gas chromatography-mass spectrometry in single ion monitoring mode. Before the analyses of different environmental samples, the protocol was evaluated in pure culture experiments. In different environmental samples a selective labelling of fatty acids demonstrated which microbial taxa were responsible for the respective chemolithoautotrophic activity. The most strongly labelled fatty acids of a sample from a sulphide treating biofilter from an animal rendering plant were cis-7-hexadecenoic acid (16:1 cis7) and 11-methyl hexadecanoic acid (16:0 11methyl), which are as-yet not known for any sulphide-oxidizing autotroph. The fatty acid labelling pattern of an experimental biotrickling filter sample supplied with dimethyl disulphide clearly indicated the presence and activity of sulphide-oxidizing bacteria of the genus Thiobacillus. For a third environmental sample from an acid mining lake sediment, the assignment of autotrophic activity to bacteria of the genus Leptospirillum but not to Acidithiobacillus could be made by this method, as the fatty acid patterns of these bacteria show clear differences.

Some taxonomic and nomenclatural changes in American Mantodea (Insecta, Dictyoptera)--Part I.

PubMed

Agudelo, Antonio A; Rivera, Julio

2015-03-20

Multiple nomenclatural problems persist in mantodean taxonomy. This constitutes an important challenge for praying mantis systematics, its forthcoming development and future consolidation. In this first contribution, we attempt solving a number of issues involving mostly Neotropical praying mantis species described by Brazilian entomologists Paulo S. Terra, Cândido F. de Mello-Leitão, Salvador de Toledo Piza Junior and Lauro J. Jantsch. We provide evidence to justify the following nomenclatural changes. In Acanthopidae, Acontiothespis travassosi Jantsch, 1986 is a new synonym of Raptrix perspicua (F. 1787). Changes in Thespidae are: Emboicy Terra, 1982 is a new synonym of Chloromiopteryx Giglio-Tos, 1915, E. mirim Terra, 1982 is transferred to Chloromiopteryx as C. mirim (Terra, 1982) (new combination); Musoniola plurilobata Mello-Leitão, 1937 is transferred to Chloromiopteryx as C. plurilobata (Mello-Leitão, 1937) (new combination); Metathespis modesta Piza, 1968 is removed from synonymy with Chloromiopteryx thalassina (Burmeister, 1838) and considered valid as C. modesta (Piza, 1968) (new combination and status revalidated); Metathespis precaria Piza, 1968 is removed from synonymy with Chloromiopteryx thalassina (Burmeister, 1838) and considered a new synonym of Miobantia rustica (Fabricius, 1781); Eumiopteryx magna Jantsch, 1991 is transferred to Anamiopteryx as A. magna (Jantsch, 1991) (new combination). For Mantidae/Amelinae, Tithrone corseuli Jantsch, 1986 and T. clauseni Jantsch, 1995 are new synonyms of Litaneutria minor (Scudder, 1872); in Mantidae/Photininae Coptopteryx gigliotosi Piza, 1960 (non Werner, 1925), its replacement name Coptopteryx ermannoi Jantsch & Corseuil, 1988 and Paraphotina precaria Piza, 1966 (the latter currently placed within Coptopteryx) are all new synonyms of Coptopteryx argentina (Burmeister, 1838), whereas Brachypteromantis bonariensis Piza 1960 (currently placed among Coptopteryx) is a new synonym of Coptopteryx gayi (Blanchard, 1851); Tithrone major Piza, 1962 is transferred to Orthoderella as O. major (Piza, 1962) (new combination); Orthoderella brasiliensis Roy & Stiewe, 2011 is a new synonym of Orthoderella major (Piza, 1962); Tithrone catharinensis Piza, 1962 is a new synonym of Photina vitrea (Burmeister, 1838); Margaromantis Piza, 1982, Rehniella Lombardo, 1999, Colombiella Koçak & Kemal, 2008 and Lombardoa Özdikmen, 2008 are all new synonyms of Photiomantis Piza, 1968 (status revalidated); Metriomantis planicephala Rehn 1916 is transferred to Photiomantis as P. planicephala (Rehn, 1916) (new combination) and Photiomantis silvai Piza, 1968 is considered a new synonym of Photiomantis planicephala (Rehn, 1916);  Margaromantis nigrolineata Menezes & Bravo, 2015 is transferred to Photiomantis as P. nigrolineata (Menezes & Bravo, 2015) (new combination). In Mantidae/Vatinae, Uromantis amazonica Jantsch, 1985 and Uromantis paraensis Jantsch, 1985 (currently placed among Stagmomantis), are new synonyms of Chopardiella latipennis (Chopard, 1911), while Pseudovates hyalostigma Mello-Leitão, 1937 and Vates obscura Toledo Piza, 1983 are new synonyms of V. biplagiata Sjöstedt, 1930. Lectotypes are designated for Chloromiopteryx thalassina (Burmeister, 1838) and Orthoderella major (Piza, 1962). Finally, we provide supplementary information about the works of S. de T. Piza and L. J. Jantsch, and a necessary critical assessment of their taxonomic contributions to the Mantodea.

Hybridisation is associated with increased fecundity and size in invasive taxa: meta-analytic support for the hybridisation-invasion hypothesis

PubMed Central

Hovick, Stephen M; Whitney, Kenneth D

2014-01-01

The hypothesis that interspecific hybridisation promotes invasiveness has received much recent attention, but tests of the hypothesis can suffer from important limitations. Here, we provide the first systematic review of studies experimentally testing the hybridisation-invasion (H-I) hypothesis in plants, animals and fungi. We identified 72 hybrid systems for which hybridisation has been putatively associated with invasiveness, weediness or range expansion. Within this group, 15 systems (comprising 34 studies) experimentally tested performance of hybrids vs. their parental species and met our other criteria. Both phylogenetic and non-phylogenetic meta-analyses demonstrated that wild hybrids were significantly more fecund and larger than their parental taxa, but did not differ in survival. Resynthesised hybrids (which typically represent earlier generations than do wild hybrids) did not consistently differ from parental species in fecundity, survival or size. Using meta-regression, we found that fecundity increased (but survival decreased) with generation in resynthesised hybrids, suggesting that natural selection can play an important role in shaping hybrid performance – and thus invasiveness – over time. We conclude that the available evidence supports the H-I hypothesis, with the caveat that our results are clearly driven by tests in plants, which are more numerous than tests in animals and fungi. PMID:25234578

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

PubMed Central

Agler, Matthew T.; Ruhe, Jonas; Kroll, Samuel; Morhenn, Constanze; Kim, Sang-Tae; Weigel, Detlef; Kemen, Eric M.

2016-01-01

Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the

Typing Candida albicans oral isolates from healthy brazilian schoolchildren using multilocus enzyme electrophoresis reveals two highly polymorphic taxa

PubMed Central

Boriollo, Marcelo Fabiano Gomes; Spolidorio, Denise Madalena Palomari; Barros, Letizia Monteiro; Bassi, Rodrigo Carlos; Garcia, José Antonio Dias; Costa, Ana Maria Duarte Dias; Rosa, Edvaldo Antonio Ribeiro; Höfling, José Francisco

2011-01-01

The genetic diversity of C. albicans oral isolates from 75 healthy schoolchildren from eight schools located in different geographic areas of Piracicaba city, São Paulo state, Brazil, was established using isoenzymes marker (Multilocus Enzyme Electrophoresis – MLEE) and cluster analysis. Patterns of monoclonal and polyclonal oral colonization by C. albicans within and between groups of schoolchildren were identified. However, significant divergence between the observed and the expected genotypic frequencies (Hardy-Weinberg equilibrium test) was not detected in the geographically adjacent groups, suggesting the hypothesis that populations of healthy schoolchildren do not correspond to the selection factor (differential survival) of strains. Two highly polymorphic and distantly genetically related taxa (A and B) were identified within the total population of yeasts, each contained subgroups (A1, A2, A3, A4, B1 and B2) and clusters of moderately related strains (from I to X), suggesting the existence of strains restricted or not to certain groups of geographically limited, healthy students. However, the coexistence of identical strains in healthy schoolchildren from the same school (geographically related) reinforces the hypothesis of oral transmission, where the sources of propagation could be explored. Furthermore, this could also be used in current and retrospective analyses of C. albicans isolated from immunocompetent and immunocompromised people, in order to detect commensal or potentially pathogenic yeast groups, predominantly in candidiasis, and in the development of strategies to prevent transmission or human propagation. PMID:24031720

Fauna Europaea – Orthopteroid orders

PubMed Central

Bohn, Horst; Haas, Fabian; Willemse, Fer

2016-01-01

Abstract Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant European terrestrial and freshwater animals, their geographical distribution at the level of countries and major islands (west of the Urals and excluding the Caucasus region), and some additional information. The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. The “Orthopteroid orders“ is one of the 58 Fauna Europaea major taxonomic groups. It contains series of mostly well-known insect orders: Embiodea (webspinners), Dermaptera (earwigs), Phasmatodea (walking sticks), Orthoptera s.s. (grasshoppers, crickets, bush-crickets) and Dictyoptera with the suborders Mantodea (mantids), Blattaria (cockroaches) and Isoptera (termites). For the Orthopteroid orders, data from 35 families containing 1,371 species are included in this paper. PMID:27660531

CAPA-peptides of praying mantids (Mantodea).

PubMed

Koehler, Rene; Predel, Reinhard

2010-03-01

Dictyoptera which consist of cockroaches, termites, and praying mantids are among the oldest pterygote insects known. Whereas the localization and sequences of neuropeptides from a number of cockroaches are very well known, nearly nothing is known about the neuropeptides typical of praying mantids. In this study, the neuroanatomy of the median neuroendocrine system in the abdominal ventral nerve cord and the sequences of the CAPA-peptides which are expressed in the respective neuroendocrine cells were analyzed. Altogether, 40 species belonging to different families of Mantodea were included. In contrast to cockroaches, the mantids mostly express two CAPA-periviscerokinins (PVKs), only in Mantis religiosa a third PVK was identified. These PVKs are sequence-related to the PVKs of basal cockroaches (Polyphagidae). In a group of closely related Mantodea (Paramantinae), extended forms of PVK-2 were observed. As shown, these forms are possibly the result of substitutions in the N-terminal cleavage sites of the respective PVKs. No trace of a CAPA-pyrokinin was found in any of the praying mantids. (c) 2009 Elsevier Inc. All rights reserved.

Reproductive biology and species geographical distribution in the Melastomataceae: a survey based on New World taxa

PubMed Central

dos Santos, Ana Paula Milla; Fracasso, Carla Magioni; Luciene dos Santos, Mirley; Romero, Rosana; Sazima, Marlies; Oliveira, Paulo Eugênio

2012-01-01

Background and Aims Apomictic plants are less dependent on pollinator services and able to occupy more diverse habitats than sexual species. However, such assumptions are based on temperate species, and comparable evaluation for species-rich Neotropical taxa is lacking. In this context, the Melastomataceae is a predominantly Neotropical angiosperm family with many apomictic species, which is common in the Campos Rupestres, endemism-rich vegetation on rocky outcrops in central Brazil. In this study, the breeding system of some Campo Rupestre Melastomataceae was evaluated, and breeding system studies for New World species were surveyed to test the hypothesis that apomixis is associated with wide distributions, whilst sexual species have more restricted areas. Methods The breeding systems of 20 Campo Rupestre Melastomataceae were studied using hand pollinations and pollen-tube growth analysis. In addition, breeding system information was compiled for 124 New World species of Melastomataceae with either wide (>1000 km) or restricted distributions. Key Results Most (80 %) of the Campo Rupestre species studied were self-compatible. Self-incompatibility in Microlicia viminalis was associated with pollen-tube arrest in the style, as described for other Melastomataceae, but most self-incompatible species analysed showed pollen-tube growth to the ovary irrespective of pollination treatment. Apomictic species showed lower pollen viability and were less frequent among the Campo Rupestre plants. Among the New World species compiled, 43 were apomictic and 77 sexual (24 self-incompatible and 53 self-compatible). Most apomictic (86 %) and self-incompatible species (71 %) presented wide distributions, whilst restricted distributions predominate only among the self-compatible ones (53 %). Conclusions Self-compatibility and dependence on biotic pollination were characteristic of Campo Rupestre and narrowly distributed New World Melastomataceae species, whilst apomictics are widely

Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean.

PubMed

Sánchez, Olga; Koblížek, Michal; Gasol, Josep M; Ferrera, Isabel

2017-06-01

Estimation of growth rates is crucial to understand the ecological role of prokaryotes and their contribution to marine biogeochemical cycling. However, there are only a few estimates for individual taxa. Two top-down (grazing) and bottom-up (phosphorus (P) availability) manipulation experiments were conducted under different light regimes in the NW Mediterranean Sea. Growth rate of different phylogenetic groups, including the Bacteroidetes, Rhodobacteraceae, SAR11, Gammaproteobacteria and its subgroups Alteromonadaceae and the NOR5/OM60 clade, were estimated from changes in cell numbers. Maximal growth rates were achieved in the P-amended treatments but when comparing values between treatments (response ratios), the response to predation removal was in general larger than to P-amendment. The Alteromonadaceae displayed the highest rates in both experiments followed by the Rhodobacteraceae, but all groups largely responded to filtration and P-amendment, even the SAR11 which presented low growth rates. Comparing light and dark treatments, growth rates were on average equal or higher in the dark than in the light for all groups, except for the Rhodobacteraceae and particularly the NOR5 clade, groups that contain photoheterotrophic species. These results are useful to evaluate the potential contributions of different bacterial types to biogeochemical processes under changing environmental conditions. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Description of two new Drepanomonas taxa and an account on features defining species in Drepanomonas Fresenius, 1858 (Ciliophora, Microthoracida).

PubMed

Omar, Atef; Foissner, Wilhelm

2013-08-01

Using standard methods, we describe two new Drepanomonas taxa: Drepanomonas hymenofera (Horváth 1956) nov. comb., which is composed of two (biogeographical?) subspecies, viz., D. hymenofera venezuelensis nov. subspec. and D. hymenofera hymenofera (Horváth 1956), was discovered in soil from Venezuela and Iceland, respectively. Both are comparatively large-sized (50×20μm and 40×18 μm in vivo), differing in the cortex pattern and the structure of kineties 3 and 4. We agree with Corliss (1979) and Chardez (1990) that the genus Pseudocristigera, which was established by Horváth (1956) for Drepanomonas hymenofera, is a junior synonym of Drepanomonas. Drepanomonas vasta nov. spec., which was discovered in the mud of a tree hole in Austria, is a middle-sized species (35×18 μm) with thick body, wide left side ridges, a single anterior dikinetid in kinety 4, and an average of 99 basal bodies; it is unique in having the dorsal side much more flattened than the ventral side, thus being cuneate in transverse view. Ontogenetic data show that the ciliary pattern of Drepanomonas is homologous to that of Leptopharynx, specifically, the structure and origin of the postoral complex. Main features for distinguishing Drepanomonas species are discussed. Copyright © 2012 Elsevier GmbH. All rights reserved.

Integrating gut microbiota immaturity and disease-discriminatory taxa to diagnose the initiation and severity of shrimp disease.

PubMed

Xiong, Jinbo; Zhu, Jinyong; Dai, Wenfang; Dong, Chunming; Qiu, Qiongfen; Li, Chenghua

2017-04-01

Increasing evidence has emerged a tight link among the gut microbiota, host age and health status. This osculating interplay impedes the definition of gut microbiome features associated with host health from that in developmental stages. Consequently, gut microbiota-based prediction of health status is promising yet not well established. Here we firstly tracked shrimp gut microbiota (N = 118) over an entire cycle of culture; shrimp either stayed healthy or progressively transitioned into severe disease. The results showed that the gut microbiota were significantly distinct over shrimp developmental stages and disease progression. Null model and phylogenetic-based mean nearest taxon distance (MNTD) analyses indicated that deterministic processes that governed gut community became less important as the shrimp aged and disease progressed. The predicted gut microbiota age (using the profiles of age-discriminatory bacterial species as independent variables) fitted well (r = 0.996; P < 0.001) with the age of healthy subjects, while this defined trend was disrupted by disease. Microbiota-for-age Z-scores (MAZ, here defined as immaturity) were relative stable among healthy shrimp, but sharply decreased when disease emerged. By distinguishing between age- and disease- discriminatory taxa, we developed a model, bacterial indicators of shrimp health status, to diagnose disease from healthy subjects with 91.5% accuracy. Notably, the relative abundances of the bacterial indicators were indicative for shrimp disease severity. These findings, in aggregate, add our understanding on the gut community assembly patterns over shrimp developmental stages and disease progression. In addition, shrimp disease initiation and severity can be accurately diagnosed using gut microbiota immaturity and bacterial indicators. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

DNA-Sequence Variation Among Schistosoma mekongi Populations and Related Taxa; Phylogeography and the Current Distribution of Asian Schistosomiasis

PubMed Central

Attwood, Stephen W.; Fatih, Farrah A.; Upatham, E. Suchart

2008-01-01

Background Schistosomiasis in humans along the lower Mekong River has proven a persistent public health problem in the region. The causative agent is the parasite Schistosoma mekongi (Trematoda: Digenea). A new transmission focus is reported, as well as the first study of genetic variation among S. mekongi populations. The aim is to confirm the identity of the species involved at each known focus of Mekong schistosomiasis transmission, to examine historical relationships among the populations and related taxa, and to provide data for use (a priori) in further studies of the origins, radiation, and future dispersal capabilities of S. mekongi. Methodology/Principal Findings DNA sequence data are presented for four populations of S. mekongi from Cambodia and southern Laos, three of which were distinguishable at the COI (cox1) and 12S (rrnS) mitochondrial loci sampled. A phylogeny was estimated for these populations and the other members of the Schistosoma sinensium group. The study provides new DNA sequence data for three new populations and one new locus/population combination. A Bayesian approach is used to estimate divergence dates for events within the S. sinensium group and among the S. mekongi populations. Conclusions/Significance The date estimates are consistent with phylogeographical hypotheses describing a Pliocene radiation of the S. sinensium group and a mid-Pleistocene invasion of Southeast Asia by S. mekongi. The date estimates also provide Bayesian priors for future work on the evolution of S. mekongi. The public health implications of S. mekongi transmission outside the lower Mekong River are also discussed. PMID:18350111

Phylogeny and classification of the Litostomatea (Protista, Ciliophora), with emphasis on free-living taxa and the 18S rRNA gene.

PubMed

Vd'ačný, Peter; Bourland, William A; Orsi, William; Epstein, Slava S; Foissner, Wilhelm

2011-05-01

The class Litostomatea is a highly diverse ciliate taxon comprising hundreds of species ranging from aerobic, free-living predators to anaerobic endocommensals. This is traditionally reflected by classifying the Litostomatea into the subclasses Haptoria and Trichostomatia. The morphological classifications of the Haptoria conflict with the molecular phylogenies, which indicate polyphyly and numerous homoplasies. Thus, we analyzed the genealogy of 53 in-group species with morphological and molecular methods, including 12 new sequences from free-living taxa. The phylogenetic analyses and some strong morphological traits show: (i) body polarization and simplification of the oral apparatus as main evolutionary trends in the Litostomatea and (ii) three distinct lineages (subclasses): the Rhynchostomatia comprising Tracheliida and Dileptida; the Haptoria comprising Lacrymariida, Haptorida, Didiniida, Pleurostomatida and Spathidiida; and the Trichostomatia. The curious Homalozoon cannot be assigned to any of the haptorian orders, but is basal to a clade containing the Didiniida and Pleurostomatida. The internal relationships of the Spathidiida remain obscure because many of them and some "traditional" haptorids form separate branches within the basal polytomy of the order, indicating one or several radiations and convergent evolution. Due to the high divergence in the 18S rRNA gene, the chaeneids and cyclotrichiids are classified incertae sedis. Copyright © 2011 Elsevier Inc. All rights reserved.

Zooxanthellae of the Montastraea annularis species complex: patterns of distribution of four taxa of Symbiodinium on different reefs and across depths.

PubMed

Toller, W W; Rowan, R; Knowlton, N

2001-12-01

Corals of the Montastraea annularis complex host several different dinoflagellates in the genus Symbiodinium. Here we address two questions arising from our previous studies of these associations on an offshore reef. First, do the same taxa and patterns of association (Symbiodinium A and B found in higher irradiance habitats than Symbiodinium C) occur on an inshore reef? Second, does M. franksi at the limits of its depth range host only Symbiodinium C, as it does at intermediate depths? In both surveys, a new Symbiodinium taxon and different patterns of distribution (assayed by analyses of small ribosomal subunit RNA genes [srDNA]) were observed. Inshore, a taxon we name Symbiodinium E predominated in higher irradiance habitats in M. franksi and its two sibling species; the only other zooxanthella observed was Symbiodinium C. Offshore, M. franksi mainly hosted Symbiodinium C, but hosted Symbiodinium A, B, C, and E in shallow water and Symbiodinium E and C in very deep water. Symbiodinium E may be stress-tolerant. Observed srDNA heterogeneity within samples of Symbiodinium B, C, and E is interpreted as variation across copies within this multigene family. Experimental bleaching of Symbiodinium C supported this interpretation. Thus sequences from natural samples should be interpreted cautiously.

Phylogenetically distant clade of Nostoc-like taxa with the description of Aliinostoc gen. nov. and Aliinostoc morphoplasticum sp. nov.

PubMed

Bagchi, Suvendra Nath; Dubey, Neelam; Singh, Prashant

2017-09-01

Nostoc is a complex and tough genus to differentiate, and its morphological plasticity makes it taxonomically complicated. Its cryptic diversity and almost no distinguishable morphological characteristics make this genus incredibly heterogeneous to evaluate on taxonomic scales. The strain NOS, isolated from a eutrophic water body, is being described as a new genus Aliinostoc with the strain showing motile hormogonia with gas vesicles as an atypical feature, which is currently considered as the diacritical feature of the genus but should be subjected to critical evaluation in the near future. The phylogenetic placement of Aliinostoc along with some other related sequences of Nostoc clearly separated this clade from Nostoc sensu stricto with high bootstrap support and robust topology in all the methods tested, thus providing strong proof of the taxa being representative of a new genus which morphologically appears to be Nostoc-like. Subsequent phylogenetic assessment using the rbcL, psbA, rpoC1 and tufA genes was done with the aim of facilitating future multi-locus studies on the proposed genus for better taxonomic clarity and resolution. Folding of the 16S-23S internal transcribed spacer region and subsequent comparisons with members of the genera Nostoc, Anabaena, Aulosira, Cylindrospermum, Sphaerospermopsis, Raphidiopsis, Desmonostoc and Mojavia gave entirely new secondary structures for the D1-D1' and box-B helix. Clear and separate clustering from Nostoc sensu stricto supports the establishment of Aliinostoc gen. nov. with the type species being Aliinostoc morphoplasticum sp. nov. in accordance with the International Code of Nomenclature for algae, fungi and plants.

Catalog of the recent taxa of the families Epitoniidae and Nystiellidae (Mollusca: Gastropoda) with a bibliography of the descriptive and systematic literature.

PubMed

Brown, Leonard G; Neville, Bruce D

2015-01-15

This catalog includes 1,487 names recent genera, subgenera, species, subspecies, varieties, and forms that have been referred to the families Epitoniidae and Nystiellidae as well as a bibliography of the descriptive and systematic literature associated with these names. For the names covered herein, we make a determination of whether the name is an available name, as that term is defined in the International Code of Zoological Nomenclature ("ICZN") and, based on a review of the literature listed in the bibliography, indicate whether the taxon is a potentially valid name or a probable synonym. This catalog includes not only includes a list of names, but also includes information on type material, type localities and species' geographic, bathymetric and size ranges. We also suggest generic assignments for many of the species level taxa listed in this work. We herein designate Scalaria acuta J. Sowerby, 1812, to be the type species of Clathrus Agassiz, 1837, designate Scalaria raricostata G.B. Sowerby II, 1844b, to be the type species of Variciscala de Boury, 1909a, designate Turbiniscala sexcosta Jousseaume, 1912, to be the type species of Turbiniscala de Boury, 1909a, and designate Scala dubia 'G. B. Sowerby II' de Boury, 1912b to be the type species of Foliaceiscala de Boury, 1912b. 

Self-pollination rate and floral-display size in Asclepias syriaca (Common Milkweed) with regard to floral-visitor taxa

PubMed Central

2014-01-01

Background Animals fertilize thousands of angiosperm species whose floral-display sizes can significantly influence pollinator behavior and plant reproductive success. Many studies have measured the interactions among pollinator behavior, floral-display size, and plant reproductive success, but few studies have been able to separate the effects of pollinator behavior and post-pollination processes on angiosperm sexual reproduction. In this study, we utilized the highly self-incompatible pollinium-pollination system of Asclepias syriaca (Common Milkweed) to quantify how insect visitors influenced male reproductive success measured as pollen removal, female reproductive success measured as pollen deposition, and self-pollination rate. We also determined how floral-display size impacts both visitor behavior and self-pollination rate. Results Four insect taxonomic orders visited A. syriaca: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We focused on three groups of visitor taxa within two orders (Hymenoptera and Lepidoptera) with sample sizes large enough for quantitative analysis: Apis mellifera (Western Honey Bee), Bombus spp. (bumble bees) and lepidopterans (butterflies and moths). Qualitatively, lepidopterans had the highest pollinator importance values, but the large variability in the lepidopteran data precluded meaningful interpretation of much of their behavior. The introduced A. mellifera was the most effective and most important diurnal pollinator with regard to both pollen removal and pollen deposition. However, when considering the self-incompatibility of A. syriaca, A. mellifera was not the most important pollinator because of its high self-pollination rate as compared to Bombus spp. Additionally, the rate of self-pollination increased more rapidly with the number of flowers per inflorescence in A. mellifera than in the native Bombus spp. Conclusions Apis mellifera’s high rate of self-pollination may have significant negative effects on both male

Self-pollination rate and floral-display size in Asclepias syriaca (Common Milkweed) with regard to floral-visitor taxa.

PubMed

Howard, Aaron F; Barrows, Edward M

2014-06-23

Animals fertilize thousands of angiosperm species whose floral-display sizes can significantly influence pollinator behavior and plant reproductive success. Many studies have measured the interactions among pollinator behavior, floral-display size, and plant reproductive success, but few studies have been able to separate the effects of pollinator behavior and post-pollination processes on angiosperm sexual reproduction. In this study, we utilized the highly self-incompatible pollinium-pollination system of Asclepias syriaca (Common Milkweed) to quantify how insect visitors influenced male reproductive success measured as pollen removal, female reproductive success measured as pollen deposition, and self-pollination rate. We also determined how floral-display size impacts both visitor behavior and self-pollination rate. Four insect taxonomic orders visited A. syriaca: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We focused on three groups of visitor taxa within two orders (Hymenoptera and Lepidoptera) with sample sizes large enough for quantitative analysis: Apis mellifera (Western Honey Bee), Bombus spp. (bumble bees) and lepidopterans (butterflies and moths). Qualitatively, lepidopterans had the highest pollinator importance values, but the large variability in the lepidopteran data precluded meaningful interpretation of much of their behavior. The introduced A. mellifera was the most effective and most important diurnal pollinator with regard to both pollen removal and pollen deposition. However, when considering the self-incompatibility of A. syriaca, A. mellifera was not the most important pollinator because of its high self-pollination rate as compared to Bombus spp. Additionally, the rate of self-pollination increased more rapidly with the number of flowers per inflorescence in A. mellifera than in the native Bombus spp. Apis mellifera's high rate of self-pollination may have significant negative effects on both male and female reproductive successes

Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton

PubMed Central

Milici, Mathias; Deng, Zhi-Luo; Tomasch, Jürgen; Decelle, Johan; Wos-Oxley, Melissa L.; Wang, Hui; Jáuregui, Ruy; Plumeier, Iris; Giebel, Helge-Ansgar; Badewien, Thomas H.; Wurst, Mascha; Pieper, Dietmar H.; Simon, Meinhard; Wagner-Döbler, Irene

2016-01-01

We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S–47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone. PMID:27199970

Head capsule, chephalic central nervous system and head circulatory system of an aberrant orthopteran, Prosarthria teretrirostris (Caelifera, Hexapoda).

PubMed

Baum, Eileen; Hertel, Wieland; Beutel, Rolf Georg

2007-01-01

The head capsule, the circulatory system and the central nervous system of the head of Prosarthria teretrirostris (Proscopiidae) is described in detail, with special consideration of modifications resulting from the aberrant head shape. The transformations of the head are completely different from those found in phasmatodeans, which are also characterised by twig mimesis. The circulatory system is distinctly modified. A hitherto undescribed additional structure in the posterior head region very likely functions as a pulsatile organ. The cephalic central nervous system is strongly elongated, with changes in the position of the suboesophageal ganglion, the corpora cardiaca and the course of the nervus mandibularis. Three-dimensional reconstructions of these two organ systems in combination with the pharynx were made using Alias Maya 6.0 software. Comparisons with other representatives of Caelifera suggest a clade comprising Proscopiidae and Morabinae. The presence of a transverse muscle connecting the antennal ampullae in Prosarthria shows that this structure likely belongs to the groundplan of Orthoptera, even though it is missing in different representatives of this group. The transverse ampullary muscle is a potential synapomorphy of Orthoptera, Phasmatodea and Dictyoptera.

Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa.

PubMed

Villegas, Luis Martínez; Pimenta, Paulo Filemon Paolucci

2014-08-01

Anophelines harbour a diverse microbial consortium that may represent an extended gene pool for the host. The proposed effects of the insect microbiota span physiological, metabolic and immune processes. Here we synthesise how current metagenomic tools combined with classical culture-dependent techniques provide new insights in the elucidation of the role of the Anopheles-associated microbiota. Many proposed malaria control strategies have been based upon the immunomodulating effects that the bacterial components of the microbiota appear to exert and their ability to express anti-Plasmodium peptides. The number of identified bacterial taxa has increased in the current "omics" era and the available data are mostly scattered or in "tables" that are difficult to exploit. Published microbiota reports for multiple anopheline species were compiled in an Excel® spreadsheet. We then filtered the microbiota data using a continent-oriented criterion and generated a visual correlation showing the exclusive and shared bacterial genera among four continents. The data suggested the existence of a core group of bacteria associated in a stable manner with their anopheline hosts. However, the lack of data from Neotropical vectors may reduce the possibility of defining the core microbiota and understanding the mosquito-bacteria interactive consortium.

Polar Lipids Analysis of Cultured Phytoplankton Reveals Significant Inter-taxa Changes, Low Influence of Growth Stage, and Usefulness in Chemotaxonomy.

PubMed

Cañavate, José Pedro; Armada, Isabel; Hachero-Cruzado, Ismael

2017-05-01

The high lipid diversity of microalgae has been used to taxonomically differentiate phytoplankton taxa at the class level. However, important lipids such as phospholipids (PL) and betaine lipids (BL) with potential chemotaxonomy application in phytoplankton ecology have been scarcely studied. The chemotaxonomy value of PL and BL depends on their intraspecific extent of variation as microalgae respond to external changing factors. To determine such effects, lipid class changes occurring at different growth stages in 15 microalgae from ten different classes were analyzed. BL occurred in 14 species and were the less affected lipids by growth stage with diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGTA) showing the highest stability. PL were more influenced by growth stage with phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidyletanolamine (PE) declining towards older culture stages in some species. Glycolipids were the more common lipids, and no evident age-related variability pattern could be associated to taxonomic diversity. Selecting BL and PL as descriptor variables optimally distinguished microalgae taxonomic variability at all growth stages. Principal coordinate analysis arranged species through a main tendency from diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGCC) containing species (mainly dinoflagellates and haptophytes) to DGTA or PC containing species (mainly cryptophytes). Two diatom classes with similar fatty acid profiles could be distinguished from their respective content in DGTA (Bacillariophyceae) or DGCC (Mediophyceae). In green lineage classes (Trebouxiophyceae, Porphyridophyceae, and Chlorodendrophyceae), PC was a better descriptor than BL. BL and PL explained a higher proportion of microalgae taxonomic variation than did fatty acids and played a complementary role as lipid markers.

Rapid sewage pollution assessment by means of the coverage of epilithic taxa in a coastal area in the SW Atlantic.

PubMed

Becherucci, M E; Jaubet, M L; Saracho Bottero, M A; Llanos, E N; Elías, R; Garaffo, G V

2018-07-01

The sewage pollution impact over coastal environment represents one of the main reasons explaining the deterioration of marine coastal ecosystems around the globe. This paper aims to detect promptly a putative sewage pollution impact in a Southwestern Atlantic coastal area of Argentina as well as to identify a straightforward way for monitoring, based on the relative abundance coverage of the intertidal epilithic taxa. Four sampling sites were distributed at increased distances from the sewage outfall where the cover of individual epilithic species was visually estimated. The surrounded outfall area (i.e. outfall site) resulted polluted with high percentages of organic matter in sediment and Enterococcus concentration in seawater. The structure of the community showed a remarkable difference between the polluted site (outfall site) and the unpolluted sites. The polychaete Boccardia proboscidea dominated the outfall site with variable abundances of the green algae Ulva sp. during the period of study, decreasing the diversity of the community, while the mussel Brachidontes rodriguezii and variable abundances of several algae species dominated the unpolluted sites. The monitoring of the benthic community represents an effective, non-destructive, relative inexpensive and rapid method to assess the health of the coastal environment in the study area. The large abundance of B. proboscidea along with the absence of B. rodriguezii individuals at <300m to the sewage outfall discharge allowed the success of this classical monitoring method in a temperate marine-coastal ecosystem with certain gradient of pollution. Copyright © 2018 Elsevier B.V. All rights reserved.

16S rRNA gene-based association study identified microbial taxa associated with pork intramuscular fat content in feces and cecum lumen.

PubMed

Fang, Shaoming; Xiong, Xingwei; Su, Ying; Huang, Lusheng; Chen, Congying

2017-07-19

Intramuscular fat (IMF) that deposits among muscle fibers or within muscle cells is an important meat quality trait in pigs. Previous studies observed the effects of dietary nutrients and additives on improving the pork IMF. Gut microbiome plays an important role in host metabolism and energy harvest. Whether gut microbiota exerts effect on IMF remains unknown. In this study, we investigated the microbial community structure of 500 samples from porcine cecum and feces using high-throughput 16S rRNA gene sequencing. We found that phylogenetic composition and potential function capacity of microbiome varied between two types of samples. Bacteria wide association study identified 119 OTUs significantly associated with IMF in the two types of samples (FDR < 0.1). Most of the IMF-associated OTUs belong to the bacteria related to polysaccharide degradation and amino acid metabolism (such as Prevotella, Treponema, Bacteroides and Clostridium). Potential function capacities related to metabolisms of carbohydrate, energy and amino acids, cell motility, and membrane transport were significantly associated with IMF content. FishTaco analysis suggested that the shifts of potential function capacities of microbiome associated with IMF might be caused by the IMF-associated microbial taxa. This study firstly evaluated the contribution of gut microbiome to porcine IMF content. The results presented a potential capacity for improving IMF through modulating gut microbiota.

Development and characterization of 16 polymorphic microsatellite markers from Taiwan cow-tail fir, Keteleeria davidiana var. formosana (Pinaceae) and cross-species amplification in other Keteleeria taxa

PubMed Central

2014-01-01

Background Keteleeria davidiana var. formosana (Pinaceae), Taiwan cow-tail fir, is an endangered species listed on the IUCN Red List of Threatened Species and only two populations remain, both on the Taiwan Island. Sixteen polymorphic microsatellite loci were developed in an endangered and endemic gymnosperm species, Keteleeria davidiana var. formosana, and were tested in an additional 6 taxa, K. davidiana var. calcarea, K. davidiana var. chienpeii, K. evelyniana, K. fortunei, K. fortunei var. cyclolepis, and K. pubescens, to evaluate the genetic variation available for conservation management and to reconstruct the phylogeographic patterns of this ancient lineage. Findings Polymorphic primer sets were developed from K. davidiana var. formosana using the modified AFLP and magnetic bead enrichment method. The number of alleles ranged from 3 to 16, with the observed heterozygosity ranging from 0.28 to 1.00. All of the loci were found to be interspecifically amplifiable. Conclusions These polymorphic and transferable loci will be potentially useful for future studies that will focus on identifying distinct evolutionary units within species and establishing the phylogeographic patterns and the process of speciation among closely related species. PMID:24755442

Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae).

PubMed

Stervander, Martin; Alström, Per; Olsson, Urban; Ottosson, Ulf; Hansson, Bengt; Bensch, Staffan

2016-09-01

The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla, C. blanfordi/C. erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C. brachydactyla and C. blanfordi, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C. brachydactyla and C. cinerea were unsupported by cytb, although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision. Copyright © 2016 Elsevier Inc. All rights reserved.

Characteristic ichthyoplankton taxa in the separation zone of the East Australian Current: Larval assemblages as tracers of coastal mixing

NASA Astrophysics Data System (ADS)

Syahailatua, Augy; Roughan, Moninya; Suthers, Iain M.

2011-03-01

Ichthyoplankton assemblages were compared between regions dominated by the oligotrophic East Australian Current (EAC) and the inner-shelf waters off southeastern Australia, to determine if the early life history of fish was related to the separation of the EAC from the coast, producing different water masses as well as characteristic taxa. Samples were collected at the surface and in sub-surface waters, at 50 and 100 m isobath stations, during two summer research voyages in November 1998 and January 1999. On both voyages the study region was characterized by coastal and EAC waters in the north (˜31°S), and in the south by topographically induced upwelling (˜31°S), associated with narrowing of the continental shelf and separation of the EAC from the coast. Among the 111 families of larval fish, we observed distinctive assemblages of ichthyoplankton associated with the two different water masses. A greater abundance of the Carangidae, Labridae, Lutjanidae, Microcanthidae, Myctophidae and Scombridae was associated with the nutrient poor EAC water mass, while the Callionymidae, Clupeidae, Platycephalidae and Sillaginidae were mostly found in the cooler and/or fresher inner-shelf water mass. We assessed these patterns with opportunistic samples from an unusual, wind-driven upwelling event in the north (˜31°S) earlier in the November voyage. The relative abundance of these 10 characteristic families distinguished this wind-driven upwelling event from the subsequent relaxation and predominance of the EAC assemblage at this location just 6 d later. Distinctive and abundant families such as larval clupeids, relative to larval carangids, could be a useful marker of inner-shelf, EAC and mixed water masses in the absence of robust hydrographic data. This and related studies indicate contrast in early life histories of Sardinops sagax and Trachurus spp., which appear to spawn respectively in the inner-shelf and outer-shelf waters. The post-flexion stages of S. sagax

Influence of codon usage bias on FGLamide-allatostatin mRNA secondary structure.

PubMed

Martínez-Pérez, Francisco; Bendena, William G; Chang, Belinda S W; Tobe, Stephen S

2011-03-01

The FGLamide allatostatins (ASTs) are invertebrate neuropeptides which inhibit juvenile hormone biosynthesis in Dictyoptera and related orders. They also show myomodulatory activity. FGLamide AST nucleotide frequencies and codon bias were investigated with respect to possible effects on mRNA secondary structure. 367 putative FGLamide ASTs and their potential endoproteolytic cleavage sites were identified from 40 species of crustaceans, chelicerates and insects. Among these, 55% comprised only 11 amino acids. An FGLamide AST consensus was identified to be (X)(1→16)Y(S/A/N/G)FGLGKR, with a strong bias for the codons UUU encoding for Phe and AAA for Lys, which can form strong Watson-Crick pairing in all peptides analyzed. The physical distance between these codons favor a loop structure from Ser/Ala-Phe to Lys-Arg. Other loop and hairpin loops were also inferred from the codon frequencies in the N-terminal motif, and the first amino acids from the C-terminal motif, or the dibasic potential endoproteolytic cleavage site. Our results indicate that nucleotide frequencies and codon usage bias in FGLamide ASTs tend to favor mRNA folds in the codon sequence in the C-terminal active peptide core and at the dibasic potential endoproteolytic cleavage site. Copyright © 2010 Elsevier Inc. All rights reserved.

Mitochondrial genomes of praying mantises (Dictyoptera, Mantodea): rearrangement, duplication, and reassignment of tRNA genes.

PubMed

Ye, Fei; Lan, Xu-E; Zhu, Wen-Bo; You, Ping

2016-05-09

Insect mitochondrial genomes (mitogenomes) contain a conserved set of 37 genes for an extensive diversity of lineages. Previously reported dictyopteran mitogenomes share this conserved mitochondrial gene arrangement, although surprisingly little is known about the mitogenome of Mantodea. We sequenced eight mantodean mitogenomes including the first representatives of two families: Hymenopodidae and Liturgusidae. Only two of these genomes retain the typical insect gene arrangement. In three Liturgusidae species, the trnM genes have translocated. Four species of mantis (Creobroter gemmata, Mantis religiosa, Statilia sp., and Theopompa sp.-HN) have multiple identical tandem duplication of trnR, and Statilia sp. additionally includes five extra duplicate trnW. These extra trnR and trnW in Statilia sp. are erratically arranged and form another novel gene order. Interestingly, the extra trnW is converted from trnR by the process of point mutation at anticodon, which is the first case of tRNA reassignment for an insect. Furthermore, no significant differences were observed amongst mantodean mitogenomes with variable copies of tRNA according to comparative analysis of codon usage. Combined with phylogenetic analysis, the characteristics of tRNA only possess limited phylogenetic information in this research. Nevertheless, these features of gene rearrangement, duplication, and reassignment provide valuable information toward understanding mitogenome evolution in insects.

Mitochondrial genomes of praying mantises (Dictyoptera, Mantodea): rearrangement, duplication, and reassignment of tRNA genes

PubMed Central

Ye, Fei; Lan, Xu-e; Zhu, Wen-bo; You, Ping

2016-01-01

Insect mitochondrial genomes (mitogenomes) contain a conserved set of 37 genes for an extensive diversity of lineages. Previously reported dictyopteran mitogenomes share this conserved mitochondrial gene arrangement, although surprisingly little is known about the mitogenome of Mantodea. We sequenced eight mantodean mitogenomes including the first representatives of two families: Hymenopodidae and Liturgusidae. Only two of these genomes retain the typical insect gene arrangement. In three Liturgusidae species, the trnM genes have translocated. Four species of mantis (Creobroter gemmata, Mantis religiosa, Statilia sp., and Theopompa sp.-HN) have multiple identical tandem duplication of trnR, and Statilia sp. additionally includes five extra duplicate trnW. These extra trnR and trnW in Statilia sp. are erratically arranged and form another novel gene order. Interestingly, the extra trnW is converted from trnR by the process of point mutation at anticodon, which is the first case of tRNA reassignment for an insect. Furthermore, no significant differences were observed amongst mantodean mitogenomes with variable copies of tRNA according to comparative analysis of codon usage. Combined with phylogenetic analysis, the characteristics of tRNA only possess limited phylogenetic information in this research. Nevertheless, these features of gene rearrangement, duplication, and reassignment provide valuable information toward understanding mitogenome evolution in insects. PMID:27157299

Comparative Mitogenomic Analyses of Praying Mantises (Dictyoptera, Mantodea): Origin and Evolution of Unusual Intergenic Gaps

PubMed Central

Zhang, Hong-Li; Ye, Fei

2017-01-01

Praying mantises are a diverse group of predatory insects. Although some Mantodea mitogenomes have been reported, a comprehensive comparative and evolutionary genomic study is lacking for this group. In the present study, four new mitogenomes were sequenced, annotated, and compared to the previously published mitogenomes of other Mantodea species. Most Mantodea mitogenomes share a typical set of mitochondrial genes and a putative control region (CR). Additionally, and most intriguingly, another large non-coding region (LNC) was detected between trnM and ND2 in all six Paramantini mitogenomes examined. The main section in this common region of Paramantini may have initially originated from the corresponding control region for each species, whereas sequence differences between the LNCs and CRs and phylogenetic analyses indicate that LNC and CR are largely independently evolving. Namely, the LNC (the duplicated CR) may have subsequently degenerated during evolution. Furthermore, evidence suggests that special intergenic gaps have been introduced in some species through gene rearrangement and duplication. These gaps are actually the original abutting sequences of migrated or duplicated genes. Some gaps (G5 and G6) are homologous to the 5' and 3' surrounding regions of the duplicated gene in the original gene order, and another specific gap (G7) has tandem repeats. We analysed the phylogenetic relationships of fifteen Mantodea species using 37 concatenated mitochondrial genes and detected several synapomorphies unique to species in some clades. PMID:28367101

Insecticide resistance and diminished secondary kill performance of bait formulations against German cockroaches (Dictyoptera: Blattellidae)

PubMed Central

Ko, Alexander E.; Bieman, Donald N.; Schal, Coby; Silverman, Jules

2015-01-01

BACKGROUND Bait formulations are considered the most effective method for reducing German cockroach infestations. An important property of some bait formulations is secondary kill, whereby active ingredient is translocated in insect-produced residues throughout the cockroach population, especially affecting relatively sedentary early instar nymphs. RESULTS Blattella germanica was collected from a location where baits containing hydramethylnon, fipronil, or indoxacarb became ineffective, and these AIs were topically applied to adult males. Results revealed the first evidence for hydramethylnon resistance, moderate resistance to fipronil and extremely high resistance to indoxacarb. Insecticide residues excreted by field-collected males that ingested commercial baits effectively killed nymphs of an insecticide-susceptible laboratory strain of B. germanica but failed to kill most nymphs of the field-collected strain. CONCLUSIONS We report three novel findings: 1) The first evidence for hydramethylnon resistance in any insect; 2) extremely high levels of indoxacarb resistance in a field population; and 3) reduced secondary mortality in an insecticide-resistant field-collected strain of B. germanica. We suggest that while secondary mortality is considered to be advantageous in cockroach interventions, the ingestion of sublethal doses of AI by nymphs may select for high insecticide resistance by increasing the frequency of AI resistance alleles within the population. PMID:26689433

Divergence of Lutzomyia (Psathyromyia) shannoni (Diptera: Psychodidae: Phlebotominae) is indicated by morphometric and molecular analyses when examined between taxa from the southeastern United States and southern Mexico.

PubMed

Florin, David A; Rebollar-Téllez, Eduardo A

2013-11-01

The medically important sand fly Lutzomyia shannoni (Dyar 1929) was collected at eight different sites: seven within the southeastern United States and one in the state of Quintana Roo, Mexico. A canonical discriminant analysis was conducted on 40 female L. shannoni specimens from each of the eight collection sites (n = 320) using 49 morphological characters. Four L. shannoni specimens from each of the eight collection sites (n = 32) were sent to the Barcode of Life Data systems where a 654-base pair segment of the cytochrome c oxidase subunit 1 (CO1) genetic marker was sequenced from each sand fly. Phylogeny estimation based on the COI segments, in addition to genetic distance, divergence, and differentiation values were calculated. Results of both the morphometric and molecular analyses indicate that the species has undergone divergence when examined between the taxa of the United States and Quintana Roo, Mexico. Although purely speculative, the arid or semiarid expanse from southern Texas to Mexico City could be an allopatric barrier that has impeded migration and hence gene flow, resulting in different morphology and genetic makeup between the two purported populations. A high degree of intragroup variability was noted in the Quintana Roo sand flies.

When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths

PubMed Central

2011-01-01

barcodes, the likelihood of assigning a query a genus name incorrectly is very low, if a genus name is provided it has a high likelihood of being accurate, and if no genus match is available the query can nevertheless be assigned to a subfamily with high accuracy regardless of library completeness. DNA barcoding often correctly assigned sphingid moths to higher taxa when species matches were unavailable, suggesting that barcode reference libraries can be useful for higher taxon assignments long before they achieve complete species coverage. PMID:21806794

The History of Tree and Shrub Taxa on Bol’shoy Lyakhovsky Island (New Siberian Archipelago) since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data

PubMed Central

Raschke, Elena; Epp, Laura S.; Stoof-Leichsenring, Kathleen R.; Schwamborn, Georg; Herzschuh, Ulrike

2017-01-01

Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol’shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns. PMID:29027988

Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium

PubMed Central

Samson, R.A.; Yilmaz, N.; Houbraken, J.; Spierenburg, H.; Seifert, K.A.; Peterson, S.W.; Varga, J.; Frisvad, J.C.

2011-01-01

The taxonomic history of anamorphic species attributed to Penicillium subgenus Biverticillium is reviewed, along with evidence supporting their relationship with teleomorphic species classified in Talaromyces. To supplement previous conclusions based on ITS, SSU and/or LSU sequencing that Talaromyces and subgenus Biverticillium comprise a monophyletic group that is distinct from Penicillium at the generic level, the phylogenetic relationships of these two groups with other genera of Trichocomaceae was further studied by sequencing a part of the RPB1 (RNA polymerase II largest subunit) gene. Talaromyces species and most species of Penicillium subgenus Biverticillium sensu Pitt reside in a monophyletic clade distant from species of other subgenera of Penicillium. For detailed phylogenetic analysis of species relationships, the ITS region (incl. 5.8S nrDNA) was sequenced for the available type strains and/or representative isolates of Talaromyces and related biverticillate anamorphic species. Extrolite profiles were compiled for all type strains and many supplementary cultures. All evidence supports our conclusions that Penicillium subgenus Biverticillium is distinct from other subgenera in Penicillium and should be taxonomically unified with the Talaromyces species that reside in the same clade. Following the concepts of nomenclatural priority and single name nomenclature, we transfer all accepted species of Penicillium subgenus Biverticillium to Talaromyces. A holomorphic generic diagnosis for the expanded concept of Talaromyces, including teleomorph and anamorph characters, is provided. A list of accepted Talaromyces names and newly combined Penicillium names is given. Species of biotechnological and medical importance, such as P. funiculosum and P. marneffei, are now combined in Talaromyces. Excluded species and taxa that need further taxonomic study are discussed. An appendix lists other generic names, usually considered synonyms of Penicillium sensu lato that

Origin and extent of resistance to fipronil in the German cockroach, Blattella germanica (L.) (Dictyoptera: Blattellidae).

PubMed

Holbrook, Glenn L; Roebuck, Jamie; Moore, Clyde B; Waldvogel, Michael G; Schal, Coby

2003-10-01

Fipronil, a phenylpyrazole insecticide, was made available in 1999 in bait formulations for use against the German cockroach, Blattella germanica (L.). We have investigated resistance to fipronil in the descendants of cockroaches collected just before, or contemporaneously with, the introduction of fipronil baits. Cockroaches were obtained in two types of settings: homes that either had or had not been serviced by a pest management professional while occupied by their current residents. Thorough inspections by us turned up no evidence that fipronil had been used in any of the homes, and in addition, no residents claimed to have used baits containing fipronil. Resistance to fipronil was detected by topically dosing adult males with the LC99 of fipronil, the value of which was determined in a dose-response assay with males of an insecticide-susceptible strain. Fewer than 99 of 100 males of all field-collected strains died within 72 h of being treated. Moreover, substantial numbers of males survived doses three and 10-fold greater than the LC99. Regression analysis showed that 67% of the variation in the percentage of males that died after being treated with fipronil was explained by a linear relationship with the percentage that died after being treated with dieldrin. Therefore, it appears that resistance to fipronil in German cockroaches--whose ancestors had never been exposed to it--is attributable to enduring resistance to the cyclodienes, which were formerly used for cockroach control and have a similar mode of action as fipronil. Lastly, we found that insects resistant to topically administered fipronil were likewise resistant, and to a similar degree, to ingested fipronil.

Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques.

PubMed

McLean, Jeffrey S; Fansler, Sarah J; Majors, Paul D; McAteer, Kathleen; Allen, Lisa Z; Shirtliff, Mark E; Lux, Renate; Shi, Wenyuan

2012-01-01

Many human microbial infectious diseases including dental caries are polymicrobial in nature. How these complex multi-species communities evolve from a healthy to a diseased state is not well understood. Although many health- or disease-associated oral bacteria have been characterized in vitro, their physiology within the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these species remain uncultivated to date with little known besides their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated species will remain enigmatic despite their apparent disease correlation. To start addressing these knowledge gaps, we applied a combination of Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for in vitro temporal monitoring of metabolites and identification of metabolically active and inactive bacterial species. Supragingival plaque samples from caries-free children incubated with (13)C-substrates under imposed healthy (buffered, pH 7) and diseased states (pH 5.5 and pH 4.5) produced lactate as the dominant organic acid from glucose metabolism. Rapid lactate utilization upon glucose depletion was observed under pH 7 conditions. SIP analyses revealed a number of genera containing cultured and uncultivated taxa with metabolic capabilities at pH 5.5. The diversity of active species decreased significantly at pH 4.5 and was dominated by Lactobacillus and Propionibacterium species, both of which have been previously found within carious lesions from children. Our approach allowed for identification of species that metabolize carbohydrates under different pH conditions and supports the importance of Lactobacilli and Propionibacterium in the development of childhood caries. Identification of species within healthy subjects that are active at low pH can lead to a better understanding of oral

Comparative analysis of Edwardsiella isolates from fish in the eastern United States identifies two distinct genetic taxa amongst organisms phenotypically classified as E. tarda

USGS Publications Warehouse

Griffin, Matt J.; Quiniou, Sylvie M.; Cody, Theresa; Tabuchi, Maki; Ware, Cynthia; Cipriano, Rocco C.; Mauel, Michael J.; Soto, Esteban

2013-01-01

Edwardsiella tarda, a Gram-negative member of the family Enterobacteriaceae, has been implicated in significant losses in aquaculture facilities worldwide. Here, we assessed the intra-specific variability of E. tarda isolates from 4 different fish species in the eastern United States. Repetitive sequence mediated PCR (rep-PCR) using 4 different primer sets (ERIC I & II, ERIC II, BOX, and GTG5) and multi-locus sequence analysis of 16S SSU rDNA, groEl, gyrA, gyrB, pho, pgi, pgm, and rpoA gene fragments identified two distinct genotypes of E. tarda (DNA group I; DNA group II). Isolates that fell into DNA group II demonstrated more similarity to E. ictaluri than DNA group I, which contained the reference E. tarda strain (ATCC #15947). Conventional PCR analysis using published E. tarda-specific primer sets yielded variable results, with several primer sets producing no observable amplification of target DNA from some isolates. Fluorometric determination of G + C content demonstrated 56.4% G + C content for DNA group I, 60.2% for DNA group II, and 58.4% for E. ictaluri. Surprisingly, these isolates were indistinguishable using conventional biochemical techniques, with all isolates demonstrating phenotypic characteristics consistent with E. tarda. Analysis using two commercial test kits identified multiple phenotypes, although no single metabolic characteristic could reliably discriminate between genetic groups. Additionally, anti-microbial susceptibility and fatty acid profiles did not demonstrate remarkable differences between groups. The significant genetic variation (<90% similarity at gyrA, gyrB, pho, phi and pgm; <40% similarity by rep-PCR) between these groups suggests organisms from DNA group II may represent an unrecognized, genetically distinct taxa of Edwardsiella that is phenotypically indistinguishable from E. tarda.

Mass extinction in poorly known taxa.

PubMed

Régnier, Claire; Achaz, Guillaume; Lambert, Amaury; Cowie, Robert H; Bouchet, Philippe; Fontaine, Benoît

2015-06-23

Since the 1980s, many have suggested we are in the midst of a massive extinction crisis, yet only 799 (0.04%) of the 1.9 million known recent species are recorded as extinct, questioning the reality of the crisis. This low figure is due to the fact that the status of very few invertebrates, which represent the bulk of biodiversity, have been evaluated. Here we show, based on extrapolation from a random sample of land snail species via two independent approaches, that we may already have lost 7% (130,000 extinctions) of the species on Earth. However, this loss is masked by the emphasis on terrestrial vertebrates, the target of most conservation actions. Projections of species extinction rates are controversial because invertebrates are essentially excluded from these scenarios. Invertebrates can and must be assessed if we are to obtain a more realistic picture of the sixth extinction crisis.

Mass extinction in poorly known taxa

PubMed Central

Régnier, Claire; Achaz, Guillaume; Lambert, Amaury; Cowie, Robert H.; Bouchet, Philippe; Fontaine, Benoît

2015-01-01

Since the 1980s, many have suggested we are in the midst of a massive extinction crisis, yet only 799 (0.04%) of the 1.9 million known recent species are recorded as extinct, questioning the reality of the crisis. This low figure is due to the fact that the status of very few invertebrates, which represent the bulk of biodiversity, have been evaluated. Here we show, based on extrapolation from a random sample of land snail species via two independent approaches, that we may already have lost 7% (130,000 extinctions) of the species on Earth. However, this loss is masked by the emphasis on terrestrial vertebrates, the target of most conservation actions. Projections of species extinction rates are controversial because invertebrates are essentially excluded from these scenarios. Invertebrates can and must be assessed if we are to obtain a more realistic picture of the sixth extinction crisis. PMID:26056308

Insular threat associations within taxa worldwide.

PubMed

Leclerc, Camille; Courchamp, Franck; Bellard, Céline

2018-04-23

The global loss of biodiversity can be attributed to numerous threats. While pioneer studies have investigated their relative importance, the majority of those studies are restricted to specific geographic regions and/or taxonomic groups and only consider a small subset of threats, generally in isolation despite their frequent interaction. Here, we investigated 11 major threats responsible for species decline on islands worldwide. We applied an innovative method of network analyses to disentangle the associations of multiple threats on vertebrates, invertebrates, and plants in 15 insular regions. Biological invasions, wildlife exploitation, and cultivation, either alone or in association, were found to be the three most important drivers of species extinction and decline on islands. Specifically, wildlife exploitation and cultivation are largely associated with the decline of threatened plants and terrestrial vertebrates, whereas biological invasions mostly threaten invertebrates and freshwater fish. Furthermore, biodiversity in the Indian Ocean and near the Asian coasts is mostly affected by wildlife exploitation and cultivation compared to biological invasions in the Pacific and Atlantic insular regions. We highlighted specific associations of threats at different scales, showing that the analysis of each threat in isolation might be inadequate for developing effective conservation policies and managements.

76 FR 20558 - Endangered and Threatened Wildlife and Plants; 44 Marine and Anadromous Taxa: Adding 10 Taxa...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-13

... Environmental Policy Act We have determined that an environmental assessment, as defined under the authority of the National Environmental Policy Act of 1969, need not be prepared in connection with regulations..., Costa Rica, Guatemala, Honduras, Mexico, Nicaragua, Panama, Venezuela, and all the islands of the West...

Genetic characterization and barcoding of taxa in the genus Wolffia Horkel ex Schleid. (Lemnaceae) as revealed by two plastidic markers and amplified fragment length polymorphism (AFLP).

PubMed

Bog, Manuela; Schneider, Philipp; Hellwig, Frank; Sachse, Svea; Kochieva, Elena Z; Martyrosian, Elena; Landolt, Elias; Appenroth, Klaus-J

2013-01-01

The genus Wolffia of the duckweed family (Lemnaceae) contains the smallest flowering plants. Presently, 11 species are recognized and categorized mainly on the basis of morphology. Because of extreme reduction of structure of all species, molecular methods are especially required for barcoding and identification of species and clones of this genus. We applied AFLP combined with Bayesian analysis of population structure to 66 clones covering all 11 species. Nine clusters were identified: (1) W. angusta and W. microscopica (only one clone), (2) W. arrhiza, (3) W. cylindracea (except one clone that might be a transition form), (4) W. australiana, (5) W. globosa, (6) W. globosa, W. neglecta, and W. borealis, (7) W. brasiliensis, and W. columbiana, (8) W. columbiana, (9) W. elongata. Furthermore, we investigated the sequences of plastidic regions rps16 (54 clones) and rpl16 (55 clones), and identified the following species: W. angusta, W. australiana, W. brasiliensis, W. cylindracea, W. elongata, W. microscopica, and W. neglecta. Wolffia globosa has been separated into two groups by both methods. One group which consists only of clones from North America and East Asia was labelled here "typical W. globosa". The other group of W. globosa, termed operationally "W. neglecta", contains also clones of W. neglecta and shows high similarity to W. borealis. None of the methods recognized W. borealis as a distinct species. Although each clone could be characterized individually by AFLP and plastidic sequences, and most species could be bar-coded, the presently available data are not sufficient to identify all taxa of Wolffia.

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

PubMed Central

2012-01-01

Introduction Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa. Results cDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature. Conclusions We generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable

Comparisons of toxic baits for controlling the cockroach, Blattella germanica: attractiveness and feeding stimulation.

PubMed

Durier, V; Rivault, C

2000-12-01

Female German cockroaches, Blattella germanica (L.) (Dictyoptera: Blattellidae) and nymphs (stages 1, 3 and 6) were used to test the attractiveness and the feeding stimulation of several commercial gel formulations of insecticide food baits in laboratory binary choice tests. The four toxic gel baits tested were: 'Avert' (0.05% abamectin=avermectin B1), 'Drax' (33.3% boric acid), 'Goliath' (0.05% fipronil) and 'Maxforce' (2.15% hydramethylnon). The attractiveness of a bait was estimated by the number of cockroaches that chose it first, and by their tendency to change to it secondarily. Feeding stimulation was estimated by the mean duration of feeding bouts and total duration of food intake. Variability of these factors was assessed in relation to age of cockroaches and to age of baits. With a few exceptions, cockroach age did not affect performance in any of these tests. Attractiveness to B. germanica ranked 'Goliath' gel higher than 'Avert', 'Drax' and 'Maxforce' gels, whether or not the active ingredient fipronil was present in 'Goliath' gel. Feeding stimulation ranked 'Avert' and 'Maxforce' gels higher than 'Goliath' gel, and 'Drax' gel was inferior. With ageing up to 3 months, the feeding stimulation power of 'Goliath' and 'Maxforce' gels increased, whereas that of 'Avert' fluctuated. Assuming that all types of bait effectively kill cockroaches once ingested, these results illustrate the importance of behavioural observations on bait efficiency and show that ranking of these different food baits varies in relation to the parameter analysed.

Efficacy of Chlorantraniliprole in Controlling Structural Infestations of the Eastern Subterranean Termite in the USA

PubMed Central

Jones, Susan C.; Vargo, Edward L.; Keefer, T. Chris; Labadie, Paul; Scherer, Clay W.; Gallagher, Nicola T.; Gold, Roger E.

2017-01-01

Subterranean termites are the most economically important structural pests in the USA, and the eastern subterranean termite, Reticulitermes flavipes (Kollar) (Dictyoptera: Rhinotermitidae) is the most widely distributed species. Soil treatment with a liquid termiticide is a widely used method for controlling subterranean termites in structures. We assessed the efficacy of a nonrepellent termiticide, Altriset® (active ingredient: chlorantraniliprole), in controlling structural infestations of R. flavipes in Texas, North Carolina, and Ohio and determined the post-treatment fate of termite colonies in and around the structures. In all three states, microsatellite markers indicated that only one R. flavipes colony was infesting each structure. A single chlorantraniliprole treatment provided effective structural protection as there was no further evidence of termite activity in and on the majority of structures from approximately 1 month to 2 years post-treatment when the study concluded. Additionally, the treatment appeared to either severely reduce the infesting colony’s footprint at monitors in the landscape or eliminate colony members from these monitors. A supplemental spot-treatment was conducted at one house each in Texas and North Carolina at 5 and 6 months post-treatment, respectively; no termites were observed thereafter in these structures and associated landscaping. The number of colonies found exclusively in the landscape (not attacking the structure) varied among the states, with the largest number of colonies in Texas (0–4) and North Carolina (0–5) as compared to 0–1 in Ohio, the most northern state. PMID:28858226

A reappraisal of the Pleurotus eryngii complex - new species and taxonomic combinations based on the application of a polyphasic approach, and an identification key to Pleurotus taxa associated with Apiaceae plants.

PubMed

Zervakis, Georgios I; Ntougias, Spyridon; Gargano, Maria Letizia; Besi, Maria I; Polemis, Elias; Typas, Milton A; Venturella, Giuseppe

2014-01-01

The Pleurotus eryngii species-complex comprises choice edible mushrooms growing on roots and lower stem residues of Apiaceae (umbellifers) plants. Material deriving from extensive sampling was studied by mating compatibility, morphological and ecological criteria, and through analysis of ITS1-5.8S-ITS2 and IGS1 rRNA sequences. Results revealed that P. eryngii sensu stricto forms a diverse and widely distributed aggregate composed of varieties elaeoselini, eryngii, ferulae, thapsiae, and tingitanus. Pleurotuseryngii subsp. tuoliensis comb. nov. is a phylogenetically sister group to the former growing only on various Ferula species in Asia. The existence of Pleurotusnebrodensis outside of Sicily (i.e., in Greece) is reported for the first time on the basis of molecular data, while P. nebrodensis subsp. fossulatus comb. nov. is a related Asiatic taxon associated with the same plant (Prangos ferulacea). Last, Pleurotusferulaginis sp. nov. grows on Ferulago campestris in northeast Italy, Slovenia and Hungary; it occupies a distinct phylogenetic position accompanied with significant differences in spore size and mating incompatibility versus other Pleurotus populations. Coevolution with umbellifers and host/substrate specificity seem to play key roles in speciation processes within this fungal group. An identification key to the nine Pleurotus taxa growing in association with Apiaceae plants is provided. Copyright © 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay.

PubMed

Dai, Tianjiao; Zhang, Yan; Tang, Yushi; Bai, Yaohui; Tao, Yile; Huang, Bei; Wen, Donghui

2016-10-01

Coastal areas are land-sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Summary of taxa-specific research: 2. pathogens

Treesearch

Ned Klopfenstein; Brian Geils

2009-01-01

Damage caused by invasive forest pathogens is widely viewed as more severe, long-term, widespread, and difficult to restore than that caused by any other biological disturbance agent. In the last century, pathogens introduced into our native forests have threatened extinction of native tree species and critically degraded many different ecosystems across North America...

Systematics of Hypocrea citrina and related taxa

PubMed Central

Overton, Barrie E.; Stewart, Elwin L.; Geiser, David M.; Jaklitsch, Walter M.

2006-01-01

Morphological studies and phylogenetic analyses of DNA sequences from three genomic regions – the internal transcribed spacer (ITS) regions of the nuclear ribosomal gene repeat, a partial sequence of RNA polymerase II subunit (rpb2), and a partial sequence of translation elongation factor (tef1) – were used to investigate the systematics of Hypocrea citrina and related species. A neotype specimen is designated for H. citrina that conforms to Persoon's description of a yellow effuse fungus occurring on leaf litter. Historical information and results obtained in this study provide the foundation for selection of a lectotype specimen from Fries's herbarium for H. lactea. The results indicate that (1) Hypocrea citrina and H. pulvinata are distinct species; (2) H. lactea sensu Fries is a synonym of the older name H. citrina; (3) H. pulvinata, H. protopulvinata, and H. americana are phylogenetically distinct species that form a well-supported polyporicolous clade; (4) H. citrina is situated in a clade closely related to H. pulvinata; and (5) H. microcitrina and H. pseudostraminea reside in a highly supported clade phylogenetically distinct from H. citrina. Hypocrea protopulvinata, H. microcitrina, H. megalocitrina, H. pseudostraminea, and a new species, H. aurantiistroma, are reported and described from North America. Variation in rpb2 and tef1 gene sequences suggests geographical subgroupings between European and North American isolates of H. pulvinata. The phylogenies inferred from ITS, rpb2, and tef1 gene sequences are concordant. Hypocrea citrina var. americana is elevated to species status, Hypocrea americana. PMID:18490988

Checklist of Fabaceae Lindley in Balaghat Ranges of Maharashtra, India

PubMed Central

2015-01-01

Abstract The present paper provides an enumeration of leguminous taxa of Balaghat Ranges of Maharashtra along with their habits, phenological deta and voucher specimen numbers. During the present work, a total of 123 species, 4 subspecies and 17 varieties of Fabaceae have been recorded for Balaghat Ranges of Maharashtra, of which 119 taxa are occurring in wild while 25 are under cultivation. The members of Fabaceae are dominant in herbaceous vegetation of the Balaghat Ranges. There are more species in genera like Crotalaria (23 taxa), Indigofera (16 taxa), Alysicarpus (14 taxa), Vigna (11 taxa) and Desmodium (8 taxa). Twelve taxa are endemic to India of which Indigofera deccanensis falls into Critically Endangered IUCN Red data category. The legumes of Balaghat Ranges have many actual and potential uses such as food, fodder and sources of edible oil, natural dyes, industrial lubricants, timber and medicines. About 19 leguminous taxa are wild relatives of food and fodder crops have resistance to pests and diseases, and abiotic stresses such as drought and salinity, can be used for crop improvement. PMID:25829859

Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction.

PubMed

Mallatt, Jon; Craig, Catherine Waggoner; Yoder, Matthew J

2010-04-01

This study (1) uses nearly complete rRNA-gene sequences from across Metazoa (197 taxa) to reconstruct animal phylogeny; (2) presents a highly annotated, manual alignment of these sequences with special reference to rRNA features including paired sites (http://purl.oclc.org/NET/rRNA/Metazoan_alignment) and (3) tests, after eliminating as few disruptive, rogue sequences as possible, if a likelihood framework can recover the main metazoan clades. We found that systematic elimination of approximately 6% of the sequences, including the divergent or unstably placed sequences of cephalopods, arrowworm, symphylan and pauropod myriapods, and of myzostomid and nemertodermatid worms, led to a tree that supported Ecdysozoa, Lophotrochozoa, Protostomia, and Bilateria. Deuterostomia, however, was never recovered, because the rRNA of urochordates goes (nonsignificantly) near the base of the Bilateria. Counterintuitively, when we modeled the evolution of the paired sites, phylogenetic resolution was not increased over traditional tree-building models that assume all sites in rRNA evolve independently. The rRNA genes of non-bilaterians contain a higher % AT than do those of most bilaterians. The rRNA genes of Acoela and Myzostomida were found to be secondarily shortened, AT-enriched, and highly modified, throwing some doubt on the location of these worms at the base of Bilateria in the rRNA tree--especially myzostomids, which other evidence suggests are annelids instead. Other findings are marsupial-with-placental mammals, arrowworms in Ecdysozoa (well supported here but contradicted by morphology), and Placozoa as sister to Cnidaria. Finally, despite the difficulties, the rRNA-gene trees are in strong concordance with trees derived from multiple protein-coding genes in supporting the new animal phylogeny. (c) 2009 Elsevier Inc. All rights reserved.

Assessing streamflow characteristics as limiting factors on benthic invertebrate assemblages in streams across the western United States

USGS Publications Warehouse

Konrad, C.P.; Brasher, A.M.D.; May, J.T.

2008-01-01

4. Relative abundance of Plecoptera, richness of non-insect taxa and relative abundance of intolerant taxa were associated with multiple streamflow metrics. Metrics of sensitive taxa (Ephemeroptera, Plecoptera and Trichoptera), and intolerant taxa generally had ceilings associated with flow metrics while metrics of tolerant taxa, non-insects, dominance and chironomids generally had floors. Broader characteristics of invertebrate assemblages such as abundance and richness had fewer limits, but these limits were nonetheless associated with a broad range of streamflow characteristics.

Investigation of taxa of the family Pasteurellaceae isolated from Syrian and European hamsters and proposal of Mesocricetibacter intestinalis gen. nov., sp. nov. and Cricetibacter osteomyelitidis gen. nov., sp. nov.

PubMed

Christensen, H; Nicklas, W; Bisgaard, M

2014-11-01

Eleven strains from hamster of Bisgaard taxa 23 and 24, also referred to as Krause's groups 2 and 1, respectively, were investigated by a polyphasic approach including data published previously. Strains showed small, regular and circular colonies with smooth and shiny appearance, typical of members of the family Pasteurellaceae. The strains formed two monophyletic groups based on 16S rRNA gene sequence comparison to other members of the family Pasteurellaceae. Partial rpoB sequencing as well as published data on DNA-DNA hybridization showed high genotypic relationships within both groups. Menaquinone 7 (MK7) was found in strains of both groups as well as an unknown ubiquinone with shorter chain length than previously reported for any other member of the family Pasteurellaceae. A new genus with one species, Mesocricetibacter intestinalis gen. nov., sp. nov., is proposed to accommodate members of taxon 24 of Bisgaard whereas members of taxon 23 of Bisgaard are proposed to represent Cricetibacter osteomyelitidis gen. nov., sp. nov. Major fatty acids of type strains of type species of both genera are C(14:0), C(14:0) 3-OH/iso-C(16:1) I, C(16:1)ω7c and C(16:0). The two genera are clearly separated by phenotype from each other and from existing genera of the family Pasteurellaceae. The type strain of Mesocricetibacter intestinalis is HIM 933/7(T) ( =Kunstyr 246/85(T) =CCUG 28030(T) =DSM 28403(T)) while the type strain of Cricetibacter osteomyelitidis is HIM943/7(T) ( =Kunstyr 507/85(T) =CCUG 36451(T) =DSM 28404(T)). © 2014 IUMS.

A synoptic account of flora of solapur district, maharashtra (India).

PubMed

Garad, Krushnadeoray U; Gore, Ramchandra D; Gaikwad, Sayajirao P

2015-01-01

The present paper provides the first systematic and comprehensive account of the flora of Solapur district of Maharashtra (India). The flora of this region demonstrates a wide range of species diversity and growth forms. The vegetation of the district mainly represents tropical dry deciduous forests, thorny open scrub and vast grasslands. During the present work, a total of 1441 taxa belonging to 699 genera and 125 families of flowering plants were recorded. A new species Crinumsolapurense Gaikwad et al. is described. Fabaceae is the dominant family with 210 taxa, followed by Poaceae (157 taxa), Asteraceae (85 taxa), Malvaceae (68 taxa) and Euphorbiaceae (48 taxa). Acacia is the largest genus with 25 taxa, followed by Euphorbia (23), Cyperus (22), Crotalaria (19) and Ipomoea (19). The herbaceous flora of the district is notable as it amounts to 56.21% of the whole of flora. The ratio of indigenous woody to herbaceous components is 1:1.28. The proportion of indigenous taxa (978) to the cultivated ones (460) is 1.35: 0.5 in the district.

A Synoptic Account of Flora of Solapur District, Maharashtra (India)

PubMed Central

Garad, Krushnadeoray U.; Gaikwad, Sayajirao P.

2015-01-01

Abstract The present paper provides the first systematic and comprehensive account of the flora of Solapur district of Maharashtra (India). The flora of this region demonstrates a wide range of species diversity and growth forms. The vegetation of the district mainly represents tropical dry deciduous forests, thorny open scrub and vast grasslands. During the present work, a total of 1441 taxa belonging to 699 genera and 125 families of flowering plants were recorded. A new species Crinum solapurense Gaikwad et al. is described. Fabaceae is the dominant family with 210 taxa, followed by Poaceae (157 taxa), Asteraceae (85 taxa), Malvaceae (68 taxa) and Euphorbiaceae (48 taxa). Acacia is the largest genus with 25 taxa, followed by Euphorbia (23), Cyperus (22), Crotalaria (19) and Ipomoea (19). The herbaceous flora of the district is notable as it amounts to 56.21% of the whole of flora. The ratio of indigenous woody to herbaceous components is 1:1.28. The proportion of indigenous taxa (978) to the cultivated ones (460) is 1.35: 0.5 in the district. PMID:25632259

Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management.

PubMed

Poudel, R; Jumpponen, A; Schlatter, D C; Paulitz, T C; Gardener, B B McSpadden; Kinkel, L L; Garrett, K A

2016-10-01

Network models of soil and plant microbiomes provide new opportunities for enhancing disease management, but also challenges for interpretation. We present a framework for interpreting microbiome networks, illustrating how observed network structures can be used to generate testable hypotheses about candidate microbes affecting plant health. The framework includes four types of network analyses. "General network analysis" identifies candidate taxa for maintaining an existing microbial community. "Host-focused analysis" includes a node representing a plant response such as yield, identifying taxa with direct or indirect associations with that node. "Pathogen-focused analysis" identifies taxa with direct or indirect associations with taxa known a priori as pathogens. "Disease-focused analysis" identifies taxa associated with disease. Positive direct or indirect associations with desirable outcomes, or negative associations with undesirable outcomes, indicate candidate taxa. Network analysis provides characterization not only of taxa with direct associations with important outcomes such as disease suppression, biofertilization, or expression of plant host resistance, but also taxa with indirect associations via their association with other key taxa. We illustrate the interpretation of network structure with analyses of microbiomes in the oak phyllosphere, and in wheat rhizosphere and bulk soil associated with the presence or absence of infection by Rhizoctonia solani.

The role of hybridization in facilitating tree invasion

PubMed Central

2017-01-01

Abstract Hybridization events can generate additional genetic diversity upon which natural selection can act and at times enhance invasiveness of the species. Invasive tree species are a growing ecological concern worldwide, and some of these invasions involve hybridization events pre- or post-introduction. There are 20 hybrid invasive tree taxa in 15 genera (11 plant families) discussed here. When reported, abundance of hybrids comprised 10–100 % of an invasion, the remainder being parental taxa. In seven hybrid taxa, researchers identified phenotypes that may make hybrids better invaders. Twelve hybrid tree taxa involved introgression and more hybrids involved all non-native taxa than native × non-native taxa. Three hybrid tree taxa were the result of intentional crosses, and all hybrid taxa involved intentional introduction of either one or more parental taxon or the hybrid itself. The knowledge gaps present in some hybrid tree taxa can weaken our effectiveness in predicting and controlling invasions, as hybrids can add a level of complexity to an invasion by being morphologically cryptic, causing genetic pollution of a native parental taxon, presenting novel genotypes for which there may not be coevolved biological control agents, or evolving adaptive traits through increased genetic variation. PMID:28028055

Vascular plant species of the Comanche National Grassland in southeastern Colorado

Treesearch

Donald L. Hazlett

2004-01-01

This checklist has 785 species and 801 taxa (for taxa, the varieties and subspecies are included in the count) in 90 plant families. The most common plant families are the grasses (Poaceae) and the sunflower family (Asteraceae). Of this total, 513 taxa are definitely known to occur on the Comanche National Grassland. The remaining 288 taxa occur in nearby areas of...

Dominant molluscan taxa in the northern Adriatic Sea over the last centuries: down-core changes in shell communities and their implications for an ecological history

NASA Astrophysics Data System (ADS)

Haselmair, Alexandra; Gallmetzer, Ivo; Tomasovych, Adam; Stachowitsch, Michael; Zuschin, Martin

2015-04-01

The northern Adriatic Sea, with its densely populated shoreline, is among the most degraded marine ecosystems worldwide and therefore particularly suited to study ecosystem modification under human pressure. In particular, the period of the last 500 to 1500 years witnessed major anthropogenic impacts here. The present study reconstructs major ecological shifts over this timespan by identifying down-core changes in molluscan death assemblages that can serve as proxies for changing environmental conditions. Here, we focus on taxonomical down-core fluctuations and changes in abundance of key bivalve and gastropod taxa found at seven sampling stations spread throughout the northern Adriatic basin. At these stations, which were chosen in order to cover different sediment types, nutrient conditions and degrees of exploitation, several cores of 1.5 m length and diameters of 90 and 160 mm were taken and sliced into smaller subsamples of 2 and 5 cm, respectively. The samples were sieved through a 1 mm mesh size and all the shells found counted and identified to species level if possible. In total, 114 bivalve and 112 gastropod species were recorded. At the Po delta and Panzano bay stations, characterized by muddy sediments, Corbula gibba and Kurtiella bidentata were the dominant bivalve species, Nassarius pygmaeus and Turritella communis the most abundand gastropods. In the sandy mud from the Brijuni islands, the bivalves Timoclea ovata and Striarca lactea were very numerous, whereas at the Piran station, characterized by a similar sediment composition, Gouldia minima and Corbula gibba reached the highest numbers. Overall abundances of bivalve and gastropod species differed markedly between stations. In all cores, the incidence of individual species varied down-core. Opposite trends were recorded for Brijuni and Piran station: at Piran, the abundance peaked in the uppermost sediment layers while at the Brijuni islands the number of most gastropod and bivalve species

Front-Eddy Influence on Water Column Properties, Phytoplankton Community Structure, and Cross-Shelf Exchange of Diatom Taxa in the Shelf-Slope Area off Concepción (˜36-37°S)

NASA Astrophysics Data System (ADS)

Morales, Carmen E.; Anabalón, Valeria; Bento, Joaquim P.; Hormazabal, Samuel; Cornejo, Marcela; Correa-Ramírez, Marco A.; Silva, Nelson

2017-11-01

In eastern boundary current systems (EBCSs), submesoscale to mesocale variability contributes to cross-shore exchanges of water properties, nutrients, and plankton. Data from a short-term summer survey and satellite time series (January-February 2014) were used to characterize submesoscale variability in oceanographic conditions and phytoplankton distribution across the coastal upwelling and coastal transition zones north of Punta Lavapié, and to explore cross-shelf exchanges of diatom taxa. A thermohaline front (FRN-1) flanked by a mesoscale anticyclonic intrathermocline eddy (ITE-1), or mode-water eddy, persisted during the time series and the survey was undertaken during a wind relaxation event. At the survey time, ITE-1 contributed to an onshore intrusion of warm oceanic waters (southern section) and an offshore advection of cold coastal waters (northern section), with the latter forming a cold, high chlorophyll-a filament. In situ phytoplankton and diatom biomasses were highest at the surface in FRN-1 and at the subsurface in ITE-1, whereas values in the coastal zone were lower and dominated by smaller cells. Diatom species typical of the coastal zone and species dominant in oceanic waters were both found in the FRN-1 and ITE-1 interaction area, suggesting that this mixture was the result of both offshore and onshore advection. Overall, front-eddy interactions in EBCSs could enhance cross-shelf exchanges of coastal and oceanic plankton, as well as sustain phytoplankton growth in the slope area through localized upward injections of nutrients in the frontal zone, combined with ITE-induced advection and vertical nutrient inputs to the surface layer.

Low doses of the pesticide lindane induce protein release by the fat body of female cockroach Blaberus craniifer (Dictyoptera).

PubMed

Goudey-Perrière, Françoise; Lemonnier, François; Bergougnoux, Véronique; Perrière, Claude

2007-11-01

In the ovoviviparous cockroach Blaberus craniifer, low doses of the pesticide lindane (1-6 microg/g of body mass) have been implicated in the enhancement of ovarian growth and vitellogenesis onset in headless female ovaries. In order to investigate lindane effects on protein release by the fat body, we used antibodies raised against egg proteins to quantify protein levels in fat body, hemolymph and ovaries of treated-fed or -decapitated females 3- or 5-days -old. In vitro assays used fat body in Grace's medium to quantify the protein amount released in the medium. Individual data for each treatment were related to their corresponding control in paired series. In vivo, ovarian enhanced protein content was linked to an enhanced protein secretion by the fat body. This was ascertained in vitro by high levels of released protein in the medium containing lindane (1 microM) by fat body from females, but not from males. This effect was inhibited by EDTA, a calcium chelator. The present results confirmed that low doses of lindane (about 3 microg/g of body mass) acted as a juvenile hormone analogue, at the level of the ovaries, by enhancing protein uptake, and also at the level of the fat body, by triggering protein release. This property is calcium-dependent.

Does responsiveness to arbuscular mycorrhizal fungi depend on plant invasive status?

PubMed

Reinhart, Kurt O; Lekberg, Ylva; Klironomos, John; Maherali, Hafiz

2017-08-01

Differences in the direction and degree to which invasive alien and native plants are influenced by mycorrhizal associations could indicate a general mechanism of plant invasion, but whether or not such differences exist is unclear. Here, we tested whether mycorrhizal responsiveness varies by plant invasive status while controlling for phylogenetic relatedness among plants with two large grassland datasets. Mycorrhizal responsiveness was measured for 68 taxa from the Northern Plains, and data for 95 taxa from the Central Plains were included. Nineteen percent of taxa from the Northern Plains had greater total biomass with mycorrhizas while 61% of taxa from the Central Plains responded positively. For the Northern Plains taxa, measurable effects often depended on the response variable (i.e., total biomass, shoot biomass, and root mass ratio) suggesting varied resource allocation strategies when roots are colonized by arbuscular mycorrhizal fungi. In both datasets, invasive status was nonrandomly distributed on the phylogeny. Invasive taxa were mainly from two clades, that is, Poaceae and Asteraceae families. In contrast, mycorrhizal responsiveness was randomly distributed over the phylogeny for taxa from the Northern Plains, but nonrandomly distributed for taxa from the Central Plains. After controlling for phylogenetic similarity, we found no evidence that invasive taxa responded differently to mycorrhizas than other taxa. Although it is possible that mycorrhizal responsiveness contributes to invasiveness in particular species, we find no evidence that invasiveness in general is associated with the degree of mycorrhizal responsiveness. However, mycorrhizal responsiveness among species grown under common conditions was highly variable, and more work is needed to determine the causes of this variation.

Morphological Analysis of Cretaceous-Paleogene Boundary Foraminiferal Taxa

NASA Astrophysics Data System (ADS)

Mikenas, M.; Hull, P. M.; Henehan, M. J.

2014-12-01

66 million years ago at the end of the Cretaceous period, an asteroid impact in the Gulf of Mexico triggered the sudden extinction of an estimated 50% of marine invertebrate species. The event profoundly affected planktonic foraminifera, marine protists with an excellent fossil records in open marine sediments. The mass extinction and expansive fossil record of foraminifera creates the opportunity for detailed studies of the way species and ecosystems evolve and respond to environmental changes. Community level research is, however, relatively rare compared to geochemical paleoceanographic approaches. This is due, in part, to the fact that community level data collection is labor intensive and only partially records all aspects of the biological response. Here, I use a new approach to quantify community change with a computer-controlled microscope able to take high-resolution images of thousands of foraminifera at a time. Analytical software is used to classify populations by morphology, and this data is compared with traditional assemblage counts from multiple oceanic core sites from the late Maastrichtian to the early Danian. Previous studies have suggested that certain phenotypic characteristics are related to ecological niches -here, the direct measurement of shape of large populations of foraminifera is used to research the possible correlation between the K-Pg boundary events and community structure. Continued study of morphological data can be used to investigate the evolution of foraminiferal phenotypes, the connection between shape and ecological behavior, and the changes they exhibit in response to both sudden and long term changes in climate such as occurred near the K/Pg boundary. The image database of Maastrichtian and early Danian foraminifera will be made available to the scientific community, enabling inter-lab and cross-site comparisons.

Morphological studies in Veluticeps, Pileodon, and related taxa

Treesearch

Karen K. Nakasone

2004-01-01

In this study, type specimens of Fomes angularis, Pileodon megasporus, Veluticeps philippinensis, V. pini, V. setosa, and V. tabacina are described and illustrated. Fomes angularis and V. pini are conspecific with V. berkeleyi. Basidia and basidiospores of V. philippinensis are described for the first time, and the new combination Pileodon philippinensis is proposed....

Discrimination, Crypticity and Incipient Taxa in Entamoeba1

PubMed Central

Espinosa, Avelina; Paz-y-Miño-C, Guillermo

2011-01-01

Persistent difficulties in resolving clear lineages in diverging populations of prokaryotes or unicellular eukaryotes (protistan polyphyletic groups) are challenging the classical species concept. Although multiple integrated approaches would render holistic taxonomies, most phylogenetic studies are still based on single-gene or morphological traits. Such methodologies conceal natural lineages, which are considered ‘cryptic’. The concept of species is considered artificial and inadequate to define natural populations. Social organisms display differential behaviors toward kin than to non-related individuals. In ‘social’ microbes, kin discrimination has been used to help resolve crypticity. Aggregative behavior could be explored in a non-social protist to define phylogenetic varieties that are considered ‘cryptic’. Two Entamoeba invadens strains, VK-1:NS and IP-1 are considered close populations of the same ‘species’. This study demonstrates that VK-1:NS and IP-1 trophozoites aggregate only with alike members and discriminate individuals from different strains based on behavioral and chemical signals. Combined morphological, behavioral/chemical and ecological studies could improve Archamoebae phylogenies and define cryptic varieties. Evolutionary processes in which selection acted continuously and cumulatively on ancestors of Entamoeba populations gave rise to behavioral and chemical signals that allowed individuals to discriminate non-population members and gradually, to new lineages; alternative views that claim a ‘Designer’ or ‘Creator’ as responsible for protistan diversity are unfounded. PMID:22299709

Detecting Horizontal Gene Transfer between Closely Related Taxa

PubMed Central

Adato, Orit; Ninyo, Noga; Gophna, Uri; Snir, Sagi

2015-01-01

Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived) genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive. We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM). Using CRM, the algorithm assigns a confidence score based on “unusual” sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set. When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain. PMID:26439115

Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region.

PubMed

Pinkney, Alfred E; Driscoll, Charles T; Evers, David C; Hooper, Michael J; Horan, Jeffrey; Jones, Jess W; Lazarus, Rebecca S; Marshall, Harold G; Milliken, Andrew; Rattner, Barnett A; Schmerfeld, John; Sparling, Donald W

2015-07-01

The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public-private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena-freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures and

Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region

USGS Publications Warehouse

Pinkney, Alfred E.; Driscoll, Charles T.; Evers, David C.; Hooper, Michael J.; Horan, Jeffrey; Jones, Jess W.; Lazarus, Rebecca S.; Marshall, Harold G.; Milliken, Andrew; Rattner, Barnett A.; Schmerfeld, John J.; Sparling, Donald W.

2015-01-01

The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public–private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena—freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures

Comparison of macroinvertebrate community structure between two riffle-based sampling protocols in Wyoming, Colorado, and Montana, 2000-2001

USGS Publications Warehouse

Peterson, David A.; Zumberge, Jeremy R.

2006-01-01

Samples of benthic macroinvertebrates were collected side-by-side from riffles at 12 stream sites in Wyoming, Colorado, and Montana during 2000-2001, following protocols established by the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program and the U.S. Environmental Protection Agency Environmental Monitoring and Assessment Program (EMAP). Samples from riffles were collected following NAWQA protocols, using a sampler with 425-micron net mesh-opening size from a total area of 1.25 m2 per sample in multiple riffles. Samples also were collected following EMAP protocols, using a sampler with 500-micron net mesh-opening size from a total area of 0.72 m2 per sample in multiple riffles. The taxonomic identification and enumeration of the samples followed procedures established for each program. Benthic macroinvertebrate community structure was compared between the data sets using individual metrics, a multimetric index, and multivariate analysis. Comparisons between the macroinvertebrate community structures were made after sequentially adjusting both data sets for: (1) ambiguous taxa, (2) taxonomic inconsistencies, and (3) differences in laboratory subsampling. After removal of ambiguous taxa, pair-wise differences in total taxa richness and Ephemeroptera taxa richness were statistically significant (p < 0.05). Differences between the data sets generally were not significant for richness of other taxa, tolerant taxa, semi-voltine taxa, functional feeding groups, diversity, and dominance. Sample scores calculated using the Wyoming Stream Integrity Index were not significantly different between the two data sets. After reconciling both data sets for taxonomic inconsistencies, total taxa richness and Ephemeroptera taxa richness remained significantly different between the data sets. After adjusting the data for differences in laboratory subsampling, the differences in taxa richness were no longer significant. Bray-Curtis similarity coefficients and non

Differences in species richness patterns between unicellular and multicellular organisms.

PubMed

Hillebrand, Helmut; Watermann, Frank; Karez, Rolf; Berninger, Ulrike-G

2001-01-01

For unicellular organisms, a lack of effects of local species richness on ecosystem function has been proposed due to their locally high species richness and their ubiquitous distribution. High dispersal ability and high individual numbers may enable unicellular taxa to occur everywhere. Using our own and published data sets on uni- and multicellular organisms, we conducted thorough statistical analyses to test whether (1) unicellular taxa show higher relative local species richness compared to multicellular taxa, (2) unicellular taxa show lower slopes of the species:area relationships and species:individuals relationships, and (3) the species composition of unicellular taxa is less influenced by geographic distance compared to multicellular taxa. We found higher local species richness compared to the global species pool for unicellular organisms than for metazoan taxa. The difference was significant if global species richness was conservatively estimated but not if extrapolated, and therefore higher richness estimates were used. Both microalgae and protozoans showed lower slopes between species richness and sample size (area or individuals) compared to macrozoobenthos, also indicating higher local species richness for unicellular taxa. The similarity of species composition of both benthic diatoms and ciliates decreased with increasing geographic distance. This indicated restricted dispersal ability of protists and the absence of ubiquity. However, a steeper slope between similarity and distance was found for polychaetes and corals, suggesting a stronger effect of distance on the dispersal of metazoans compared to unicellular taxa. In conclusion, we found partly different species richness patterns among uni- and multicellular eukaryotes, but no strict ubiquity of unicellular taxa. Therefore, the effect of local unicellular species richness on ecosystem function has to be reanalyzed. Macroecological patterns suggested for multicellular organisms may differ in

The Long Term Response of Birds to Climate Change: New Results from a Cold Stage Avifauna in Northern England

PubMed Central

Stewart, John R.

2015-01-01

The early MIS 3 (55–40 Kyr BP associated with Middle Palaeolithic archaeology) bird remains from Pin Hole, Creswell Crags, Derbyshire, England are analysed in the context of the new dating of the site’s stratigraphy. The analysis is restricted to the material from the early MIS 3 level of the cave because the upper fauna is now known to include Holocene material as well as that from the Late Glacial. The results of the analysis confirm the presence of the taxa, possibly unexpected for a Late Pleistocene glacial deposit including records such as Alpine swift, demoiselle crane and long-legged buzzard with southern and/or eastern distributions today. These taxa are accompanied by more expected ones such as willow ptarmigan /red grouse and rock ptarmigan living today in northern and montane areas. Finally, there are temperate taxa normally requiring trees for nesting such as wood pigeon and grey heron. Therefore, the result of the analysis is that the avifauna of early MIS 3 in England included taxa whose ranges today do not overlap making it a non-analogue community similar to the many steppe-tundra mammalian faunas of the time. The inclusion of more temperate and woodland taxa is discussed in the light that parts of northern Europe may have acted as cryptic northern refugia for some such taxa during the last glacial. These records showing former ranges of taxa are considered in the light of modern phylogeographic studies as these often assume former ranges without considering the fossil record of those taxa. In addition to the anomalous combination of taxa during MIS 3 living in Derbyshire, the individuals of a number of the taxa are different in size and shape to members of the species today probably due to the high carrying capacity of the steppe-tundra. PMID:25992609

Amplified plant turnover in response to climate change forecast by Late Quaternary records

NASA Astrophysics Data System (ADS)

Nogués-Bravo, D.; Veloz, S.; Holt, B. G.; Singarayer, J.; Valdes, P.; Davis, B.; Brewer, S. C.; Williams, J. W.; Rahbek, C.

2016-12-01

Conservation decisions are informed by twenty-first-century climate impact projections that typically predict high extinction risk. Conversely, the palaeorecord shows strong sensitivity of species abundances and distributions to past climate changes, but few clear instances of extinctions attributable to rising temperatures. However, few studies have incorporated palaeoecological data into projections of future distributions. Here we project changes in abundance and conservation status under a climate warming scenario for 187 European and North American plant taxa using niche-based models calibrated against taxa-climate relationships for the past 21,000 years. We find that incorporating long-term data into niche-based models increases the magnitude of projected future changes for plant abundances and community turnover. The larger projected changes in abundances and community turnover translate into different, and often more threatened, projected IUCN conservation status for declining tree taxa, compared with traditional approaches. An average of 18.4% (North America) and 15.5% (Europe) of taxa switch IUCN categories when compared with single-time model results. When taxa categorized as `Least Concern' are excluded, the palaeo-calibrated models increase, on average, the conservation threat status of 33.2% and 56.8% of taxa. Notably, however, few models predict total disappearance of taxa, suggesting resilience for these taxa, if climate were the only extinction driver. Long-term studies linking palaeorecords and forecasting techniques have the potential to improve conservation assessments.

The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony.

PubMed

Debry, Ronald W

2005-06-01

The effect of taxonomic sampling on phylogenetic accuracy under parsimony is examined by simulating nucleotide sequence evolution. Random error is minimized by using very large numbers of simulated characters. This allows estimation of the consistency behavior of parsimony, even for trees with up to 100 taxa. Data were simulated on 8 distinct 100-taxon model trees and analyzed as stratified subsets containing either 25 or 50 taxa, in addition to the full 100-taxon data set. Overall accuracy decreased in a majority of cases when taxa were added. However, the magnitude of change in the cases in which accuracy increased was larger than the magnitude of change in the cases in which accuracy decreased, so, on average, overall accuracy increased as more taxa were included. A stratified sampling scheme was used to assess accuracy for an initial subsample of 25 taxa. The 25-taxon analyses were compared to 50- and 100-taxon analyses that were pruned to include only the original 25 taxa. On average, accuracy for the 25 taxa was improved by taxon addition, but there was considerable variation in the degree of improvement among the model trees and across different rates of substitution.

Utility of DNA barcoding for rapid and accurate assessment of bat diversity in Malaysia in the absence of formally described species.

PubMed

Wilson, J-J; Sing, K-W; Halim, M R A; Ramli, R; Hashim, R; Sofian-Azirun, M

2014-02-19

Bats are important flagship species for biodiversity research; however, diversity in Southeast Asia is considerably underestimated in the current checklists and field guides. Incorporation of DNA barcoding into surveys has revealed numerous species-level taxa overlooked by conventional methods. Inclusion of these taxa in inventories provides a more informative record of diversity, but is problematic as these species lack formal description. We investigated how frequently documented, but undescribed, bat taxa are encountered in Peninsular Malaysia. We discuss whether a barcode library provides a means of recognizing and recording these taxa across biodiversity inventories. Tissue was sampled from bats trapped at Pasir Raja, Dungun Terengganu, Peninsular Malaysia. The DNA was extracted and the COI barcode region amplified and sequenced. We identified 9 species-level taxa within our samples, based on analysis of the DNA barcodes. Six specimens matched to four previously documented taxa considered candidate species but currently lacking formal taxonomic status. This study confirms the high diversity of bats within Peninsular Malaysia (9 species in 13 samples) and demonstrates how DNA barcoding allows for inventory and documentation of known taxa lacking formal taxonomic status.

Evidence of taxon cycles in an Indo-Pacific passerine bird radiation (Aves: Pachycephala)

PubMed Central

Jønsson, Knud Andreas; Irestedt, Martin; Christidis, Les; Clegg, Sonya M.; Holt, Ben G.; Fjeldså, Jon

2014-01-01

Many insular taxa possess extraordinary abilities to disperse but may differ in their abilities to diversify and compete. While some taxa are widespread across archipelagos, others have disjunct (relictual) populations. These types of taxa, exemplified in the literature by selections of unrelated taxa, have been interpreted as representing a continuum of expansions and contractions (i.e. taxon cycles). Here, we use molecular data of 35 out of 40 species of the avian genus Pachycephala (including 54 out of 66 taxa in Pachycephala pectoralis (sensu lato), to assess the spatio-temporal evolution of the group. We also include data on species distributions, morphology, habitat and elevational ranges to test a number of predictions associated with the taxon-cycle hypothesis. We demonstrate that relictual species persist on the largest and highest islands across the Indo-Pacific, whereas recent archipelago expansions resulted in colonization of all islands in a region. For co-occurring island taxa, the earliest colonists generally inhabit the interior and highest parts of an island, with little spatial overlap with later colonists. Collectively, our data support the idea that taxa continuously pass through phases of expansions and contractions (i.e. taxon cycles). PMID:24403319

Checklist of beetles (Coleoptera) of Canada and Alaska. Second edition

PubMed Central

Bousquet, Yves; Bouchard, Patrice; Davies, Anthony E.; Sikes, Derek S.

2013-01-01

Abstract All 8237 species-group taxa of Coleoptera known to occur in Canada and Alaska are recorded by province/territory or state, along with their author(s) and year of publication, in a classification framework. Only presence of taxa in each Canadian province or territory and Alaska is noted. Labrador is considered a distinct geographical entity. Adventive and Holarctic species-group taxa are indicated. References to pertinent identification keys are given under the corresponding supraspecific taxa in the data archive. PMID:24363590

Cockroach Oothecal Parasitoid, Evania appendigaster (Hymenoptera: Evaniidae) Exhibits Oviposition Preference Towards Oothecal Age Most Vulnerable to Host Cannibalism.

PubMed

Tee, Hui-Siang; Lee, Chow-Yang

2017-12-05

Many female parasitoid wasps optimize host selection to balance the benefits of high-quality hosts and the costs of predator- or hyperparasitoid-induced mortality risks to maximize their fitness. Cannibalism exists in many insect species and affects survival of parasitoid larvae developing in or on parasitized hosts. However, little is known about how parasitoid wasps resolve the fitness consequence of host cannibalism-induced mortality risk during host selection. We examined the effect of oothecal age on cannibalism in the American cockroach Periplaneta americana (L.) (Dictyoptera: Blattidae) and its effect on host age selection and fitness of its oothecal parasitoid Evania appendigaster (L.) (Hymenoptera: Evaniidae). P. americana differentially cannibalized 1-d-old (30‒60%) versus 10- to 40-d-old oothecae (<9%). However, parasitoid females did not avoid but still preferred to parasitize 1-d-old (45%) over 10- to 40-d-old oothecae (1.6‒20%). The parasitism rate was greater and the handling time was shorter on 1-d-old compared to older oothecae. For parasitoid progeny emerging from different-aged oothecae, regression analysis showed that development time increased and body size (measured as hind tibia length) and longevity decreased with oothecal age. These results demonstrate that reduced parasitoid progeny survival due to host cannibalism did not change the parasitoid's oviposition preference for newly laid oothecae, and that E. appendigaster females traded progeny survival for fitness gains for themselves and their progeny. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Preliminary data from IODP Site U1338 of the Pacific Equatorial Age Transect (PEAT IODP Expedition 320/321): a study on the interaction between paleoenvironment and evolution of selected calcareous nannofossil taxa

NASA Astrophysics Data System (ADS)

Raffi, I.; Ciummelli, M.; Backman, J.; Iodp Expedition 320/321 Shipboard Scientific Party

2010-12-01

A continuous Cenozoic sediment record of the paleoequatorial Pacific ocean was recovered during IODP Expedition 320/321 (March-June 2009). The Pacific Equatorial Age Transect (PEAT) includes eight sites (U1331 to U1338), cored above the paleo-position of the equator at successive crustal ages on the Pacific plate, with records from the sediment surface to basement, with basalt aged between 53 to 18 Ma. The present study is focused on IODP Site 1338 that collected a 3-18 Ma segment of the PEAT equatorial megasplice. Although the target equatorial interval of Site 1338 was the middle and late Miocene, ~415 m of a complete sedimentary succession from Pleistocene to lower Miocene was recovered. Sediments are nannofossil ooze and chalk with varying concentrations (often relatively high abundances) of biosiliceous components, and show decimeter to meter lithological cycles that possibly reflect changes in production, dissolution, photic zone paleoecology. Ongoing analysis on nannofossil assemblages and selected taxa are providing distribution and abundance data that, combined with geochemical proxies, will unravel the biotic response to different climatic and oceanographic conditions. Biometric analysis and quantitative abundance analysis are used for providing a clear taxonomy of an important Neogene component of the nannofossil assemblages, the genus Discoaster, and for delineating in detail the evolutionary trends within the taxon. Moreover, we will try to relate the evolutionary signal observed in Discoaster lineage to the environmental evolution, namely to significant events such as the carbonate crash (Vincent and Berger, 1985; Lyle, et al., in prep.), the fluctuation and shallowing of the Calcite Compensation Depth (CCD) (Lyle, 2003), and deposition of diatom enriched intervals (Kemp and Baldauf, 1993).

Breeding system variation in 10 evening primroses (Oenothera sections Anogra and Kleinia; Onagraceae).

PubMed

Theiss, Kathryn E; Holsinger, Kent E; Evans, Margaret E K

2010-06-01

We examined two accounts of the relationship between breeding system and life history variation in a clade of evening primroses (Oenothera, Onagraceae): (1) selection for reproductive assurance should generate an association between self-compatibility and monocarpy and (2) phylogenetic conservatism leads to retention of breeding system and life history traits among closely related taxa. • We performed over 4000 hand pollinations under greenhouse conditions to determine the compatibility of 10 Oenothera taxa (sections Anogra [17 taxa] and Kleinia [2 taxa)] for which breeding systems had not previously been reported. We used generalized linear mixed models to evaluate the influence of pollination treatment, parents, and population on fruiting success. • Among the taxa tested, six were self-incompatible, two were variable in compatibility, and two were self-compatible. We combined these data with published studies in Anogra and Kleinia and mapped breeding system and life history onto a published phylogeny. • We found no evidence for phylogenetic conservatism, but detected considerable evolutionary lability in both traits. Additionally, we found no evidence for a consistent relationship between breeding system and life history. Only eight of 19 taxa followed the predicted association between self-incompatibility and polycarpy vs. self-compatibility and monocarpy. Instead, many taxa have retained self-incompatibility, regardless of monocarpy or polycarpy.

Influence of seasonal, diel, lunar, and other environmental factors on upstream fish passage in the igarapava fish ladder, Brazil

USGS Publications Warehouse

Bizzotto, P.M.; Godinho, Alexandre L.; Vono, V.; Kynard, B.; Godinho, Hugo P.

2009-01-01

Upstream fish passage was evaluated during 12 months in the vertical-slot Igarapava Fish Ladder constructed around Igarapava Dam, in the heavily dammed Grande River, Southeast Brazil. A video monitoring system was used to observe 61,621 fish that passed the ladder, of which 93.5% were identified to 15 taxa. Among the migratory species, the most abundant were Pimelodus maculatus (33.6% of all fish), Leporinus octofasciatus (31.4%), Leporinus friderici (4.5%), and Prochilodus lineatus (3.1%). Seven taxa were classified as nonmigratory, and of these taxa, the small Bryconamericus stramineus was the most abundant (12.7%) of all fishes. Passage of the 'nonmigratory' taxa upstream in the ladder shows they are migratory in this system and have a strong behavioural drive to move to upstream habitat. Passage of most taxa had a strong seasonal pattern. While some species passed primarily during the day, others showed a distinct nocturnal pattern. Lunar phase and water temperature also strongly affected passage of some taxa. Rainfall and dam discharge had a small or null influence on most taxa; perhaps due to the fairly small catchment area of the reservoir and the highly regulated discharge at Igarapava Dam. ?? 2009 John Wiley & Sons A/S.

Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation

PubMed Central

Lammers, Youri; Yoccoz, Nigel Giles; Jørgensen, Tina; Sjögren, Per; Gielly, Ludovic; Edwards, Mary E.

2018-01-01

Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation. PMID:29664954

Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation.

PubMed

Alsos, Inger Greve; Lammers, Youri; Yoccoz, Nigel Giles; Jørgensen, Tina; Sjögren, Per; Gielly, Ludovic; Edwards, Mary E

2018-01-01

Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17-49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.

Evidence for progenitor–derivative speciation in sexually deceptive orchids

PubMed Central

Schlüter, Philipp M.; Ruas, Paulo M.; Kohl, Gudrun; Ruas, Claudete F.; Stuessy, Tod F.; Paulus, Hannes F.

2011-01-01

Background and Aims Sexually deceptive orchids of the genus Ophrys use mimicry of pollinator females to attract specific pollinators. Pollinator shifts may drive speciation in Ophrys, since novel pollinators may in principle act as isolating factors immediately. It is thus possible that evolution of novel species occurs rapidly and with a progenitor–derivative pattern. The aims of this study are to compare genetic structure and diversity among widespread and geographically restricted Ophrys taxa, to test whether genetic structure is associated with specific pollinators, and to investigate whether any widespread species may have acted as a progenitor for the evolution of more restricted taxa. Methods Genetic differentiation and diversity were investigated in O. leucadica and O. cinereophila, the two taxa of the Ophrys fusca sensu lato complex widespread in the Aegean, and three geographically restricted taxa from Rhodes, O. attaviria, O. parvula and O. persephonae, all differing in their specific pollinators. This was done using amplified fragment length polymorphism (AFLP) DNA fingerprinting, and sequencing of the low-copy nuclear gene LEAFY (LFY). Key Results All taxa were found to be separate genetic entities, with O. leucadica forming two geographic groups from the west and east of the Aegean. Genetic structure was significantly shaped by pollinators and geography, and comparison of sequence and AFLP data revealed ancestral polymorphisms shared among several taxa. Among the sampled taxa, O. leucadica harbours the greatest genetic differentiation and geographic structure, and the highest genetic diversity. Part of the genome of O. parvula, endemic to Rhodes, may be derived from O. leucadica. Conclusions Pollinators probably influence the genetic structure of the investigated Ophrys species. The genetic pattern identified is consistent with O. leucadica being the oldest of the sampled taxa, making O. leucadica a candidate progenitor species from which more

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

Andersen, Gary L.; Dubinsky, Eric A.

Herein are described 1058 different bacterial taxa that were unique to either human, grazing mammal, or bird fecal wastes. These identified taxa can serve as specific identifier taxa for these sources in environmental waters. Two field tests in marine waters demonstrate the capacity of phylogenetic microarray analysis to track multiple sources with one test.

Landscape-scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton.

PubMed

Niño-García, Juan Pablo; Ruiz-González, Clara; Del Giorgio, Paul A

2016-12-01

Aquatic bacterial communities harbour thousands of coexisting taxa. To meet the challenge of discriminating between a 'core' and a sporadically occurring 'random' component of these communities, we explored the spatial abundance distribution of individual bacterioplankton taxa across 198 boreal lakes and their associated fluvial networks (188 rivers). We found that all taxa could be grouped into four distinct categories based on model statistical distributions (normal like, bimodal, logistic and lognormal). The distribution patterns across lakes and their associated river networks showed that lake communities are composed of a core of taxa whose distribution appears to be linked to in-lake environmental sorting (normal-like and bimodal categories), and a large fraction of mostly rare bacteria (94% of all taxa) whose presence appears to be largely random and linked to downstream transport in aquatic networks (logistic and lognormal categories). These rare taxa are thus likely to reflect species sorting at upstream locations, providing a perspective of the conditions prevailing in entire aquatic networks rather than only in lakes. © 2016 John Wiley & Sons Ltd/CNRS.

Temperature threshold models for benthic macroinvertebrates in Idaho wadeable streams and neighboring ecoregions.

PubMed

Richards, David C; Lester, Gary; Pfeiffer, John; Pappani, Jason

2018-02-07

Water temperatures are warming throughout the world including the Pacific Northwest, USA. Benthic macroinvertebrates are one of the most important and widely used indicators of freshwater impairment; however, their response to increased water temperatures and their use for monitoring water temperature impairment has been hindered by lack of knowledge of temperature occurrences, threshold change points, or indicator taxa. We present new analysis of a large macroinvertebrate database provided by Idaho Department of Environmental Quality from wadeable streams in Idaho that is to be used in conjunction with our previous analyses. This new analysis provides threshold change points for over 400 taxa along an increasing temperature gradient and provides a list of statistically important indicator taxa. The macroinvertebrate assemblage temperature change point for the taxa that decreased with increased temperatures was determined to be about 20.5 °C and for the taxa assemblage that increased with increased temperatures was about 11.5 °C. Results of this new analysis combined with our previous analysis will also be useful for others in neighboring regions where these taxa occur.

New pasture plants intensify invasive species risk.

PubMed

Driscoll, Don A; Catford, Jane A; Barney, Jacob N; Hulme, Philip E; Inderjit; Martin, Tara G; Pauchard, Aníbal; Pyšek, Petr; Richardson, David M; Riley, Sophie; Visser, Vernon

2014-11-18

Agricultural intensification is critical to meet global food demand, but intensification threatens native species and degrades ecosystems. Sustainable intensification (SI) is heralded as a new approach for enabling growth in agriculture while minimizing environmental impacts. However, the SI literature has overlooked a major environmental risk. Using data from eight countries on six continents, we show that few governments regulate conventionally bred pasture taxa to limit threats to natural areas, even though most agribusinesses promote taxa with substantial weed risk. New pasture taxa (including species, subspecies, varieties, cultivars, and plant-endophyte combinations) are bred with characteristics typical of invasive species and environmental weeds. By introducing novel genetic and endophyte variation, pasture taxa are imbued with additional capacity for invasion and environmental impact. New strategies to prevent future problems are urgently needed. We highlight opportunities for researchers, agribusiness, and consumers to reduce environmental risks associated with new pasture taxa. We also emphasize four main approaches that governments could consider as they build new policies to limit weed risks, including (i) national lists of taxa that are prohibited based on environmental risk; (ii) a weed risk assessment for all new taxa; (iii) a program to rapidly detect and control new taxa that invade natural areas; and (iv) the polluter-pays principle, so that if a taxon becomes an environmental weed, industry pays for its management. There is mounting pressure to increase livestock production. With foresight and planning, growth in agriculture can be achieved sustainably provided that the scope of SI expands to encompass environmental weed risks.

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa.

PubMed

Geisen, S; Laros, I; Vizcaíno, A; Bonkowski, M; de Groot, G A

2015-09-01

Protists, the most diverse eukaryotes, are largely considered to be free-living bacterivores, but vast numbers of taxa are known to parasitize plants or animals. High-throughput sequencing (HTS) approaches now commonly replace cultivation-based approaches in studying soil protists, but insights into common biases associated with this method are limited to aquatic taxa and samples. We created a mock community of common free-living soil protists (amoebae, flagellates, ciliates), extracted DNA and amplified it in the presence of metazoan DNA using 454 HTS. We aimed at evaluating whether HTS quantitatively reveals true relative abundances of soil protists and at investigating whether the expected protist community structure is altered by the co-amplification of metazoan-associated protist taxa. Indeed, HTS revealed fundamentally different protist communities from those expected. Ciliate sequences were highly over-represented, while those of most amoebae and flagellates were under-represented or totally absent. These results underpin the biases introduced by HTS that prevent reliable quantitative estimations of free-living protist communities. Furthermore, we detected a wide range of nonadded protist taxa probably introduced along with metazoan DNA, which altered the protist community structure. Among those, 20 taxa most closely resembled parasitic, often pathogenic taxa. Therewith, we provide the first HTS data in support of classical observational studies that showed that potential protist parasites are hosted by soil metazoa. Taken together, profound differences in amplification success between protist taxa and an inevitable co-extraction of protist taxa parasitizing soil metazoa obscure the true diversity of free-living soil protist communities. © 2015 John Wiley & Sons Ltd.

New pasture plants intensify invasive species risk

PubMed Central

Driscoll, Don A.; Catford, Jane A.; Barney, Jacob N.; Hulme, Philip E.; Inderjit; Martin, Tara G.; Pauchard, Aníbal; Pyšek, Petr; Richardson, David M.; Riley, Sophie; Visser, Vernon

2014-01-01

Agricultural intensification is critical to meet global food demand, but intensification threatens native species and degrades ecosystems. Sustainable intensification (SI) is heralded as a new approach for enabling growth in agriculture while minimizing environmental impacts. However, the SI literature has overlooked a major environmental risk. Using data from eight countries on six continents, we show that few governments regulate conventionally bred pasture taxa to limit threats to natural areas, even though most agribusinesses promote taxa with substantial weed risk. New pasture taxa (including species, subspecies, varieties, cultivars, and plant-endophyte combinations) are bred with characteristics typical of invasive species and environmental weeds. By introducing novel genetic and endophyte variation, pasture taxa are imbued with additional capacity for invasion and environmental impact. New strategies to prevent future problems are urgently needed. We highlight opportunities for researchers, agribusiness, and consumers to reduce environmental risks associated with new pasture taxa. We also emphasize four main approaches that governments could consider as they build new policies to limit weed risks, including (i) national lists of taxa that are prohibited based on environmental risk; (ii) a weed risk assessment for all new taxa; (iii) a program to rapidly detect and control new taxa that invade natural areas; and (iv) the polluter-pays principle, so that if a taxon becomes an environmental weed, industry pays for its management. There is mounting pressure to increase livestock production. With foresight and planning, growth in agriculture can be achieved sustainably provided that the scope of SI expands to encompass environmental weed risks. PMID:25368175

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia.

PubMed

Kumar, Manoj; van Elsas, Jan Dirk; Nissinen, Riitta

2017-01-01

as well as the endosphere communities in the Mayrhofen region were all characterized by high relative abundances of nifH sequences related to Geobacter . In contrast, the endosphere and soil (bulk or rhizosphere soil) communities in the High Arctic were highly divergent: endosphere communities in the arctic regions were shaped by Clostridium spp., while nifH sequences representing δ- Proteobacteria , β- Proteobacteria, Cyanobacteria (in Ny-Ålesund), and Verrucomicrobia (in Kilpisjärvi) dominated the soil communities. Interestingly, the major PNFB genera identified in this study have been previously identified as members of conserved core microbiomes in the endospheres and seeds of these plants by 16S rRNA gene based analyses combined with bacterial isolation, suggesting a very tight interaction between diazotrophic bacteria and these arctic pioneer plants. Overall, anaerobic bacterial taxa dominated the PNFB communities of the endospheres and rhizospheres of the two plant species in all study sites. This could indicate anoxic conditions in and around plant roots at the time of sampling (early growth season), created by melting snow and underlying permafrost.

Plant endemism in the Sierras of Córdoba and San Luis (Argentina): understanding links between phylogeny and regional biogeographical patterns.

PubMed

Chiapella, Jorge O; Demaio, Pablo H

2015-01-01

We compiled a checklist with all known endemic plants occurring in the Sierras of Córdoba and San Luis, an isolated mountainous range located in central Argentina. In order to obtain a better understanding of the evolutionary history, relationships and age of the regional flora, we gathered basic information on the biogeographical and floristic affinities of the endemics, and documented the inclusion of each taxon in molecular phylogenies. We listed 89 taxa (including 69 species and 20 infraspecific taxa) belonging to 53 genera and 29 families. The endemics are not distributed evenly, being more abundant in the lower than in the middle and upper vegetation belts. Thirty-two genera (60.3%) have been included in phylogenetic analyses, but only ten (18.8%) included local endemic taxa. A total of 28 endemic taxa of the Sierras CSL have a clear relationship with a widespread species of the same genus, or with one found close to the area. Available phylogenies for some taxa show divergence times between 7.0 - 1.8 Ma; all endemic taxa are most probably neoendemics sensu Stebbins and Major. Our analysis was specifically aimed at a particular geographic area, but the approach of analyzing phylogenetic patterns together with floristic or biogeographical relationships of the endemic taxa of an area, delimited by clear geomorphological features, could reveal evolutionary trends shaping the area.

Phytoplankton Assemblages in Selected Freshwaters of New Jersey

NASA Astrophysics Data System (ADS)

Caraballo, Y. A.; Wu, M. S.

2017-12-01

Characterizing phytoplankton assemblages in freshwaters is crucial for future management and monitoring of drinking and recreational freshwaters of New Jersey. New Jersey freshwater phytoplankton assemblages are poorly known and there is no list of freshwater phytoplankton taxa in New Jersey. This study seeks to describe phytoplankton assemblages of freshwaters in New Jersey. Results will help address public health, economic and environmental threats related to harmful algal blooms in New Jersey. A total of 49 freshwater sites, including ponds, rivers and reservoirs, were used for this study. Overall results showed 66 taxa of freshwater phytoplankton in 6 major groups and 29 different orders. Green algae had the highest number of taxa, followed by diatoms and blue-greens (cyanobacteria). The most common freshwater taxa in NJ are Synedra spp., Fragilaria spp., Selenastrum capricornutum, Scenedesmus spp., and Anabaena spp. Cyanobacteria species are present in more than half of the sites examined in this study. All ten cyanobacteria taxa present in New Jersey freshwaters are capable of producing the endotoxin lipopolysaccharides (LPS), eight can produce the hepatotoxins and six can produce neutoroxins. In addition, some taxa such as Anabaena spp. are capable of simultaneously producing endotoxins, hepatotoxins, neurotoxins and taste and odor compounds. The presence of taxa capable of producing multiple toxins infers the difficulty of management and treatment as well as increased public health effects.

Plant endemism in the Sierras of Córdoba and San Luis (Argentina): understanding links between phylogeny and regional biogeographical patterns1

PubMed Central

Chiapella, Jorge O.; Demaio, Pablo H.

2015-01-01

Abstract We compiled a checklist with all known endemic plants occurring in the Sierras of Córdoba and San Luis, an isolated mountainous range located in central Argentina. In order to obtain a better understanding of the evolutionary history, relationships and age of the regional flora, we gathered basic information on the biogeographical and floristic affinities of the endemics, and documented the inclusion of each taxon in molecular phylogenies. We listed 89 taxa (including 69 species and 20 infraspecific taxa) belonging to 53 genera and 29 families. The endemics are not distributed evenly, being more abundant in the lower than in the middle and upper vegetation belts. Thirty-two genera (60.3%) have been included in phylogenetic analyses, but only ten (18.8%) included local endemic taxa. A total of 28 endemic taxa of the Sierras CSL have a clear relationship with a widespread species of the same genus, or with one found close to the area. Available phylogenies for some taxa show divergence times between 7.0 – 1.8 Ma; all endemic taxa are most probably neoendemics sensu Stebbins and Major. Our analysis was specifically aimed at a particular geographic area, but the approach of analyzing phylogenetic patterns together with floristic or biogeographical relationships of the endemic taxa of an area, delimited by clear geomorphological features, could reveal evolutionary trends shaping the area. PMID:25878555

Phenological sensitivity to climate across taxa and trophic levels.

PubMed

Thackeray, Stephen J; Henrys, Peter A; Hemming, Deborah; Bell, James R; Botham, Marc S; Burthe, Sarah; Helaouet, Pierre; Johns, David G; Jones, Ian D; Leech, David I; Mackay, Eleanor B; Massimino, Dario; Atkinson, Sian; Bacon, Philip J; Brereton, Tom M; Carvalho, Laurence; Clutton-Brock, Tim H; Duck, Callan; Edwards, Martin; Elliott, J Malcolm; Hall, Stephen J G; Harrington, Richard; Pearce-Higgins, James W; Høye, Toke T; Kruuk, Loeske E B; Pemberton, Josephine M; Sparks, Tim H; Thompson, Paul M; White, Ian; Winfield, Ian J; Wanless, Sarah

2016-07-14

Differences in phenological responses to climate change among species can desynchronise ecological interactions and thereby threaten ecosystem function. To assess these threats, we must quantify the relative impact of climate change on species at different trophic levels. Here, we apply a Climate Sensitivity Profile approach to 10,003 terrestrial and aquatic phenological data sets, spatially matched to temperature and precipitation data, to quantify variation in climate sensitivity. The direction, magnitude and timing of climate sensitivity varied markedly among organisms within taxonomic and trophic groups. Despite this variability, we detected systematic variation in the direction and magnitude of phenological climate sensitivity. Secondary consumers showed consistently lower climate sensitivity than other groups. We used mid-century climate change projections to estimate that the timing of phenological events could change more for primary consumers than for species in other trophic levels (6.2 versus 2.5-2.9 days earlier on average), with substantial taxonomic variation (1.1-14.8 days earlier on average).

Using extant taxa to inform studies of fossil footprints

NASA Astrophysics Data System (ADS)

Falkingham, Peter; Gatesy, Stephen

2016-04-01

Attempting to use the fossilized footprints of extinct animals to study their palaeobiology and palaeoecology is notoriously difficult. The inconvenient extinction of the trackmaker makes direct correlation between footprints and foot far from straightforward. However, footprints are the only direct evidence of vertebrate motion recorded in the fossil record, and are potentially a source of data on palaeobiology that cannot be obtained from osteological remains alone. Our interests lie in recovering information about the movements of dinosaurs from their tracks. In particular, the Hitchcock collection of early Jurassic tracks held at the Beneski Museum of Natural History, Amherst, provide a rare look into the 3D form of tracks at and below the surface the animal walked on. Breaking naturally along laminations into 'track books', the specimens present sediment deformation at multiple levels, and in doing so record more of the foot's motion than a single surface might. In order to utilize this rich information source to study the now extinct trackmakers, the process of track formation must be understood at a fundamental level; the interaction of the moving foot and compliant substrate. We used bi-planar X-ray techniques (X-ray Reconstruction of Moving Morphology) to record the limb and foot motions of a Guineafowl traversing both granular and cohesive substrates. This data was supplemented with photogrammetric records of the resultant track surfaces, as well as the motion of metal beads within the sediment, to provide a full experimental dataset of foot and footprint formation. The physical experimental data was used to generate computer simulations of the process using high performance computing and the Discrete Element Method. The resultant simulations showed excellent congruence with reality, and enabled visualization within the sediment volume, and throughout the track-forming process. This physical and virtual experimental set-up has provided major insight into how to interpret the track-books within the Amherst Collection, and as such begin to understand how these early Jurassic dinosaurs moved. More broadly, this complete view of track formation afforded by experimental techniques will aid in interpretation of fossil vertebrate tracks throughout the fossil record.

Characterizing Specimens of Kudzu and Related Taxa with RAPD's

Treesearch

D.K. Jewett; C.J. Jiang; K.O. Britton; J.H. Sun; J. Tang

2003-01-01

Kudzu [Pueraria montana (Lour.) Merr. var. lobata (Willd.) Maesen and Almeidal is a perennial, semi-woody, climbing legume in the tribe Phaseoleae Benth., subtribe Glycininae Benth. (Maesen 1985, Maesen and Almeida 1988, Ward 1998). It is native to China, where an abundance of natural enemies (Pemberton 1988) and its cultivation...

New taxa of Orthoptera (Insecta Tettigoniidae Phaneropterinae) from Madagascar.

PubMed

Massa, Bruno

2017-03-10

The author reports the results of a study on Orthoptera collected in Madagascar and preserved in two European Natural History museums. He describes Symmetroraggea depravata n. sp., Parapyrrhicia longipodex n. sp., Madagascarantia bartolozzii n. gen. n. sp., Mimoscudderia spinicercata n. sp. In addition, he lists new records or unknown taxonomical characters of Xenodus nobilis Carl, 1914 and Parapyrrhicia virilis Carl, 1914.

Multi-taxa population connectivity in the northern Rocky Mountains

Treesearch

Samuel A. Cushman; Erin L. Landguth

2012-01-01

Effective broad-spectrum biodiversity conservation requires that conservation strategies simultaneously meet the needs of multiple species. However, little is known about how maintaining habitat connectivity for one species or species group may also act as an umbrella for other species. We evaluated the degree to which predicted connected habitat for each of 144...

Phylogenetic classification of yeasts and related taxa within Pucciniomycotina

PubMed Central

Wang, Q.-M.; Yurkov, A.M.; Göker, M.; Lumbsch, H.T.; Leavitt, S.D.; Groenewald, M.; Theelen, B.; Liu, X.-Z.; Boekhout, T.; Bai, F.-Y.

2016-01-01

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the “One Fungus = One Name” nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study. PMID:26951631

Citrus cyopreservation: viability of diverse taxa and histological observations

USDA-ARS?s Scientific Manuscript database

Diverse citrus cultivars maintained clonally within gene banks serve as valuable resources for research and breeding programs worldwide. These critical collections are kept as trees within field, screenhouse, or greenhouse collections. These ex situ collections are at risk of being lost due to unfor...

Phylogenetic classification of yeasts and related taxa within Pucciniomycotina.

PubMed

Wang, Q-M; Yurkov, A M; Göker, M; Lumbsch, H T; Leavitt, S D; Groenewald, M; Theelen, B; Liu, X-Z; Boekhout, T; Bai, F-Y

2015-06-01

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the "One Fungus = One Name" nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.

Vascular flora of the Penobscot Experimental Forest, with provisional lists of lichens and bryophytes

Treesearch

Alison C. Dibble

2014-01-01

A compilation of plant lists from all available sources since the 1950s represents the flora of the Penobscot Experimental Forest (PEF), Bradley, Maine. More than 300 taxa of vascular plants in 71 families and 186 genera are included. Approximately 85 percent of the taxa are native to Maine. Ten of 45 nonnative species are considered invasive. Infraspecific taxa have...

Taxonomic composition of phytoplankton in the Vakh River (Western Siberia)

NASA Astrophysics Data System (ADS)

Skorobogatova, O. N.

2018-03-01

This paper provides data on the hydrological and hydrochemical parameters of the Vakh River in the Middle Ob region. In 2005-2008 we have identified 404 taxonomic units represented by 463 species, types and forms of algae, belonging to 140 genera, 52 families, 13 classes and 7 divisions. 386 species were identified for the first time, 141 taxa were identified as rare and 22 taxa as new for Western Siberia. Leading divisions, Bacillariophyta and Chlorophyta, make up for 78.9% of total phytoplankton diversity. Cyanobacteria, Chrysophyta and Euglenophyta form a community of 88 taxonomic units having a rank lower than genus level, and represent 19.0% of the total number. The floral role of Xanthophyta and Dinophyta is insignificant (2.1%). The main structure-forming species are 14: vegetating throughout the year (Aulacoseira italica, Asterionella formosa), summer taxa (Microcystis aeruginosa, Melosira varians, Aulacoseira granulata, Pandorina morum, Pediastrum boryanum, P. duplex, Lacunastrum gracillimum, Scenedesmus quadricauda) and summer-autumn (Microcystis pulverea, Tabellaria fenestrata, T. flocculosa, Mucidosphaerium pulchellum). The Vakh River demonstrates specific characteristics of boreal flowing waterways. The northern composition is represented in a big rate of families (44.2%) and genera (109 77.9) with one to three species. The richest genera Closterium (31 taxa), Eunotia (27 taxa), Pinnularia (22 taxa), Desmidium (11 taxa) and the family Desmidiaceae (45 taxa) ensure diversity of phytoplankton. Ecological and geographical analysis demonstrates predominance of cosmopolitan algae (56.6%). Plankton represents 44.7% of all algae, oligogalobs - 78.8% and indifferent algae – 36.7%. Water meets the requirements for β-mezosaprobian pollution zone, class of satisfactory purity (III class).

Floristic summary of 22 National Parks in the Midwestern United States

USGS Publications Warehouse

Bennett, J.P.

1996-01-01

Biological diversity is studied at many geographical scales, but specimen collecting is invariably done at a local level. Collecting of animal and plant specimens leads to the compilation of checklists for multiple small areas, which are sometimes merged to produce larger, regional checklists. Such an approach was employed to study the regional vascular flora of 22 national parks of the midwestern United States. Total number of plant taxa (species level and below) ranged from 86 at Hopewell Culture National Historical Park to 1,399 at Indiana Dunes National Lakeshore and averaged 520 per park. Infraspecific taxa were 12% or less of all taxa at all parks and averaged 7%. Genera per parkranged from 70 to 562, and families ranged from 41 to 145. Non-native species averaged 95 per park, or about 27% on average of the total number of taxa per park. The aggregated regional flora contained just over 2,900 taxa, 828 genera and 160 families. Eleven percent of the taxa were below the species level. Almost 17% of the taxa were non-native, a relatively large percentage, but not out of the range of percentages reported in the literature. The observed and estimated numbers of taxa for this region were in good agreement with other estimates for these latitudes and for a standard regional size. However, the parks do not represent their respective state floras very well when they are aggregated at that scale. Indiana was the best represented state with 65% of the state flora found in the parks, while only 25% of each state's flora were represented by parks in Iowa, Kansas, and Nebraska, and the average representation was only 42%.

An annotated type catalogue of the anguid, dibamid, scincid and varanid lizards in the Department of Herpetology, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia (Reptilia: Sauria: Anguidae, Dibamidae, Scincidae and Varanidae).

PubMed

Barabanov, Andrei; Milto, Konstantin

2017-03-17

A complete catalogue is provided for the type specimens of anguid, dibamid, scincid and varanid lizards in the herpetological collection of the Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia (ZISP), as of January 2017. The collection contains a total of 170 type specimens, representing 50 taxa in the four lizard families under consideration. Thirty-one of these taxa are regarded currently as valid. The types of four taxa (one holotype, one lectotype and two paralectotypes) could not be located in the ZISP collections in January 2017. A majority of the types are skinks (43 taxa, 155 types), many of which were described by the late Ilya Darevsky (1924-2009).

Annotated checklist of the recent and extinct pythons (Serpentes, Pythonidae), with notes on nomenclature, taxonomy, and distribution

PubMed Central

Schleip, Wulf D.; O’Shea, Mark

2010-01-01

Abstract McDiarmid et al. (1999) published the first part of their planned taxonomic catalog of the snakes of the world. Since then, several new python taxa have been described in both the scientific literature and non-peer-reviewed publications. This checklist evaluates the nomenclatural status of the names and discusses the taxonomic status of the new taxa, and aims to continue the work of McDiarmid et al. (1999) for the family Pythonidae, covering the period 1999 to 2010. Numerous new taxa are listed, and where appropriate recent synonymies are included and annotations are made. A checklist and a taxonomic identification key of valid taxa are provided. PMID:21594030

Linking NCBI to Wikipedia: a wiki-based approach.

PubMed

Page, Roderic D M

2011-03-31

The NCBI Taxonomy underpins many bioinformatics and phyloinformatics databases, but by itself provides limited information on the taxa it contains. One readily available source of information on many taxa is Wikipedia. This paper describes iPhylo Linkout, a Semantic wiki that maps taxa in NCBI's taxonomy database onto corresponding pages in Wikipedia. Storing the mapping in a wiki makes it easy to edit, correct, or otherwise annotate the links between NCBI and Wikipedia. The mapping currently comprises some 53,000 taxa, and is available at http://iphylo.org/linkout. The links between NCBI and Wikipedia are also made available to NCBI users through the NCBI LinkOut service.

Folk knowledge of invertebrates in Central Europe - folk taxonomy, nomenclature, medicinal and other uses, folklore, and nature conservation.

PubMed

Ulicsni, Viktor; Svanberg, Ingvar; Molnár, Zsolt

2016-10-11

There is scarce information about European folk knowledge of wild invertebrate fauna. We have documented such folk knowledge in three regions, in Romania, Slovakia and Croatia. We provide a list of folk taxa, and discuss folk biological classification and nomenclature, salient features, uses, related proverbs and sayings, and conservation. We collected data among Hungarian-speaking people practising small-scale, traditional agriculture. We studied "all" invertebrate species (species groups) potentially occurring in the vicinity of the settlements. We used photos, held semi-structured interviews, and conducted picture sorting. We documented 208 invertebrate folk taxa. Many species were known which have, to our knowledge, no economic significance. 36 % of the species were known to at least half of the informants. Knowledge reliability was high, although informants were sometimes prone to exaggeration. 93 % of folk taxa had their own individual names, and 90 % of the taxa were embedded in the folk taxonomy. Twenty four species were of direct use to humans (4 medicinal, 5 consumed, 11 as bait, 2 as playthings). Completely new was the discovery that the honey stomachs of black-coloured carpenter bees (Xylocopa violacea, X. valga) were consumed. 30 taxa were associated with a proverb or used for weather forecasting, or predicting harvests. Conscious ideas about conserving invertebrates only occurred with a few taxa, but informants would generally refrain from harming firebugs (Pyrrhocoris apterus), field crickets (Gryllus campestris) and most butterflies. We did not find any mythical creatures among invertebrate folk taxa. Almost every invertebrate species was regarded as basically harmful. Where possible, they were destroyed or at least regarded as worth eradicating. However, we could find no evidence to suggest any invertebrate species had suffered population loss as a result of conscious destruction. Sometimes knowledge pertaining to the taxa could have more

The use of invertebrates as indicators of environmental change in alpine rivers and lakes.

PubMed

Khamis, K; Hannah, D M; Brown, L E; Tiberti, R; Milner, A M

2014-09-15

In alpine regions climatic change will alter the balance between water sources (rainfall, ice-melt, snowmelt, and groundwater) for aquatic systems, particularly modifying the relative contributions of meltwater, groundwater and rain to both rivers and lakes. While these changes are expected to have implications for alpine aquatic ecosystems, little is known about potential ecological tipping points and associated indicator taxa. We examined changes in biotic communities along a gradient of glacier influence for two study systems: (1) a stream network in the French Pyrénées; and (2) a network of lakes in the Italian Alps, with the aim of identifying potential indicator taxa (macroinvertebrates and zooplankton) of glacier retreat in these environments. To assess parallels in biotic responses across streams and lakes, both primary data and findings from other publications were synthesised. Using TITAN (Threshold Indicator Taxa ANalysis) changes in community composition of river taxa were identified at thresholds of <5.1% glacier cover and <66.6% meltwater contribution. Below these thresholds the loss of cold stenothermic benthic invertebrate taxa, Diamesa spp. and the Pyrenean endemic Rhyacophila angelieri was apparent. Some generalist taxa including Protonemura sp., Perla grandis, Baetis alpinus, Rhithrogena loyolaea and Microspectra sp. increased when glacier cover was <2.7% and <52% meltwater. Patterns were not as distinct for the alpine lakes, due to fewer sampling sites; however, Daphnia longispina grp. and the benthic invertebrate groups Plectopera and Planaria were identified as potential indicator taxa. While further work is required to assess potential indicator taxa for alpine lake systems, findings from alpine river systems were consistent between methods for assessing glacier influence (meltwater contribution/glacier cover). Hence, it is clear that TITAN could become a useful management tool, enabling: (i) the identification of taxa particularly

Two new fossil flowers of magnoliid affinity from the Late Cretaceous of New Jersey.

PubMed

Crepet, W L; Nixon, K C

1998-09-01

Two taxa of cupulate magnoliid fossil flowers, Cronquistiflora and Detrusandra, are described from the Late Cretaceous (Turonian, ∼90 million years before present [MYBP]) Raritan (or lower Magothy) Formation of New Jersey. The fossil taxa are represented by flowers at various stages of development, associated fragments of cup-shaped floral receptacles with attached anthers, and isolated anthers. Both taxa have laminar stamens with adaxial thecae and valvate dehiscence. Pollen is boat-shaped and foveolate in anthers associated with Cronquistiflora and spherical with reticulate ornamentation in Detrusandra. Cup-shaped receptacles are externally bracteose in both taxa. The receptacle of Cronquistiflora is broader than the campanulate one of Detrusandra. Cronquistiflora also has more carpels (∼50 in a spiral vs. ∼5 in a whorl or tight spiral). In Detrusandra the carpels are surrounded by dorsiventrally flattened structures (pistillodes?) that are remote from the attachment of the stamens near the distal rim of the receptacular cupule. Detrusandra stigmas are rounded and bilobed, while those of Cronquistiflora, although bilateral in symmetry, are somewhat peltate. The fossil taxa share prominent characters with extant cupulate magnoliids (e.g., Eupomatia, Calycanthus), but also share characters with other magnoliids including Winteraceae. These fossils represent taxa that are character mosaics relative to currently recognized families. Inclusion of these fossils in existing data matrices and ensuing phylogenetic analyses effect changes in tree topologies consistent with their mosaicism relative to modern taxa. But such analyses do not definitively demonstrate the affinities of the fossils other than illustrating that these fossils are generalized magnoliids. Additional analysis of modern and fossil magnoliids is necessary to fully appreciate the phylogenetic significance and positions of these fossil taxa. However, the results of the phylogenetic analyses do

Phytoplankton assemblages in high-elevation lakes in the northern Cascade Mountains, Washington State, USA

USGS Publications Warehouse

Larson, Gary L.; McIntire, C.D.; Truitt, R.E.; Liss, W.J.; Hoffman, Robert L.; Deimling, E.; Lomnicky, G.A.

1998-01-01

Phytoplankton assemblages in high-elevation lakes of North Cascades National Park Service Complex were studied during the open-water period in 1989. Collectively, 93 taxa were identified in 55 samples from 51 lakes. Based on cell densities, cyanobacteria had the highest relative abundance (36.7 %), followed by chlorophytes (29.8 %), and chrysophytes (19.6 %). Aphanocapsa delicatissima had the highest proportional abundance (14.0 %). Only 15.1 % percent of the taxa occurred in more than 20 samples. Phytoplankton cell densities increased following a gradient of increasing lake-water temperature, alkalinity, and concentration of total Kjeldahl-N with decreasing lake elevation. Chrysophytes and cyanobacteria were quantitatively (relative abundance) the most important taxa in alpine and subalpine lakes, whereas cyanobacteria had the highest relative abundances in high-forest and low-forest lakes. Chlorophytes had their highest relative abundance in high-forest lakes. Although low in relative abundance, diatoms and dinoflagellates were most abundant in alpine lakes. An ordination by correspondence analysis indicated that most alpine, subalpine, and high-forest lakes had similar floras. Although a few subalpine lakes exhibited deviations from this pattern, the main differences in phytoplankton composition were found in a group of low-forest and high-forest lakes. Canonical correspondence analysis (CCA) provided evidence that the distribution of samples and taxa in ordination space was correlated with a gradient of decreasing lake elevation and increasing water temperature, alkalinity, and concentration of nitrogen. When CCA was used to examine relationships among phytoplankton taxa and vegetation zones, a continuous distribution of taxa was found from the low-forest zone to the subalpine zone, with a large number of taxa occurring primarily in the subalpine and high-forest zones. Three phytoplankton taxa occurred primarily in alpine lakes, whereas five taxa co-occurred in

Development of Diagnostic Insecticide Concentrations and Assessment of Insecticide Susceptibility in German Cockroach (Dictyoptera: Blattellidae) Field Strains Collected From Public Housing.

PubMed

Fardisi, Mahsa; Gondhalekar, Ameya D; Scharf, Michael E

2017-06-01

Insecticide resistance in German cockroaches (Blattella germanica (L.)) has been a barrier to effective control since its first documentation in the 1950s. A necessary first step toward managing resistance is to understand insecticide susceptibility profiles in field-collected strains so that active ingredients (AIs) with lowest resistance levels can be identified. As a first step in this study, diagnostic concentrations (DCs) were determined for 14 insecticide AIs based on lethal concentrations that killed 99% or 90% of the individuals from a susceptible lab strain (JWax-S). Next, cockroaches were collected from two low-income multifamily housing complexes in Danville, IL, and Indianapolis, IN, and used to establish laboratory strains. These strains were screened against the 14 AI-DCs in vial bioassays, and susceptibility profiles were determined by comparing percent mortalities between the field strains relative to the JWax-S strain. Results revealed lowest resistance of field strains to boric acid, abamectin, dinotefuran, clothianidin, thiamethoxam, and chlorfenapyr. For the AIs hydramethylnon and imidacloprid, field strains did not display survivorship different than the lab strain, but >90% mortality was never achieved. Lastly, both field strains displayed resistance to indoxacarb, fipronil, acetamiprid, beta-cyfluthrin, bifenthrin, and lambda-cyhalothrin, but at varying levels. These results satisfy two objectives. First, baseline monitoring DCs were established for 14 insecticides presently registered for use against cockroaches, which represents a useful resource. Second, our findings reveal insecticide AIs with lowest resistance levels for use in forthcoming field studies that will investigate impacts of different insecticide deployment strategies on resistance management and evolution in cockroach field populations. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

Development of Diagnostic Insecticide Concentrations and Assessment of Insecticide Susceptibility in German Cockroach (Dictyoptera: Blattellidae) Field Strains Collected From Public Housing

PubMed Central

Fardisi, Mahsa; Gondhalekar, Ameya D.

2017-01-01

Abstract Insecticide resistance in German cockroaches (Blattella germanica (L.)) has been a barrier to effective control since its first documentation in the 1950s. A necessary first step toward managing resistance is to understand insecticide susceptibility profiles in field-collected strains so that active ingredients (AIs) with lowest resistance levels can be identified. As a first step in this study, diagnostic concentrations (DCs) were determined for 14 insecticide AIs based on lethal concentrations that killed 99% or 90% of the individuals from a susceptible lab strain (JWax-S). Next, cockroaches were collected from two low-income multifamily housing complexes in Danville, IL, and Indianapolis, IN, and used to establish laboratory strains. These strains were screened against the 14 AI-DCs in vial bioassays, and susceptibility profiles were determined by comparing percent mortalities between the field strains relative to the JWax-S strain. Results revealed lowest resistance of field strains to boric acid, abamectin, dinotefuran, clothianidin, thiamethoxam, and chlorfenapyr. For the AIs hydramethylnon and imidacloprid, field strains did not display survivorship different than the lab strain, but >90% mortality was never achieved. Lastly, both field strains displayed resistance to indoxacarb, fipronil, acetamiprid, beta-cyfluthrin, bifenthrin, and lambda-cyhalothrin, but at varying levels. These results satisfy two objectives. First, baseline monitoring DCs were established for 14 insecticides presently registered for use against cockroaches, which represents a useful resource. Second, our findings reveal insecticide AIs with lowest resistance levels for use in forthcoming field studies that will investigate impacts of different insecticide deployment strategies on resistance management and evolution in cockroach field populations. PMID:28334270

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling

PubMed Central

Chesters, Douglas

2017-01-01

Abstract Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies

Mass coral bleaching in 2010 in the southern Caribbean.

PubMed

Alemu I, Jahson Berhane; Clement, Ysharda

2014-01-01

Ocean temperatures are increasing globally and the Caribbean is no exception. An extreme ocean warming event in 2010 placed Tobago's coral reefs under severe stress resulting in widespread coral bleaching and threatening the livelihoods that rely on them. The bleaching response of four reef building taxa was monitored over a six month period across three major reefs systems in Tobago. By identifying taxa resilient to bleaching we propose to assist local coral reef managers in the decision making process to cope with mass bleaching events. The bleaching signal (length of exposure to high ocean temperatures) varied widely between the Atlantic and Caribbean reefs, but regardless of this variation most taxa bleached. Colpophyllia natans, Montastraea faveolata and Siderastrea siderea were considered the most bleaching vulnerable taxa. Interestingly, reefs with the highest coral cover showed the greatest decline reef building taxa, and conversely, reefs with the lowest coral cover showed the most bleaching but lowest change in coral cover with little algal overgrowth post-bleaching.

Novelties in secretory structures and anatomy of Rhynchosia (Fabaceae).

PubMed

De Vargas, Wanderleia; Sartori, Ângela L B; Dias, Edna S

2015-03-01

A comparative anatomical study was carried out on the secretory structures of leaflets from taxa belonging to the genus Rhynchosia - taxa difficult to delimit because of uncertain interspecific relations - in order to evaluate the potential diagnostic value of these anatomical traits for taxonomic assignment. A further objective was to establish consensual denomination for these secretory structures. The new anatomical features found in these taxa were sufficiently consistent to separate the species evaluated. The presence and localization of glandular-punctate structures bulbous-based trichomes, the number of layers in the palisade parenchyma and the arrangement of vascular units distinguish the taxa investigated and these characteristics can be extended to other species of Papilionoideae. The trichomes analyzed were described and classified into five types. Depicted in diagrams, photomicrographs, and by scanning electron microscopy, and listed for the first time at the genus and species levels. The information obtained served to effectively distinguish the taxa investigated among species of Papilonoideae.

Mass Coral Bleaching in 2010 in the Southern Caribbean

PubMed Central

Alemu I, Jahson Berhane; Clement, Ysharda

2014-01-01

Ocean temperatures are increasing globally and the Caribbean is no exception. An extreme ocean warming event in 2010 placed Tobago's coral reefs under severe stress resulting in widespread coral bleaching and threatening the livelihoods that rely on them. The bleaching response of four reef building taxa was monitored over a six month period across three major reefs systems in Tobago. By identifying taxa resilient to bleaching we propose to assist local coral reef managers in the decision making process to cope with mass bleaching events. The bleaching signal (length of exposure to high ocean temperatures) varied widely between the Atlantic and Caribbean reefs, but regardless of this variation most taxa bleached. Colpophyllia natans, Montastraea faveolata and Siderastrea siderea were considered the most bleaching vulnerable taxa. Interestingly, reefs with the highest coral cover showed the greatest decline reef building taxa, and conversely, reefs with the lowest coral cover showed the most bleaching but lowest change in coral cover with little algal overgrowth post-bleaching. PMID:24400078

Flora and threatened and endangered plants of John F. Kennedy Space Center, Florida

NASA Technical Reports Server (NTRS)

Schmalzer, Paul A.; Hinkle, C. Ross

1990-01-01

The vascular flora of the Kennedy Space Center (KSC) area was first studied in the 1970's. Nomenclatural and taxonomic changes as well as additional collections required revision of this list. The revised list includes 1045 taxa of which 850 are native and 195 are introduced. This appears to be a substantial proportion of the regional flora. Forty six taxa are endemic or nearly endemic to Florida, a level of endemism that appears high for the east coast of central Florida. Seventy three taxa (69 native) are listed as threatened, endangered, or of special concern on Federal or state lists. Taxa of special concern occur in all major habitats, but many are restricted to hammocks and hardwood swamps that constitute a minor proportion of the terrestrial vegetation. For some of these taxa, populations on KSC appear to be important for their regional and global survival. The bryophyte flora of the KSC area include 23 mosses and 20 liverworts and hornworts. The lichen flora is currently unknown.

Quantitative studies of Savannah River aquatic insects, 1959--1985

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

Soltis, R.; Hart, D.; Nagy, T.

1986-10-30

As part of a long-term study of water quality patterns, scientists from the Academy of Natural Sciences have collected aquatic insects from artificial substrates placed at several stations in Savannah River. This report presents the first detailed compilation and analysis of this substantial data base, and examines patterns of variations of insect distribution and abundance (both spatial and temporal) during the last quarter century. Data on the number of individuals of various taxa found in the insect traps were obtained from tables in the Academy`s cursory reports. Computer data files created from these records were subjected to extensive statistical analysesmore » in order to examine variation among stations, seasons and years in the abundances of major taxa and various aggregate properties of the insect assemblage. Although a total of 83 taxa were collected over the 27-year study, 10 taxa accounted for nearly 80% of the individuals collected from the traps, hence there 10 taxa were analyzed more intensively.« less

Quantitative studies of Savannah River aquatic insects, 1959--1985

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

Soltis, R.; Hart, D.; Nagy, T.

1986-10-30

As part of a long-term study of water quality patterns, scientists from the Academy of Natural Sciences have collected aquatic insects from artificial substrates placed at several stations in Savannah River. This report presents the first detailed compilation and analysis of this substantial data base, and examines patterns of variations of insect distribution and abundance (both spatial and temporal) during the last quarter century. Data on the number of individuals of various taxa found in the insect traps were obtained from tables in the Academy's cursory reports. Computer data files created from these records were subjected to extensive statistical analysesmore » in order to examine variation among stations, seasons and years in the abundances of major taxa and various aggregate properties of the insect assemblage. Although a total of 83 taxa were collected over the 27-year study, 10 taxa accounted for nearly 80% of the individuals collected from the traps, hence there 10 taxa were analyzed more intensively.« less

A revision of the genus Antepione Packard with description of the new genus Pionenta Ferris (Lepidoptera, Geometridae, Ennominae).

PubMed

Ferris, Clifford D

2010-12-14

Based on genitalic studies, the new genus Pionenta is established for two taxa formerly placed under Antepione. The taxa hewesata and ochreata (and previously associated synonyms) are now synonomized as Pionenta ochreata. Three species of Antepione are now recognized: Antepione thisoaria, Antepione imitata, Antepione tiselaaria with the taxa comstocki, constans, and indiscretata synonomized under Antepione imitata. No new species are described. Adults and genitalia are illustrated, including type specimens.

Can Global Weed Assemblages Be Used to Predict Future Weeds?

PubMed Central

Morin, Louise; Paini, Dean R.; Randall, Roderick P.

2013-01-01

Predicting which plant taxa are more likely to become weeds in a region presents significant challenges to both researchers and government agencies. Often it is done in a qualitative or semi-quantitative way. In this study, we explored the potential of using the quantitative self-organising map (SOM) approach to analyse global weed assemblages and estimate likelihoods of plant taxa becoming weeds before and after they have been moved to a new region. The SOM approach examines plant taxa associations by analysing where a taxon is recorded as a weed and what other taxa are recorded as weeds in those regions. The dataset analysed was extracted from a pre-existing, extensive worldwide database of plant taxa recorded as weeds or other related status and, following reformatting, included 187 regions and 6690 plant taxa. To assess the value of the SOM approach we selected Australia as a case study. We found that the key and most important limitation in using such analytical approach lies with the dataset used. The classification of a taxon as a weed in the literature is not often based on actual data that document the economic, environmental and/or social impact of the taxon, but mostly based on human perceptions that the taxon is troublesome or simply not wanted in a particular situation. The adoption of consistent and objective criteria that incorporate a standardized approach for impact assessment of plant taxa will be necessary to develop a new global database suitable to make predictions regarding weediness using methods like SOM. It may however, be more realistic to opt for a classification system that focuses on the invasive characteristics of plant taxa without any inference to impacts, which to be defined would require some level of research to avoid bias from human perceptions and value systems. PMID:23393591

Impacts of phylogenetic nomenclature on the efficacy of the U.S. Endangered Species Act.

PubMed

Leslie, Matthew S

2015-02-01

Cataloging biodiversity is critical to conservation efforts because accurate taxonomy is often a precondition for protection under laws designed for species conservation, such as the U.S. Endangered Species Act (ESA). Traditional nomenclatural codes governing the taxonomic process have recently come under scrutiny because taxon names are more closely linked to hierarchical ranks than to the taxa themselves. A new approach to naming biological groups, called phylogenetic nomenclature (PN), explicitly names taxa by defining their names in terms of ancestry and descent. PN has the potential to increase nomenclatural stability and decrease confusion induced by the rank-based codes. But proponents of PN have struggled with whether species and infraspecific taxa should be governed by the same rules as other taxa or should have special rules. Some proponents advocate the wholesale abandonment of rank labels (including species); this could have consequences for the implementation of taxon-based conservation legislation. I examined the principles of PN as embodied in the PhyloCode (an alternative to traditional rank-based nomenclature that names biological groups based on the results of phylogenetic analyses and does not associate taxa with ranks) and assessed how this novel approach to naming taxa might affect the implementation of species-based legislation by providing a case study of the ESA. The latest version of the PhyloCode relies on the traditional rank-based codes to name species and infraspecific taxa; thus, little will change regarding the main targets of the ESA because they will retain rank labels. For this reason, and because knowledge of evolutionary relationships is of greater importance than nomenclatural procedures for initial protection of endangered taxa under the ESA, I conclude that PN under the PhyloCode will have little impact on implementation of the ESA. © 2014 Society for Conservation Biology.

Guide to the Vascular Flora of the Savannas and Flatwoods of Shaken Creek Preserve and Vicinity (Pender & Onslow Counties, North Carolina, U.S.A.)

PubMed Central

Krings, Alexander; Lindbo, David; Stucky, Jon

2014-01-01

Abstract Shaken Creek Preserve (“SCP”) is a 2,448 ha (6,050 ac) natural area in Pender and Onslow Counties, North Carolina (U.S.A). Best known for its high-quality longleaf pine savanna habitat, the site contains seven savanna or savanna-like plant community types (i.e., flatwoods or sandhills), three of which are globally critically imperiled (G1): Sandy Pine Savanna (Rush Featherling subtype), Wet Loamy Pine Savanna, and Very Wet Loamy Pine Savanna. SCP hosts three Federally Endangered plant species and six Federal Species of Concern. Formerly a private hunting club, the site was virtually unknown to scientists until the 1990s; consequently, few biological inventories of SCP have been conducted. In particular, no systematic floristic inventories of the species-rich savannas have been undertaken, despite the fact that floristic data is critical to the effective management of any natural area. The goals of this study were to (1) inventory the vascular flora of the savannas, flatwoods, and sandhill community types on site through the collection of voucher specimens; (2) provide a comprehensive checklist of the flora based on collections and reports made from the site and from the same or similar habitats in the vicinity (i.e., within 2 miles of SCP); and (3) create an illustrated guide based on the checklist. In order to increase the usefulness of the guide, taxa not currently known from SCP but collected or reported from the same or similar habitats within two miles of SCP, are included in the guide. Eighty-three families containing 450 taxa, including thirty-two Significantly Rare and thirty-eight Watch List taxa, were collected or reported from SCP; an additional seven families containing a total of 102 taxa, including eighteen Significantly Rare and seven Watch List taxa, were collected or reported from the vicinity. In total, ninety families containing 552 taxa, including fifty Significantly Rare and forty-five Watch List taxa, are treated in the guide

Relations of habitat-specific algal assemblages to land use and water chemistry in the Willamette Basin, Oregon

USGS Publications Warehouse

Carpenter, K.D.; Waite, I.R.

2000-01-01

Benthic algal assemblages, water chemistry, and habitat were characterized at 25 stream sites in the Willamette Basin, Oregon, during low flow in 1994. Seventy-three algal samples yielded 420 taxa - Mostly diatoms, blue-green algae, and green algae. Algal assemblages from depositional samples were strongly dominated by diatoms (76% mean relative abundance), whereas erosional samples were dominated by blue-green algae (68% mean relative abundance). Canonical correspondence analysis (CCA) of semiquantitative and qualitative (presence/absence) data sets identified four environmental variables (maximum specific conductance, % open canopy, pH, and drainage area) that were significant in describing patterns of algal taxa among sites. Based on CCA, four groups of sites were identified: Streams in forested basins that supported oligotrophic taxa, such as Diatoma mesodon; small streams in agricultural and urban basins that contained a variety of eutrophic and nitrogen-heterotrophic algal taxa; larger rivers draining areas of mixed land use that supported planktonic, eutrophic, and nitrogen-heterotrophic algal taxa; and streams with severely degraded or absent riparian vegetation (> 75% open canopy) that were dominated by other planktonic, eutrophic, and nitrogen-heterotrophic algal taxa. Patterns in water chemistry were consistent with the algal autecological interpretations and clearly demonstrated relationships between land use, water quality, and algal distribution patterns.

Ecogeography and utility to plant breeding of the crop wild relatives of sunflower (Helianthus annuus L.)

PubMed Central

Kantar, Michael B.; Sosa, Chrystian C.; Khoury, Colin K.; Castañeda-Álvarez, Nora P.; Achicanoy, Harold A.; Bernau, Vivian; Kane, Nolan C.; Marek, Laura; Seiler, Gerald; Rieseberg, Loren H.

2015-01-01

Crop wild relatives (CWR) are a rich source of genetic diversity for crop improvement. Combining ecogeographic and phylogenetic techniques can inform both conservation and breeding. Geographic occurrence, bioclimatic, and biophysical data were used to predict species distributions, range overlap and niche occupancy in 36 taxa closely related to sunflower (Helianthus annuus L.). Taxa lacking comprehensive ex situ conservation were identified. The predicted distributions for 36 Helianthus taxa identified substantial range overlap, range asymmetry and niche conservatism. Specific taxa (e.g., Helianthus deblis Nutt., Helianthus anomalus Blake, and Helianthus divaricatus L.) were identified as targets for traits of interest, particularly for abiotic stress tolerance, and adaptation to extreme soil properties. The combination of techniques demonstrates the potential for publicly available ecogeographic and phylogenetic data to facilitate the identification of possible sources of abiotic stress traits for plant breeding programs. Much of the primary genepool (wild H. annuus) occurs in extreme environments indicating that introgression of targeted traits may be relatively straightforward. Sister taxa in Helianthus have greater range overlap than more distantly related taxa within the genus. This adds to a growing body of literature suggesting that in plants (unlike some animal groups), geographic isolation may not be necessary for speciation. PMID:26500675

Ecogeography and utility to plant breeding of the crop wild relatives of sunflower (Helianthus annuus L.).

PubMed

Kantar, Michael B; Sosa, Chrystian C; Khoury, Colin K; Castañeda-Álvarez, Nora P; Achicanoy, Harold A; Bernau, Vivian; Kane, Nolan C; Marek, Laura; Seiler, Gerald; Rieseberg, Loren H

2015-01-01

Crop wild relatives (CWR) are a rich source of genetic diversity for crop improvement. Combining ecogeographic and phylogenetic techniques can inform both conservation and breeding. Geographic occurrence, bioclimatic, and biophysical data were used to predict species distributions, range overlap and niche occupancy in 36 taxa closely related to sunflower (Helianthus annuus L.). Taxa lacking comprehensive ex situ conservation were identified. The predicted distributions for 36 Helianthus taxa identified substantial range overlap, range asymmetry and niche conservatism. Specific taxa (e.g., Helianthus deblis Nutt., Helianthus anomalus Blake, and Helianthus divaricatus L.) were identified as targets for traits of interest, particularly for abiotic stress tolerance, and adaptation to extreme soil properties. The combination of techniques demonstrates the potential for publicly available ecogeographic and phylogenetic data to facilitate the identification of possible sources of abiotic stress traits for plant breeding programs. Much of the primary genepool (wild H. annuus) occurs in extreme environments indicating that introgression of targeted traits may be relatively straightforward. Sister taxa in Helianthus have greater range overlap than more distantly related taxa within the genus. This adds to a growing body of literature suggesting that in plants (unlike some animal groups), geographic isolation may not be necessary for speciation.

Zooplankton assemblages in montane lakes and ponds of Mount Rainier National Park, Washington State, USA

USGS Publications Warehouse

Larson, G.L.; Hoffman, R.; McIntire, C.D.; Lienkaemper, G.; Samora, B.

2009-01-01

Water quality and zooplankton samples were collected during the ice-free periods between 1988 and 2005 from 103 oligotrophic montane lakes and ponds located in low forest to alpine vegetation zones in Mount Rainier National Park, Washington State, USA. Collectively, 45 rotifer and 44 crustacean taxa were identified. Most of the numerically dominant taxa appeared to have wide niche breadths. The average number of taxa per lake decreased with elevation and generally increased as maximum lake depths increased (especially for rotifers). With one exception, fish presence/absence did not explain the taxonomic compositions of crustacean zooplankton assemblages. Many rotifer species were common members of zooplankton assemblages in montane lakes and ponds in western North America, whereas the crustacean taxa were common to some areas of the west, but not others. Constraints of the environmental variables did not appear to provide strong gradients to separate the distributions of most zooplankton species. This suggests that interspecific competitive interactions and stochastic processes regulate the taxonomic structures of the zooplankton assemblages at the landscape level. Crustacean species that had broad niche breadths were associated with different rotifer taxa across the environmental gradients. Studies of zooplankton assemblages need to address both crustacean and rotifer taxa, not one or the other.

Detecting macroecological patterns in bacterial communities across independent studies of global soils.

PubMed

Ramirez, Kelly S; Knight, Christopher G; de Hollander, Mattias; Brearley, Francis Q; Constantinides, Bede; Cotton, Anne; Creer, Si; Crowther, Thomas W; Davison, John; Delgado-Baquerizo, Manuel; Dorrepaal, Ellen; Elliott, David R; Fox, Graeme; Griffiths, Robert I; Hale, Chris; Hartman, Kyle; Houlden, Ashley; Jones, David L; Krab, Eveline J; Maestre, Fernando T; McGuire, Krista L; Monteux, Sylvain; Orr, Caroline H; van der Putten, Wim H; Roberts, Ian S; Robinson, David A; Rocca, Jennifer D; Rowntree, Jennifer; Schlaeppi, Klaus; Shepherd, Matthew; Singh, Brajesh K; Straathof, Angela L; Bhatnagar, Jennifer M; Thion, Cécile; van der Heijden, Marcel G A; de Vries, Franciska T

2018-02-01

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Alteration of Neutrophil Reactive Oxygen Species Production by Extracts of Devil's Claw (Harpagophytum).

PubMed

Muzila, Mbaki; Rumpunen, Kimmo; Wright, Helen; Roberts, Helen; Grant, Melissa; Nybom, Hilde; Sehic, Jasna; Ekholm, Anders; Widén, Cecilia

2016-01-01

Harpagophytum, Devil's Claw, is a genus of tuberiferous xerophytic plants native to southern Africa. Some of the taxa are appreciated for their medicinal effects and have been traditionally used to relieve symptoms of inflammation. The objectives of this pilot study were to investigate the antioxidant capacity and the content of total phenols, verbascoside, isoverbascoside, and selected iridoids, as well as to investigate the capacity of various Harpagophytum taxa in suppressing respiratory burst in terms of reactive oxygen species produced by human neutrophils challenged with phorbol myristate acetate (PMA), opsonised Staphylococcus aureus, and Fusobacterium nucleatum. Harpagophytum plants were classified into different taxa according to morphology, and DNA analysis was used to confirm the classification. A putative new variety of H. procumbens showed the highest degree of antioxidative capacity. Using PMA, three Harpagophytum taxa showed anti-inflammatory effects with regard to the PBS control. A putative hybrid between H. procumbens and H. zeyheri in contrast showed proinflammatory effect on the response of neutrophils to F. nucleatum in comparison with treatment with vehicle control. Harpagophytum taxa were biochemically very variable and the response in suppressing respiratory burst differed. Further studies with larger number of subjects are needed to corroborate anti-inflammatory effects of different taxa of Harpagophytum.

Alteration of Neutrophil Reactive Oxygen Species Production by Extracts of Devil's Claw (Harpagophytum)

PubMed Central

Muzila, Mbaki; Wright, Helen; Roberts, Helen; Grant, Melissa; Nybom, Hilde; Sehic, Jasna; Ekholm, Anders

2016-01-01

Harpagophytum, Devil's Claw, is a genus of tuberiferous xerophytic plants native to southern Africa. Some of the taxa are appreciated for their medicinal effects and have been traditionally used to relieve symptoms of inflammation. The objectives of this pilot study were to investigate the antioxidant capacity and the content of total phenols, verbascoside, isoverbascoside, and selected iridoids, as well as to investigate the capacity of various Harpagophytum taxa in suppressing respiratory burst in terms of reactive oxygen species produced by human neutrophils challenged with phorbol myristate acetate (PMA), opsonised Staphylococcus aureus, and Fusobacterium nucleatum. Harpagophytum plants were classified into different taxa according to morphology, and DNA analysis was used to confirm the classification. A putative new variety of H. procumbens showed the highest degree of antioxidative capacity. Using PMA, three Harpagophytum taxa showed anti-inflammatory effects with regard to the PBS control. A putative hybrid between H. procumbens and H. zeyheri in contrast showed proinflammatory effect on the response of neutrophils to F. nucleatum in comparison with treatment with vehicle control. Harpagophytum taxa were biochemically very variable and the response in suppressing respiratory burst differed. Further studies with larger number of subjects are needed to corroborate anti-inflammatory effects of different taxa of Harpagophytum. PMID:27429708

EVALUATING MACROINVERTEBRATE COMMUNITY ...

EPA Pesticide Factsheets

Since 2010, new construction in California is required to include stormwater detention and infiltration that is designed to capture rainfall from the 85th percentile of storm events in the region, preferably through green infrastructure. This study used recent macroinvertebrate community monitoring data to determine the ecological threshold for percent impervious cover prior to large scale adoption of green infrastructure using Threshold Indicator Taxa Analysis (TITAN). TITAN uses an environmental gradient and biological community data to determine individual taxa change points with respect to changes in taxa abundance and frequency across that gradient. Individual taxa change points are then aggregated to calculate the ecological threshold. This study used impervious cover data from National Land Cover Datasets and macroinvertebrate community data from California Environmental Data Exchange Network and Southern California Coastal Water Research Project. Preliminary TITAN runs for California’s Chaparral region indicated that both increasing and decreasing taxa had ecological thresholds of <1% watershed impervious cover. Next, TITAN will be used to determine shifts in the ecological threshold after the implementation of green infrastructure on a large scale. This presentation for the Society for Freshwater Scientists will discuss initial evaluation of community and taxa-specific thresholds of impairment for macroinvertebrates in California streams along

Field Surveys of Rare Plants on Santa Cruz Island, California, 2003-2006: Historical Records and Current Distributions

USGS Publications Warehouse

McEachern, A. Kathryn; Chess, Katherine A.; Niessen, Ken

2010-01-01

Santa Cruz Island is the largest of the northern Channel Islands located off the coast of California. It is owned and managed as a conservation reserve by The Nature Conservancy and the Channel Islands National Park. The island is home to nine plant taxa listed in 1997 as threatened or endangered under the federal Endangered Species Act, because of declines related to nearly 150 years of ranching on the island. Feral livestock were removed from the island as a major conservation step, which was part of a program completed in early 2007 with the eradication of pigs and turkeys. For the first time in more than a century, the rare plants of Santa Cruz Island have a chance to recover in the wild. This study provides survey information and living plant materials needed for recovery management of the listed taxa. We developed a database containing information about historical collections of the nine taxa and used it to plan a survey strategy. Our objectives were to relocate as many of the previously known populations as possible, with emphasis on documenting sites not visited in several decades, sites that were poorly documented in the historical record, and sites spanning the range of environmental conditions inhabited by the taxa. From 2003 through 2006, we searched for and found 39 populations of the taxa, indicating that nearly 80 percent of the populations known earlier in the 1900s still existed. Most populations are small and isolated, occupying native-dominated habitat patches in a highly fragmented and invaded landscape; they are still at risk of declining through population losses. Most are not expanding beyond the edges of their habitat patches. However, most taxa appeared to have good seed production and a range of size classes in populations, indicating a good capacity for plant recruitment and population growth in these restricted sites. For these taxa, seed collection and outplanting might be a good strategy to increase numbers of populations for species

Abundance and stratification of soil macroarthropods in a Caatinga Forest in Northeast Brazil.

PubMed

Araújo, V F P; Bandeira, A G; Vasconcellos, A

2010-10-01

In arid and semiarid environments, seasonality usually exerts a strong influence on the composition and dynamics of the soil community. The soil macroarthropods were studied in a Caatinga forest located in the Reserva Particular do Patrimônio Natural (RPPN) Fazenda Almas, São José dos Cordeiros, Paraíba, Brazil. Samples were collected during the dry and rainy seasons following the method proposed by the Tropical Soil Biology and Fertility Program (TSBF), with minor modifications. At each station, 15 soil blocks (20 × 20 × 30 cm: 12 L) were extracted and divided into three layers: A (0-10 cm), B (10-20 cm), and C (20-30 cm). In the rainy and dry seasons 1,306 ± 543(se) and 458 ± 212 ind.m-2 macroarthropods were found, respectively, with 35 and 18 respective taxa recorded. The abundance of individuals and taxa were significantly higher in the rainy season. Isoptera (57.8%) was the most abundant taxon, followed by Hymenoptera: Formicidae (17.2%), Coleoptera larvae (7.3%), and Araneae (3.5%). In the rainy season, abundance in layer A (576 ± 138 ind.m-2) was significantly higher than that of layer C (117 ± 64 ind.m-2), but was not different from layer B (613 ± 480 ind.m-2). There was also no difference between the layer B and C abundances. In the dry season, abundance in layer B (232 ± 120 ind.m-2) was not significantly different compared to layer A (182 ± 129 ind.m-2), but was significantly higher than abundance in layer C (44 ± 35 ind.m-2). During the rainy season, layer A (34 taxa) was significantly richer in taxa than layers B (19 taxa) and C (11 taxa). On the other hand, during the dry season the richness of layers A (12 taxa) and B (12 taxa) was equal, but significantly higher than that of layer C (6 taxa). Richness of taxa and abundance were positively correlated with soil organic matter and negatively correlated with soil temperature. The community of soil macroarthropods in the area of Caatinga studied has taxonomic and functional structures that

A revision of the genus Antepione Packard with description of the new genus Pionenta Ferris (Lepidoptera, Geometridae, Ennominae)

PubMed Central

Ferris, Clifford D.

2010-01-01

Abstract Based on genitalic studies, the new genus Pionenta is established for two taxa formerly placed under Antepione. The taxa hewesata and ochreata (and previously associated synonyms) are now synonomized as Pionenta ochreata. Three species of Antepione are now recognized: Antepione thisoaria, Antepione imitata, Antepione tiselaaria with the taxa comstocki, constans, and indiscretata synonomized under Antepione imitata. No new species are described. Adults and genitalia are illustrated, including type specimens. PMID:21594048

Does the Cave Environment Reduce Functional Diversity?

PubMed Central

Fernandes, Camile Sorbo; Batalha, Marco Antonio; Bichuette, Maria Elina

2016-01-01

Caves are not colonised by all taxa present in the surface species pool, due to absence of light and the tendency to food limitation when compared to surface communities. Under strong species sorting during colonisation and later by the restrictive environmental filter, traits that are not adaptive in subterranean habitats may be filtered out. We tested whether cave communities were assembled by the restrictive regime propitiated by permanent darkness or by competitive exclusion due to resource scarcity. When compared to surface communities, the restrictive subterranean regime would lead to lower functional diversity and phenotypic clustering inside the caves, and the opposite should be expected in the case of competitive exclusion. Using isopods (Oniscidea) as model taxa, we measured several niche descriptors of taxa from surface and cave habitats, used a multivariate measure of functional diversity, and compared their widths. We found phenotypic overdispersion and higher functional diversity in cave taxa when compared to surface taxa. On the one hand, the dry climate outside of caves hampered the survival of several taxa and their ecological strategies, not viable under severe desiccation risk, culminating in the clustering of functional traits. In contrast, this restriction does not occur inside of caves, where isopods find favourable conditions under lower predation pressures and more amenable environmental parameters that allow occupation and subsequent diversification. Our results showed that, at least for some taxa, caves may not be such a harsh environment as previously thought. The high functional diversity we found inside caves adds an additional reason for the conservation of these sensitive environments. PMID:27003837

Diversity, Abundance and Community Structure of Benthic Macro- and Megafauna on the Beaufort Shelf and Slope

PubMed Central

Nephin, Jessica; Juniper, S. Kim; Archambault, Philippe

2014-01-01

Diversity and community patterns of macro- and megafauna were compared on the Canadian Beaufort shelf and slope. Faunal sampling collected 247 taxa from 48 stations with box core and trawl gear over the summers of 2009–2011 between 50 and 1,000 m in depth. Of the 80 macrofaunal and 167 megafaunal taxa, 23% were uniques, present at only one station. Rare taxa were found to increase proportional to total taxa richness and differ between the shelf ( 100 m) where they tended to be sparse and the slope where they were relatively abundant. The macrofauna principally comprised polychaetes with nephtyid polychaetes dominant on the shelf and maldanid polychaetes (up to 92% in relative abundance/station) dominant on the slope. The megafauna principally comprised echinoderms with Ophiocten sp. (up to 90% in relative abundance/station) dominant on the shelf and Ophiopleura sp. dominant on the slope. Macro- and megafauna had divergent patterns of abundance, taxa richness ( diversity) and diversity. A greater degree of macrofaunal than megafaunal variation in abundance, richness and diversity was explained by confounding factors: location (east-west), sampling year and the timing of sampling with respect to sea-ice conditions. Change in megafaunal abundance, richness and diversity was greatest across the depth gradient, with total abundance and richness elevated on the shelf compared to the slope. We conclude that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appears to be the main driver of megafaunal diversity across the depth gradient. PMID:25007347

Diversity, abundance and community structure of benthic macro- and megafauna on the Beaufort shelf and slope.

PubMed

Nephin, Jessica; Juniper, S Kim; Archambault, Philippe

2014-01-01

Diversity and community patterns of macro- and megafauna were compared on the Canadian Beaufort shelf and slope. Faunal sampling collected 247 taxa from 48 stations with box core and trawl gear over the summers of 2009-2011 between 50 and 1,000 m in depth. Of the 80 macrofaunal and 167 megafaunal taxa, 23% were uniques, present at only one station. Rare taxa were found to increase proportional to total taxa richness and differ between the shelf (< 100 m) where they tended to be sparse and the slope where they were relatively abundant. The macrofauna principally comprised polychaetes with nephtyid polychaetes dominant on the shelf and maldanid polychaetes (up to 92% in relative abundance/station) dominant on the slope. The megafauna principally comprised echinoderms with Ophiocten sp. (up to 90% in relative abundance/station) dominant on the shelf and Ophiopleura sp. dominant on the slope. Macro- and megafauna had divergent patterns of abundance, taxa richness (α diversity) and β diversity. A greater degree of macrofaunal than megafaunal variation in abundance, richness and β diversity was explained by confounding factors: location (east-west), sampling year and the timing of sampling with respect to sea-ice conditions. Change in megafaunal abundance, richness and β diversity was greatest across the depth gradient, with total abundance and richness elevated on the shelf compared to the slope. We conclude that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appears to be the main driver of megafaunal β diversity across the depth gradient.

Data characterizing the chloroplast genomes of extinct and endangered Hawaiian endemic mints (Lamiaceae) and their close relatives.

PubMed

Welch, Andreanna J; Collins, Katherine; Ratan, Aakrosh; Drautz-Moses, Daniela I; Schuster, Stephan C; Lindqvist, Charlotte

2016-06-01

These data are presented in support of a plastid phylogenomic analysis of the recent radiation of the Hawaiian endemic mints (Lamiaceae), and their close relatives in the genus Stachys, "The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)" [1]. Here we describe the chloroplast genome sequences for 12 mint taxa. Data presented include summaries of gene content and length for these taxa, structural comparison of the mint chloroplast genomes with published sequences from other species in the order Lamiales, and comparisons of variability among three Hawaiian taxa vs. three outgroup taxa. Finally, we provide a list of 108 primer pairs targeting the most variable regions within this group and designed specifically for amplification of DNA extracted from degraded herbarium material.

Revisiting the Estimation of Dinosaur Growth Rates

PubMed Central

Myhrvold, Nathan P.

2013-01-01

Previous growth-rate studies covering 14 dinosaur taxa, as represented by 31 data sets, are critically examined and reanalyzed by using improved statistical techniques. The examination reveals that some previously reported results cannot be replicated by using the methods originally reported; results from new methods are in many cases different, in both the quantitative rates and the qualitative nature of the growth, from results in the prior literature. Asymptotic growth curves, which have been hypothesized to be ubiquitous, are shown to provide best fits for only four of the 14 taxa. Possible reasons for non-asymptotic growth patterns are discussed; they include systematic errors in the age-estimation process and, more likely, a bias toward younger ages among the specimens analyzed. Analysis of the data sets finds that only three taxa include specimens that could be considered skeletally mature (i.e., having attained 90% of maximum body size predicted by asymptotic curve fits), and eleven taxa are quite immature, with the largest specimen having attained less than 62% of predicted asymptotic size. The three taxa that include skeletally mature specimens are included in the four taxa that are best fit by asymptotic curves. The totality of results presented here suggests that previous estimates of both maximum dinosaur growth rates and maximum dinosaur sizes have little statistical support. Suggestions for future research are presented. PMID:24358133

Occurrence of polycyclic aromatic hydrocarbons below coal-tar-sealed parking lots and effects on stream benthic macroinvertebrate communities

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

Scoggins, M.; McClintock, N.L.; Gosselink, L.

2007-12-15

Parking-lot pavement sealants recently have been recognized as a major source of polycyclic aromatic hydrocarbons (PAHs) in urban stream sediments in Austin, Texas. Laboratory and field studies have shown that PAHs in sediments can be toxic to aquatic organisms and can degrade aquatic communities. After identifying increases in concentrations of PAHs in sediments below seal-coated parking lots, we investigated whether the increases had significant effects on stream biota in 5 Austin streams. We sampled sediment chemistry and biological communities above and below the point at which stormwater runoff from the parking lots discharged into the streams, thus providing 5 upstreammore » reference sites and 5 downstream treatment sites. Differences between upstream and downstream concentrations of total PAH ranged from 3.9 to 32 mg/kg. Analysis of the species occurrence data from pool and riffle habitats indicated a significant decrease in community health at the downstream sites, including decreases in richness, intolerant taxa, Diptera taxa, and density. In pool sediments, Chironomidae density was negatively correlated with PAH concentrations, whereas Oligochaeta density responded positively to PAH concentrations. In general, pool taxa responded more strongly than riffle taxa to PAHs, but riffle taxa responded more broadly than pool taxa. Increases in PAH sediment-toxicity units between upstream and downstream sites explained decreases in taxon richness and density in pools between upstream and downstream sites.« less

A Benthic Community Index for streams in the Northern Lakes and Forests Ecoregion

USGS Publications Warehouse

Butcher, Jason T.; Stewart, Paul M.; Simon, Thomas P.

2003-01-01

Encompassing the northern glaciated section of the Midwest United States, the Northern Lakes and Forests Ecoregion is characterized by mixed conifer and deciduous forests and wetlands. Sites were randomly selected in the ecoregion using the Environmental Protection Agency's Environmental Monitoring and Assessment Program designed to develop an index of biotic integrity for wadeable streams. Macroinvertebrates were sampled during the fall of 1998 and 1999 using a multi-habitat, composite-sample method. Two hundred forty-six invertebrate taxa in 97 families were collected from 94 sites. Ten of 42 candidate metrics satisfied metric selection criteria, including six structural metrics (number of Ephemeroptera taxa, number of Diptera taxa, richness, Shannon-Wiener diversity, percent Trichoptera abundance, and percent Crustacea and Mollusca abundance), two functional metrics (number of Filterer taxa and number of Scraper taxa), and two conditional metrics (number of Ephemeroptera, Trichoptera, and Plecoptera taxa and Hilsenhoff Biotic Index). These metrics were used to develop a Benthic Community Index to assess the biological integrity of wadeable streams in the ecoregion. Index values ranged from 10 to 50, and scores from impaired sites were significantly different than non-impaired sites (P<0.001). Index values were divided into three narrative interpretations of biological integrity (poor, fair, and good). After further testing, the index may provide a useful biological assessment tool for resource managers in the ecoregion.

Co-Occurrence Patterns of Common and Rare Leaf-Litter Frogs, Epiphytic Ferns and Dung Beetles across a Gradient of Human Disturbance

PubMed Central

Oldekop, Johan A.; Bebbington, Anthony J.; Truelove, Nathan K.; Tysklind, Niklas; Villamarín, Santiago; Preziosi, Richard F.

2012-01-01

Indicator taxa are commonly used to identify priority areas for conservation or to measure biological responses to environmental change. Despite their widespread use, there is no general consensus about the ability of indicator taxa to predict wider trends in biodiversity. Many studies have focused on large-scale patterns of species co-occurrence to identify areas of high biodiversity, threat or endemism, but there is much less information about patterns of species co-occurrence at local scales. In this study, we assess fine-scale co-occurrence patterns of three indicator taxa (epiphytic ferns, leaf litter frogs and dung beetles) across a remotely sensed gradient of human disturbance in the Ecuadorian Amazon. We measure the relative contribution of rare and common species to patterns of total richness in each taxon and determine the ability of common and rare species to act as surrogate measures of human disturbance and each other. We find that the species richness of indicator taxa changed across the human disturbance gradient but that the response differed among taxa, and between rare and common species. Although we find several patterns of co-occurrence, these patterns differed between common and rare species. Despite showing complex patterns of species co-occurrence, our results suggest that species or taxa can act as reliable indicators of each other but that this relationship must be established and not assumed. PMID:22701730

Taxocoenosis and distribution of nektonic fauna in the rice fields of Kashmir (J and K) India.

PubMed

Bahaar, S W N; Bhat, G A

2011-04-15

Present study attempts to identify the taxocoenosis and distribution of nektonic fauna harbouring the rice field ecosystems of Kashmir. The main objective of the study was to provide an overview of the nektonic community composition and physicochemical characteristics of flood waters. 6 sites were selected in Kupwara, Bandipora, Budgam, Srinagar, Pulwama and Anantnag districts of valley Kashmir. A total of 26 taxa belonging to 13 different orders were reported during the study which commenced through 2 consecutive crop cycles. The taxocoenosis was dominated by Coleoptera (10 taxa) followed by Hemiptera (3 taxa), Diptera (2 taxa), Diplostraca (2 taxa), Acarina, Anostraca, Anura, Amphipoda, Basommatophora, Cypriniformes, Cyprinodontiformes, Odonata and Pulmonata (1 taxa each). Diversity was calculated using Simpsons Index (D), Simpsons Index of Diversity (1-D), Simpsons Reciprocal Index (1/D), Shannon-Weiner Index (H'), Margalef Richness Index (d) and Evenness Index (e). Kupwara (34 degrees 02'N; 74 degrees 16'E) formed the most diverse site registering a total of 2384 individuals belonging to 24 taxa. A perusal of the primary data related to the physicochemical attributes of flood waters exhibited that average water temperature varied between 19-30 degrees C, average air temperature varied between 21 and 33 degrees C. pH depicted a variation between 6.0 and 9.0, Dissolved Oxygen varied between a minimum of 1.0 mg L(-1) and a maximum of 10 mg L(-1). Free CO2 ranged between 0 mg L(-1) and 6.1 mg(-1). The results pressed the need for recognizing and preserving rice fields as potential habitats for organisms that have successfully adapted to the highly manipulated and eutrophic conditions of rice paddies.

A comparative approach expands the protein-protein interaction node of the immune receptor XA21 in wheat and rice

PubMed Central

Yang, Baoju; Ruan, Randy; Cantu, Dario; Wang, Xiaodong; Ji, Wanquan; Ronald, Pamela C; Dubcovsky, Jorge

2016-01-01

The rice (Oryza sativa) OsXA21 receptor kinase is a well-studied immune receptor that initiates a signal transduction pathway leading to resistance to Xanthomonas oryzae pv. oryzae. Two homologs of OsXA21 were identified in wheat (Triticum aestivum): TaXA21-like1 located in a syntenic region with OsXA21, and TaXA21-like2 located in a non-syntenic region. Proteins encoded by these two wheat genes interact with four wheat orthologs of known OsXA21 interactors. In this study, we screened a wheat yeast-two-hybrid (Y2H) library using the cytosolic portion of TaXA21-like1 as bait to identify additional interactors. Using full-length T. aestivum and T. monococcum proteins and Y2H assays we identified three novel TaXA21-like1 interactors (TaARG, TaPR2, TmSKL1) plus one previously known in rice (TaSGT1). An additional full-length wheat protein (TaCIPK14) interacted with TaXA21-like2 and OsXA21 but not with TaXA21-like1. The interactions of TaXA21-like1 with TmSKL1 and TaSGT1 were also observed in rice protoplasts using bimolecular fluorescence complementation (BiFC) assays. We then cloned the rice homologs of the novel wheat interactors and confirmed that they all interact with OsXA21. This last result suggests that inter-specific comparative interactome analyses can be used not only to transfer known interactions from rice to wheat, but also to identify novel interactions in rice. PMID:23957671

Campanulaceae: a family with small seeds that require light for germination

PubMed Central

Koutsovoulou, Katerina; Daws, Matthew I.; Thanos, Costas A.

2014-01-01

Background and Aims The Campanulaceae is a large cosmopolitan family, but is understudied in terms of germination, and seed biology in general. Small seed mass (usually in the range 10–200 µg) is a noteworthy trait of the family, and having small seeds is commonly associated with a light requirement. Thus, the purpose of this study was to investigate the effect of light on germination in 131 taxa of the Campanulaceae family, from all five continents of its distribution. Methods For all taxa, seed germination was tested in light (8 or 12 h photoperiod) and continuous darkness under constant and alternating temperatures. For four taxa, the effect of light on germination was examined over a wide range of temperatures on a thermogradient plate, and the possible substitution of the light requirement by gibberellic acid and nitrate was examined in ten taxa. Key Results For all 131 taxa, seed germination was higher in light than in darkness for every temperature tested. Across species, the light requirement decreased significantly with increasing seed mass. For larger seeded species, germination in the dark reached higher levels under alternating than under constant temperatures. Gibberellic acid promoted germination in darkness whereas nitrates partially substituted for a light requirement only in species showing some dark germination. Conclusions A light requirement for germination, observed in virtually all taxa examined, constitutes a collective characteristic of the family. It is postulated that smaller seeded taxa might germinate only on the soil surface or at shallow depths, while larger seeded species might additionally germinate when buried in the soil if cued to do so by fluctuating temperatures. PMID:24232382

Dietary changes of large herbivores in the Turkana Basin, Kenya from 4 to 1 Ma

NASA Astrophysics Data System (ADS)

Cerling, Thure E.; Andanje, Samuel A.; Blumenthal, Scott A.; Brown, Francis H.; Chritz, Kendra L.; Harris, John M.; Hart, John A.; Kirera, Francis M.; Kaleme, Prince; Leakey, Louise N.; Leakey, Meave G.; Levin, Naomi E.; Kyalo Manthi, Fredrick; Passey, Benjamin H.; Uno, Kevin T.

2015-09-01

A large stable isotope dataset from East and Central Africa from ca. 30 regional collection sites that range from forest to grassland shows that most extant East and Central African large herbivore taxa have diets dominated by C4 grazing or C3 browsing. Comparison with the fossil record shows that faunal assemblages from ca. 4.1-2.35 Ma in the Turkana Basin had a greater diversity of C3-C4 mixed feeding taxa than is presently found in modern East and Central African environments. In contrast, the period from 2.35 to 1.0 Ma had more C4-grazing taxa, especially nonruminant C4-grazing taxa, than are found in modern environments in East and Central Africa. Many nonbovid C4 grazers became extinct in Africa, notably the suid Notochoerus, the hipparion equid Eurygnathohippus, the giraffid Sivatherium, and the elephantid Elephas. Other important nonruminant C4-grazing taxa switched to browsing, including suids in the lineage Kolpochoerus-Hylochoerus and the elephant Loxodonta. Many modern herbivore taxa in Africa have diets that differ significantly from their fossil relatives. Elephants and tragelaphin bovids are two groups often used for paleoecological insight, yet their fossil diets were very different from their modern closest relatives; therefore, their taxonomic presence in a fossil assemblage does not indicate they had a similar ecological function in the past as they do at present. Overall, we find ecological assemblages of C3-browsing, C3-C4-mixed feeding, and C4-grazing taxa in the Turkana Basin fossil record that are different from any modern ecosystem in East or Central Africa.

Big cat, small cat: reconstructing body size evolution in living and extinct Felidae.

PubMed

Cuff, A R; Randau, M; Head, J; Hutchinson, J R; Pierce, S E; Goswami, A

2015-08-01

The evolution of body mass is a fundamental topic in evolutionary biology, because it is closely linked to manifold life history and ecological traits and is readily estimable for many extinct taxa. In this study, we examine patterns of body mass evolution in Felidae (Placentalia, Carnivora) to assess the effects of phylogeny, mode of evolution, and the relationship between body mass and prey choice in this charismatic mammalian clade. Our data set includes 39 extant and 26 extinct taxa, with published body mass data supplemented by estimates based on condylobasal length. These data were run through 'SURFACE' and 'bayou' to test for patterns of body mass evolution and convergence between taxa. Body masses of felids are significantly different among prey choice groupings (small, mixed and large). We find that body mass evolution in cats is strongly influenced by phylogeny, but different patterns emerged depending on inclusion of extinct taxa and assumptions about branch lengths. A single Ornstein-Uhlenbeck optimum best explains the distribution of body masses when first-occurrence data were used for the fossil taxa. However, when mean occurrence dates or last known occurrence dates were used, two selective optima for felid body mass were recovered in most analyses: a small optimum around 5 kg and a large one around 100 kg. Across living and extinct cats, we infer repeated evolutionary convergences towards both of these optima, but, likely due to biased extinction of large taxa, our results shift to supporting a Brownian motion model when only extant taxa are included in analyses. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Dietary changes of large herbivores in the Turkana Basin, Kenya from 4 to 1 Ma

PubMed Central

Cerling, Thure E.; Andanje, Samuel A.; Blumenthal, Scott A.; Brown, Francis H.; Chritz, Kendra L.; Harris, John M.; Hart, John A.; Kirera, Francis M.; Kaleme, Prince; Leakey, Louise N.; Leakey, Meave G.; Levin, Naomi E.; Manthi, Fredrick Kyalo; Passey, Benjamin H.; Uno, Kevin T.

2015-01-01

A large stable isotope dataset from East and Central Africa from ca. 30 regional collection sites that range from forest to grassland shows that most extant East and Central African large herbivore taxa have diets dominated by C4 grazing or C3 browsing. Comparison with the fossil record shows that faunal assemblages from ca. 4.1–2.35 Ma in the Turkana Basin had a greater diversity of C3–C4 mixed feeding taxa than is presently found in modern East and Central African environments. In contrast, the period from 2.35 to 1.0 Ma had more C4-grazing taxa, especially nonruminant C4-grazing taxa, than are found in modern environments in East and Central Africa. Many nonbovid C4 grazers became extinct in Africa, notably the suid Notochoerus, the hipparion equid Eurygnathohippus, the giraffid Sivatherium, and the elephantid Elephas. Other important nonruminant C4-grazing taxa switched to browsing, including suids in the lineage Kolpochoerus-Hylochoerus and the elephant Loxodonta. Many modern herbivore taxa in Africa have diets that differ significantly from their fossil relatives. Elephants and tragelaphin bovids are two groups often used for paleoecological insight, yet their fossil diets were very different from their modern closest relatives; therefore, their taxonomic presence in a fossil assemblage does not indicate they had a similar ecological function in the past as they do at present. Overall, we find ecological assemblages of C3-browsing, C3–C4-mixed feeding, and C4-grazing taxa in the Turkana Basin fossil record that are different from any modern ecosystem in East or Central Africa. PMID:26240344

Nearshore biological communities prior to the removal of the Elwha River dams: Chapter 6 in Coastal habitats of the Elwha River, Washington--biological and physical patterns and processes prior to dam removal

USGS Publications Warehouse

Rubin, Stephen P.; Miller, Ian M.; Elder, Nancy; Reisenbichler, Reginald R.; Duda, Jeffrey J.; Duda, Jeffrey J.; Warrick, Jonathan A.; Magirl, Christopher S.

2011-01-01

(3–18 m) near the mouth of the Elwha River, between the west end of Freshwater Bay and the base of Ediz Hook, were surveyed in August and September 2008, to establish baselines prior to dam removal. Density was estimated for 9 kelp taxa, 65 taxa of invertebrates larger than 2.5 cm any dimension and 24 fish taxa. Density averaged over all sites was 3.1 per square meter (/m2) for kelp, 2.7/m2 for invertebrates, and 0.1/m2 for fish. Community structure was partly controlled by substrate type, seafloor relief, and depth. On average, 12 more taxa occurred where boulders were present compared to areas lacking boulders but with similar base substrate. Four habitat types were identified: (1) Bedrock/boulder reefs had the highest kelp density and taxa richness, and were characterized by a canopy of Nereocystis leutkeana (bull kelp) at the water surface and a secondary canopy of perennial kelp 1–2 m above the seafloor; (2) Mixed sand and gravel-cobble habitats with moderate relief provided by boulders had the highest density of invertebrates and a taxa richness nearly equivalent to that for bedrock/boulder reefs; (3) Mixed sand and gravel-cobble habitats lacking boulders supported a moderate density of kelp, primarily annual species with low growth forms (blades close to the seafloor), and the lowest invertebrate density among habitats; and (4) Sand habitats had the lowest kelp density and taxa richness among habitats and a moderate density of invertebrates. Uncertainties about nearshore community responses to increases in deposited and suspended sediments highlight the opportunity to advance scientific understanding by measuring responses following dam removal.

Fungal diversity, dominance, and community structure in the rhizosphere of clonal Picea mariana plants throughout nursery production chronosequences.

PubMed

Vujanovic, V; Hamelin, R C; Bernier, L; Vujanovic, G; St-Arnaud, M

2007-11-01

Fungal diversity in the rhizosphere of healthy and diseased clonal black spruce (Picea mariana) plants was analyzed with regard to nursery production chronosequences. The four key production stages were sampled: mother plants (MP), 8-week-old cuttings (B + 0), second-year cuttings (B + 1), and third-year cuttings (B + 2). A total of 45 fungal taxa were isolated and identified based on cultural, phenotypic, and molecular characters. Members of phylum Ascomycota dominated, followed by Basidiomycota and Zygomycota. Diagnosis characters and distance analysis of the internal transcribed spacer rDNA sequences allowed the identification of 39 ascomycetous taxa. Many belong to the order Hypocreales, families Hypocreaceae and Nectriaceae, which contain many clusters of potentially pathogenic taxa (Cylindrocladium, Fusarium, and Neonectria) and are also ecologically associated with antagonistic taxa (Chaetomium, Hypocrea, Microsphaeropsis, Penicillium, Paecilomyces, Verticillium, Trichoderma, and Sporothrix). This is also the first report of a Cylindrocladium canadense association with disease symptoms and relation with Pestalotiopsis, Fusarium, Exserochilum, Rhizoctonia, and Xenochalara fungal consortia. Both production chronosequence and plant health considerably influenced fungal taxa assemblages. Unweighted pair-group arithmetic average clustering showed that isolates from MP, B + 0, and B + 1 plant rhizospheres clustered together within healthy or diseased health classes, whereas isolates from healthy and diseased B + 2 plants clustered together. Canonical correspondence analysis revealed substantial alteration in community assemblages with regard to plant health and yielded a principal axis direction that regrouped taxa associated with diseased plant rhizosphere soil, whereas the opposite axis direction was associated with healthy plants. Two diversity indices were defined and applied to assess the fungal taxa contribution (Tc) and persistence (Pi) throughout the

Patterns of Freshwater Species Richness, Endemism, and Vulnerability in California

PubMed Central

Furnish, Joseph; Gardali, Thomas; Grantham, Ted; Katz, Jacob V. E.; Kupferberg, Sarah; McIntyre, Patrick; Moyle, Peter B.; Ode, Peter R.; Peek, Ryan; Quiñones, Rebecca M.; Rehn, Andrew C.; Santos, Nick; Schoenig, Steve; Serpa, Larry; Shedd, Jackson D.; Slusark, Joe; Viers, Joshua H.; Wright, Amber; Morrison, Scott A.

2015-01-01

The ranges and abundances of species that depend on freshwater habitats are declining worldwide. Efforts to counteract those trends are often hampered by a lack of information about species distribution and conservation status and are often strongly biased toward a few well-studied groups. We identified the 3,906 vascular plants, macroinvertebrates, and vertebrates native to California, USA, that depend on fresh water for at least one stage of their life history. We evaluated the conservation status for these taxa using existing government and non-governmental organization assessments (e.g., endangered species act, NatureServe), created a spatial database of locality observations or distribution information from ~400 data sources, and mapped patterns of richness, endemism, and vulnerability. Although nearly half of all taxa with conservation status (n = 1,939) are vulnerable to extinction, only 114 (6%) of those vulnerable taxa have a legal mandate for protection in the form of formal inclusion on a state or federal endangered species list. Endemic taxa are at greater risk than non-endemics, with 90% of the 927 endemic taxa vulnerable to extinction. Records with spatial data were available for a total of 2,276 species (61%). The patterns of species richness differ depending on the taxonomic group analyzed, but are similar across taxonomic level. No particular taxonomic group represents an umbrella for all species, but hotspots of high richness for listed species cover 40% of the hotspots for all other species and 58% of the hotspots for vulnerable freshwater species. By mapping freshwater species hotspots we show locations that represent the top priority for conservation action in the state. This study identifies opportunities to fill gaps in the evaluation of conservation status for freshwater taxa in California, to address the lack of occurrence information for nearly 40% of freshwater taxa and nearly 40% of watersheds in the state, and to implement adequate

Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf.

PubMed

Cardona, Gabriel; Mir, Arnau; Rosselló, Francesc; Rotger, Lucía; Sánchez, David

2013-01-16

Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to measure quantitatively the difference between a pair of phylogenetic trees by first encoding them by means of their half-matrices of cophenetic values, and then comparing these matrices. This idea has been used several times since then to define dissimilarity measures between phylogenetic trees but, to our knowledge, no proper metric on weighted phylogenetic trees with nested taxa based on this idea has been formally defined and studied yet. Actually, the cophenetic values of pairs of different taxa alone are not enough to single out phylogenetic trees with weighted arcs or nested taxa. For every (rooted) phylogenetic tree T, let its cophenetic vectorφ(T) consist of all pairs of cophenetic values between pairs of taxa in T and all depths of taxa in T. It turns out that these cophenetic vectors single out weighted phylogenetic trees with nested taxa. We then define a family of cophenetic metrics dφ,p by comparing these cophenetic vectors by means of Lp norms, and we study, either analytically or numerically, some of their basic properties: neighbors, diameter, distribution, and their rank correlation with each other and with other metrics. The cophenetic metrics can be safely used on weighted phylogenetic trees with nested taxa and no restriction on degrees, and they can be computed in O(n2) time, where n stands for the number of taxa. The metrics dφ,1 and dφ,2 have positive skewed distributions, and they show a low rank correlation with the Robinson-Foulds metric and the nodal metrics, and a very high correlation with each other and with the splitted nodal metrics. The diameter of dφ,p, for p⩾1 , is in O(n(p+2)/p), and thus for low p they are more discriminative, having a wider range of values.

Mapping evolutionary process: a multi-taxa approach to conservation prioritization

PubMed Central

Thomassen, Henri A; Fuller, Trevon; Buermann, Wolfgang; Milá, Borja; Kieswetter, Charles M; Jarrín-V, Pablo; Cameron, Susan E; Mason, Eliza; Schweizer, Rena; Schlunegger, Jasmin; Chan, Janice; Wang, Ophelia; Peralvo, Manuel; Schneider, Christopher J; Graham, Catherine H; Pollinger, John P; Saatchi, Sassan; Wayne, Robert K; Smith, Thomas B

2011-01-01

Human-induced land use changes are causing extensive habitat fragmentation. As a result, many species are not able to shift their ranges in response to climate change and will likely need to adapt in situ to changing climate conditions. Consequently, a prudent strategy to maintain the ability of populations to adapt is to focus conservation efforts on areas where levels of intraspecific variation are high. By doing so, the potential for an evolutionary response to environmental change is maximized. Here, we use modeling approaches in conjunction with environmental variables to model species distributions and patterns of genetic and morphological variation in seven Ecuadorian amphibian, bird, and mammal species. We then used reserve selection software to prioritize areas for conservation based on intraspecific variation or species-level diversity. Reserves selected using species richness and complementarity showed little overlap with those based on genetic and morphological variation. Priority areas for intraspecific variation were mainly located along the slopes of the Andes and were largely concordant among species, but were not well represented in existing reserves. Our results imply that in order to maximize representation of intraspecific variation in reserves, genetic and morphological variation should be included in conservation prioritization. PMID:25567981

Microdistillation and analysis of volatiles from eight ornamental salvia taxa

USDA-ARS?s Scientific Manuscript database

Volatile compounds from seven Salvia species and one interspecific hybrid growing at the Dallas Arboretum and Botanical Garden, Texas, US, S. coccinea, S. farinacea, S. greggii, S. leucantha, S. longispicata × farinacea, S. madrensis, S. roemeriana and S. splendens were investigated for their chemic...

Circadian Disruption Changes Gut Microbiome Taxa and Functional Gene Composition.

PubMed

Deaver, Jessica A; Eum, Sung Y; Toborek, Michal

2018-01-01

Disrupted circadian rhythms and alterations of the gut microbiome composition were proposed to affect host health. Therefore, the aim of this research was to identify whether these events are connected and if circadian rhythm disruption by abnormal light-dark (LD) cycles affects microbial community gene expression and host vulnerability to intestinal dysfunction. Mice were subjected to either a 4-week period of constant 24-h light or of normal 12-h LD cycles. Stool samples were collected at the beginning and after the circadian rhythm disruption. A metatranscriptomic analysis revealed an increase in Ruminococcus torques , a bacterial species known to decrease gut barrier integrity, and a decrease in Lactobacillus johnsonii , a bacterium that helps maintain the intestinal epithelial cell layer, after circadian rhythm disruption. In addition, genes involved in pathways promoting host beneficial immune responses were downregulated, while genes involved in the synthesis and transportation of the endotoxin lipopolysaccharide were upregulated in mice with disrupted circadian cycles. Importantly, these mice were also more prone to dysfunction of the intestinal barrier. These results further elucidate the impact of light-cycle disruption on the gut microbiome and its connection with increased incidence of disease in response to circadian rhythm disturbances.

Circadian Disruption Changes Gut Microbiome Taxa and Functional Gene Composition

PubMed Central

Deaver, Jessica A.; Eum, Sung Y.; Toborek, Michal

2018-01-01

Disrupted circadian rhythms and alterations of the gut microbiome composition were proposed to affect host health. Therefore, the aim of this research was to identify whether these events are connected and if circadian rhythm disruption by abnormal light–dark (LD) cycles affects microbial community gene expression and host vulnerability to intestinal dysfunction. Mice were subjected to either a 4-week period of constant 24-h light or of normal 12-h LD cycles. Stool samples were collected at the beginning and after the circadian rhythm disruption. A metatranscriptomic analysis revealed an increase in Ruminococcus torques, a bacterial species known to decrease gut barrier integrity, and a decrease in Lactobacillus johnsonii, a bacterium that helps maintain the intestinal epithelial cell layer, after circadian rhythm disruption. In addition, genes involved in pathways promoting host beneficial immune responses were downregulated, while genes involved in the synthesis and transportation of the endotoxin lipopolysaccharide were upregulated in mice with disrupted circadian cycles. Importantly, these mice were also more prone to dysfunction of the intestinal barrier. These results further elucidate the impact of light-cycle disruption on the gut microbiome and its connection with increased incidence of disease in response to circadian rhythm disturbances. PMID:29706947

Mapping evolutionary process: a multi-taxa approach to conservation prioritization.

PubMed

Thomassen, Henri A; Fuller, Trevon; Buermann, Wolfgang; Milá, Borja; Kieswetter, Charles M; Jarrín-V, Pablo; Cameron, Susan E; Mason, Eliza; Schweizer, Rena; Schlunegger, Jasmin; Chan, Janice; Wang, Ophelia; Peralvo, Manuel; Schneider, Christopher J; Graham, Catherine H; Pollinger, John P; Saatchi, Sassan; Wayne, Robert K; Smith, Thomas B

2011-03-01

Human-induced land use changes are causing extensive habitat fragmentation. As a result, many species are not able to shift their ranges in response to climate change and will likely need to adapt in situ to changing climate conditions. Consequently, a prudent strategy to maintain the ability of populations to adapt is to focus conservation efforts on areas where levels of intraspecific variation are high. By doing so, the potential for an evolutionary response to environmental change is maximized. Here, we use modeling approaches in conjunction with environmental variables to model species distributions and patterns of genetic and morphological variation in seven Ecuadorian amphibian, bird, and mammal species. We then used reserve selection software to prioritize areas for conservation based on intraspecific variation or species-level diversity. Reserves selected using species richness and complementarity showed little overlap with those based on genetic and morphological variation. Priority areas for intraspecific variation were mainly located along the slopes of the Andes and were largely concordant among species, but were not well represented in existing reserves. Our results imply that in order to maximize representation of intraspecific variation in reserves, genetic and morphological variation should be included in conservation prioritization.

Lectotypifications of six taxa in the Boraginales (Cordiaceae and Heliotropiaceae)

PubMed Central

Feuillet, Christian

2016-01-01

Abstract A large number of specimens used as original material for the description of new species were destroyed in the bombing of the Berlin-Dahlem herbarium, B, in 1943. Six lectotypes are designated here for Cordia discolor Cham., Cordia multispicata Cham., Cordia tobagensis Urb. and its variety broadwayi Urb. in the Cordiaceae and for Tournefortia paniculata Cham. and Tournefortia ulei Vaupel in the Heliotropiaceae. PMID:27212885

A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL ANALYSIS OF GENETIC DIVERSITY

EPA Science Inventory

In addition to measuring spatial patterns of genetic diversity, population genetic measures of biological resources should include temporal data that indicate whether the observed patterns are the result of historical or contemporary processes. In general, genetic measures focus...

Concentrated evolutionary novelties in the foot musculature of Odontophrynidae (Anura: Neobatrachia), with comments on adaptations for burrowing.

PubMed

Blotto, Boris L; Pereyra, Martin O; Faivovich, Julián; Dias, Pedro Henrique Dos Santos; Grant, Taran

2017-05-02

We studied the foot musculature of the fossorial family Odontophrynidae (composed of the genera Macrogenioglottus, Odontophrynus, and Proceratophrys) plus several outgroup taxa from Hyloidea and other burrowing taxa from across Anura. We found novel character-states supporting the monophyly of Odontophrynus, Proceratophrys, and Odontophrynus + Macrogenioglottus. The character-states observed in O. cultripes support conflicting phylogenetic positions within Odontophrynus. A comparison of some novel character-states with a diverse sample of burrowing taxa suggests that some modifications of the foot musculature might be involved in digging.

Effect of investigator disturbance in experimental forensic entomology: succession and community composition.

PubMed

De Jong, G D; Hoback, W W

2006-06-01

Carrion insect succession studies have historically used repeated sampling of single or a few carcasses to produce data, either weighing the carcasses, removing a qualitative subsample of the fauna present, or both, on every visit over the course of decomposition and succession. This study, conducted in a set of related experimental hypotheses with two trials in a single season, investigated the effect that repeated sampling has on insect succession, determined by the number of taxa collected on each visit and by community composition. Each trial lasted at least 21 days, with daily visits on the first 14 days. Rat carcasses used in this study were all placed in the field on the same day, but then either sampled qualitatively on every visit (similar to most succession studies) or ignored until a given day of succession, when they were sampled qualitatively (a subsample) and then destructively sampled in their entirety. Carcasses sampled on every visit were in two groups: those from which only a sample of the fauna was taken and those from which a sample of fauna was taken and the carcass was weighed for biomass determination. Of the carcasses visited only once, the number of taxa in subsamples was compared to the actual number of taxa present when the carcass was destructively sampled to determine if the subsamples adequately represented the total carcass fauna. Data from the qualitative subsamples of those carcasses visited only once were also compared to data collected from carcasses that were sampled on every visit to investigate the effect of the repeated sampling. A total of 39 taxa were collected from carcasses during the study and the component taxa are discussed individually in relation to their role in succession. Number of taxa differed on only one visit between the qualitative subsamples and the actual number of taxa present, primarily because the organisms missed by the qualitative sampling were cryptic (hidden deep within body cavities) or rare (only

Analyses of the Microbial Diversity across the Human Microbiome

PubMed Central

Li, Kelvin; Bihan, Monika; Yooseph, Shibu; Methé, Barbara A.

2012-01-01

Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, Smax, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, (“τ”), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ’s greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next

The lichens of the Alps – an annotated checklist

PubMed Central

Nimis, Pier Luigi; Hafellner, Josef; Roux, Claude; Clerc, Philippe; Helmut Mayrhofer; Martellos, Stefano; Bilovitz, Peter O.

2018-01-01

Abstract This is the first attempt to provide an overview of the lichen diversity of the Alps, one of the biogegraphically most important and emblematic mountain systems worldwide. The checklist includes all lichenised species, plus a set of non- or doubtfully lichenised taxa frequently treated by lichenologists, excluding non-lichenised lichenicolous fungi. Largely based on recent national or regional checklists, it provides a list of all infrageneric taxa (with synonyms) hitherto reported from the Alps, with data on their distribution in eight countries (Austria, France, Germany, Liechtenstein, Monaco, Italy, Slovenia, Switzerland) and in 42 Operational Geographic Units, mostly corresponding to administrative subdivisions within the countries. Data on the main substrates and on the altitudinal distribution are also provided. A short note points to the main ecological requirements of each taxon and/or to open taxonomic problems. Particularly poorly known taxa are flagged and often provided with a short description, to attract the attention of specialists. The total number of infrageneric taxa is 3,163, including 117 non- or doubtfully lichenised taxa. The richness of the lichen biota fairly well corresponds with the percent of the Alpine area occupied by each country: Austria (2,337 taxa), Italy (2,169), France (2,028), Switzerland (1,835), Germany (1,168), Slovenia (890) and Lichtenstein (152), no lichen having ever been reported from Monaco. The number of poorly known taxa is quite high (604, 19.1% of the total), which indicates that, in spite of the Alps being one of the lichenologically most studied mountain systems worldwide, much work is still needed to reach a satisfactory picture of their real lichen diversity. Thirteen new combinations are proposed in the genera Agonimia, Aspicilia, Bagliettoa, Bellemerea, Carbonea, Lepra, Miriquidica, Polysporina, Protothelenella, Pseudosagedia and Thelidium. PMID:29706791

Colonization of habitat islands in the deep sea: recruitment to glass sponge stalks

NASA Astrophysics Data System (ADS)

Beaulieu, Stace E.

2001-04-01

Biogenic structures in the deep sea often act as hard substratum 'islands' for the attachment of encrusting fauna. At an abyssal station in the NE Pacific, stalks of hexactinellid sponges in the genus Hyalonema are habitat islands for species-rich epifaunal communities. An experimental study was conducted to (1) determine the colonization rates of artificial Hyalonema stalks, (2) compare the species composition and diversity of recruits to newly available substrata to that of the natural communities, and (3) examine the vertical distribution of recruits. Four sets of six artificial sponge stalks, constructed of Hyalonema spicules, were deployed at 4100 m depth for 3- to 5-month periods. There was no difference in net colonization or immigration rate among the four deployments. Colonization rates were similar to those reported for other deep-sea, hard substratum recruitment experiments. The taxa that recruited to the artificial stalks were a subset of the taxa found in natural communities. However, several taxa important in structuring natural communities did not recruit to the artificial stalks. The two taxa with the highest invasion rates, a calcareous foraminiferan ( Cibicides lobatulus) and a serpulid polychaete ( Bathyvermilia sp.), also were the two taxa with greatest relative abundance in natural communities. Vertical distributions of Cibicides and an agglutinated foraminiferan ( Telammina sp.) were skewed towards the top of the artificial stalks, potentially because of active habitat selection. These results have several implications for natural Hyalonema stalk communities. Most importantly, species composition and abundance of individuals in the stalk communities appear to be maintained by frequent recruitment of a few common taxa and infrequent recruitment of many rare taxa. An argument is presented for temporal-mosaic maintenance of diversity in these deep-sea, hard substratum communities.

Investigating the Host-Range of the Rust Fungus Puccinia psidii sensu lato across Tribes of the Family Myrtaceae Present in Australia

PubMed Central

Morin, Louise; Aveyard, Ruth; Lidbetter, Jonathan R.; Wilson, Peter G.

2012-01-01

The exotic rust fungus Puccinia psidii sensu lato was first detected in Australia in April 2010. This study aimed to determine the host-range potential of this accession of the rust by testing its pathogenicity on plants of 122 taxa, representative of the 15 tribes of the subfamily Myrtoideae in the family Myrtaceae. Each taxon was tested in two separate trials (unless indicated otherwise) that comprised up to five replicates per taxon and six replicates of a positive control (Syzygium jambos). No visible symptoms were observed on the following four taxa in either trial: Eucalyptus grandis×camaldulensis, E. moluccana, Lophostemon confertus and Sannantha angusta. Only small chlorotic or necrotic flecks without any uredinia (rust fruiting bodies) were observed on inoculated leaves of seven other taxa (Acca sellowiana, Corymbia calophylla ‘Rosea’, Lophostemon suaveolens, Psidium cattleyanum, P. guajava ‘Hawaiian’ and ‘Indian’, Syzygium unipunctatum). Fully-developed uredinia were observed on all replicates across both trials of 28 taxa from 8 tribes belonging to the following 17 genera: Agonis, Austromyrtus, Beaufortia, Callistemon, Calothamnus, Chamelaucium, Darwinia, Eucalyptus, Gossia, Kunzea, Leptospermum, Melaleuca, Metrosideros, Syzygium, Thryptomene, Tristania, Verticordia. In contrast, the remaining 83 taxa inoculated, including the majority of Corymbia and Eucalyptus species, developed a broad range of symptoms, often across the full spectrum, from fully-developed uredinia to no visible symptoms. These results were encouraging as they indicate that some levels of genetic resistance to the rust possibly exist in these taxa. Overall, our results indicated no apparent association between the presence or absence of disease symptoms and the phylogenetic relatedness of taxa. It is most likely that the majority of the thousands of Myrtaceae species found in Australia have the potential to become infected to some degree by the rust, although this wide

Polymicrobial airway bacterial communities in adult bronchiectasis patients

PubMed Central

2014-01-01

Background Chronic airway infection contributes to the underlying pathogenesis of non-cystic fibrosis bronchiectasis (NCFBr). In contrast to other chronic airway infections, associated with COPD and CF bronchiectasis, where polymicrobial communities have been implicated in lung damage due to the vicious circle of recurrent bacterial infections and inflammation, there is sparse information on the composition of bacterial communities in NCFBr. Seventy consecutive patients were recruited from an outpatient adult NCFBr clinic. Bacterial communities in sputum samples were analysed by culture and pyrosequencing approaches. Bacterial sequences were analysed using partial least square discrimination analyses to investigate trends in community composition and identify those taxa that contribute most to community variation. Results The lower airway in NCFBr is dominated by three bacterial taxa Pasteurellaceae, Streptococcaceae and Pseudomonadaceae. Moreover, the bacterial community is much more diverse than indicated by culture and contains significant numbers of other genera including anaerobic Prevotellaceae, Veillonellaceae and Actinomycetaceae. We found particular taxa are correlated with different clinical states, 27 taxa were associated with acute exacerbations, whereas 11 taxa correlated with stable clinical states. We were unable to demonstrate a significant effect of antibiotic therapy, gender, or lung function on the diversity of the bacterial community. However, presence of clinically significant culturable taxa; particularly Pseudomonas aeruginosa and Haemophilus influenzae correlated with a significant change in the diversity of the bacterial community in the lung. Conclusions We have demonstrated that acute exacerbations, the frequency of exacerbation and episodes of clinical stability are correlated, in some patients, with a significantly different bacterial community structure, that are associated with a presence of particular taxa in the NCFBr lung. Moreover

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

PubMed

Bryant, Harold N; Cantino, Philip D

2002-02-01

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.

Givetian ostracods of the Candás Formation (Asturias, North-western Spain): taxonomy, stratigraphy, palaeoecology, relationship to global events and palaeogeographical implications.

PubMed

Maillet, Sebastien; Milhau, Bruno; Vreulx, Michel; Posada, Luis-Carlos Sánchez De

2016-01-27

Asturian ostracods of the Givetian carbonate Candás Formation are documented for the first time from the Peran-Perlora and Carranques reference sections. More than 1,200 specimens were extracted from 44 samples by means of the hot acetolysis method. In all, 75 taxa are described herein, of which 21 are formally described and one, Evlanella peranensis Maillet n. sp., is new. All the taxa are marine benthic and belong to the Eifelian Mega-Assemblage. The assemblages recognized are representative of semi-restricted to shallow open-marine palaeoenvironments above the storm wave base. The stratigraphical distribution of the taxa shows a strong faunal renewal in the top of the Candás Formation. Long-ranging taxa found at the base of the formation, of which many are known from the base of the Middle Devonian, disappear within the base of the member C and are replaced above, around the Middle/Upper Givetian boundary, by more cosmopolitan taxa characteristic of the Frasnian. The lower half of the member C is also characterized both by unstable environments and occurrence of some short-ranging opportunistic ostracod taxa. This renewal within shallow water ostracod communities is probably a consequence of the global Taghanic Biocrisis, leading world-widely to extinctions in several faunal groups. Faunal affinities with Givetian ostracod taxa reported in other areas of the world reflect the commonly accepted palaeogeographical patterns. Close relations between the Cantabrian Zone (NW-Spain), the Armorican Massif (W-France), the Mouthoumet Massif (S-France) and North Africa (Morocco and Algeria) suggest a narrow oceanic space between the western European terranes and the northern Gondwanan margin that involves an advanced phase of closure of the Medio-European Ocean.

Only multi-taxon studies show the full range of arthropod responses to fire

PubMed Central

Pryke, James S.; Gaigher, René; Samways, Michael J.

2018-01-01

Fire is a major driver in many ecosystems. Yet, little is known about how different ground-living arthropods survive fire. Using three sampling methods, and time-since-fire (last fire event: 3 months, 1 year, and 7 years), we investigate how ground-living arthropod diversity responds to fire, and how species richness, diversity, abundance, and composition of the four dominant taxa: ants, beetles, cockroaches and mites, respond. We did this in the naturally fire-prone Mediterranean-type scrubland vegetation (fynbos) of the Cape Floristic Region. Surprisingly, overall species richness and diversity was the same for all time-since-fire categories. However, when each dominant taxon was analysed separately, effect of fire on species richness and abundance varied among taxa. This emphasizes that many taxa must be investigated to really understand fire-driven events. We also highlight the importance of using different diversity measures, as fire did not influence species richness and abundance of particular taxa, while it affected others, overall greatly affecting assemblages of all taxa. Rockiness affected species richness, abundance and composition of a few taxa. We found that all time-since-fire categories supported distinctive assemblages. Some indicator species occurred across all time-since-fire categories, while others were restricted to a single time-since-fire category, showing that there is a wide range of responses to fire between taxa. Details of local landscape structure, abiotic and biotic, and frequency and intensity of fire add complexity to the fire-arthropod interaction. Overall, we show that the relationship between fire and arthropods is phylogenetically constrained, having been honed by many millennia of fire events, and highly complex. Present-day species manifest a variety of adaptations for surviving the great natural selective force of fire. PMID:29614132

Potentially harmful microalgal distribution in an area of the NW Adriatic coastline: Sampling procedure and correlations with environmental factors

NASA Astrophysics Data System (ADS)

Penna, Antonella; Ingarao, Cristina; Ercolessi, Manuela; Rocchi, Marco; Penna, Nunzio

2006-10-01

In this study, the trend of potentially Harmful Algal (HA) taxa (genera and species), was analysed along a coastal area of the NW Adriatic Sea on a monthly scale. The study included the use of a phytoplankton net for sample collection. The investigation was carried out in four sampling stations characterised by different ecological features. The composition of potentially HA phytoplankton taxa and their succession were related to the environmental factors. The potentially HA group abundance accounted for 8% of all the phytoplankton taxa considered. Multivariate analyses of environmental factors suggested that potentially HA taxa are sensitive to phosphate content: potential DSP-YTX (Diarrhetic Shellfish Poisoning-Yessotoxin) producers were positively correlated with P content ( p = 0.023), while potential ASP (Amnesic Shellfish Poisoning) producers were negatively correlated with P content ( p = 0.006). Phosphorus could be considered to be the limiting factor for phytoplankton taxa density in the NW Adriatic Sea. There was a highly positive correlation between the occurrences of potentially HA taxa and low values of salinity ( p = 0.001 for potential producers of ASP, p = 0.029 for potential DSP-YTX producers). The counting of potential HA dinoflagellates in net samples represented a more accurate estimation of potential HA abundances in the water column making it possible to concentrate a greater number of potential HA dinoflagellate cells by net sampling along the entire water column rather than by sampling only at the surface as in routine monitoring procedures.

Ectomycorrhizal fungi associated with ponderosa pine and Douglas-fir: a comparison of species richness in native western North American forests and Patagonian plantations from Argentina.

PubMed

Barroetaveña, C; Cázares, E; Rajchenberg, M

2007-07-01

The putative ectomycorrhizal fungal species registered from sporocarps associated with ponderosa pine and Douglas-fir forests in their natural range distribution (i.e., western Canada, USA, and Mexico) and from plantations in south Argentina and other parts of the world are listed. One hundred and fifty seven taxa are reported for native ponderosa pine forests and 514 taxa for native Douglas-fir forests based on available literature and databases. A small group of genera comprises a high proportion of the species richness for native Douglas-fir (i.e., Cortinarius, Inocybe, and Russula), whereas in native ponderosa pine, the species richness is more evenly distributed among several genera. The comparison between ectomycorrhizal species richness associated with both trees in native forests and in Patagonia (Argentina) shows far fewer species in the latter, with 18 taxa for the ponderosa pine and 15 for the Douglas-fir. Epigeous species richness is clearly dominant in native Douglas-fir, whereas a more balanced relation epigeous/hypogeous richness is observed for native ponderosa pine; a similar trend was observed for Patagonian plantations. Most fungi in Patagonian Douglas-fir plantations have not been recorded in plantations elsewhere, except Suillus lakei and Thelephora terrestris, and only 56% of the fungal taxa recorded in Douglas-fir plantations around the world are known from native forests, the other taxa being new associations for this host, suggesting that new tree + ectomycorrhizal fungal taxa associations are favored in artificial situations as plantations.

Headwater riparian invertebrate communities associated with red alder and conifer wood and leaf litter in southeastern Alaska

USGS Publications Warehouse

LeSage, C.M.; Merritt, R.W.; Wipfli, M.S.

2005-01-01

We examined how management of young upland forests in southeastern Alaska affect riparian invertebrate taxa richness, density, and biomass, in turn, potentially influencing food abundance for fish and wildlife. Southeastern Alaska forests are dominated by coniferous trees including Sitka spruce (Picea sitchensis (Bong.) Carr.), western hemlock (Tsuga heterophylla (Raf.) Sarg.), with mixed stands of red cedar (Thuja plicata Donn.). Red alder (Alnus rubra Bong.) is hypothesized to influence the productivity of young-growth conifer forests and through forest management may provide increased riparian invertebrate abundance. To compare and contrast invertebrate densities between coniferous and alder riparian habitats, leaf litter and wood debris (early and late decay classes) samples were collected along eleven headwater streams on Prince of Wales Island, Alaska, during the summers of 2000 and 2001. Members of Acarina and Collembola were the most abundant taxa collected in leaf litter with alder litter having significantly higher mean taxa richness than conifer litter. Members of Acarina were the most abundant group collected on wood debris and alder wood had significantly higher mean taxa richness and biomass than conifer wood. Alder wood debris in more advanced decay stages had the highest mean taxa richness and biomass, compared to other wood types, while conifer late decay wood debris had the highest densities of invertebrates. The inclusion of alder in young-growth conifer forests can benefit forest ecosystems by enhancing taxa richness and biomass of riparian forest invertebrates. ?? 2005 by the Northwest Scientific Association. All rights reserved.

Plants remember past weather: a study for atmospheric pollen concentrations of Ambrosia, Poaceae and Populus

NASA Astrophysics Data System (ADS)

Matyasovszky, István; Makra, László; Csépe, Zoltán; Sümeghy, Zoltán; Deák, Áron József; Pál-Molnár, Elemér; Tusnády, Gábor

2015-10-01

After extreme dry (wet) summers or years, pollen production of different taxa may decrease (increase) substantially. Accordingly, studying effects of current and past meteorological conditions on current pollen concentrations for different taxa have of major importance. The purpose of this study is separating the weight of current and past weather conditions influencing current pollen productions of three taxa. Two procedures, namely multiple correlations and factor analysis with special transformation are used. The 11-year (1997-2007) data sets include daily pollen counts of Ambrosia (ragweed), Poaceae (grasses) and Populus (poplar), as well as daily values of four climate variables (temperature, relative humidity, global solar flux and precipitation). Multiple correlations of daily pollen counts with simultaneous values of daily meteorological variables do not show annual course for Ambrosia, but do show definite trends for Populus and Poaceae. Results received using the two methods revealed characteristic similarities. For all the three taxa, the continental rainfall peak and additional local showers in the growing season can strengthen the weight of the current meteorological elements. However, due to the precipitation, big amount of water can be stored in the soil contributing to the effect of the past climate elements during dry periods. Higher climate sensitivity (especially water sensitivity) of the herbaceous taxa ( Ambrosia and Poaceae) can be definitely established compared to the arboreal Populus. Separation of the weight of the current and past weather conditions for different taxa involves practical importance both for health care and agricultural production.

Influence of biotic variables on invertebrate size structure and diversity in coastal wetlands of Southeastern Spain

NASA Astrophysics Data System (ADS)

Antón-Pardo, María; Armengol, Xavier

2016-10-01

Biomass and size-based estimations provide relevant information regarding ecosystem functioning and biotic interactions. Our aims were to study the effect of fish and macrophytes on the size structure of invertebrate assemblages (from rotifers to insects) in a set of coastal water bodies, estimating the biomass (total and main invertebrate groups), the biomass-size spectra (model of Pareto) and size diversity. In fishless ponds, cladoceran and ostracod biomass were higher, and they presented greater size diversity. In fish ponds, rotifer biomass presented greater proportion; while in fishless ponds, cladocerans were usually the most abundant taxa and the largest organisms. The biomass size spectra showed more irregularities in fishless ponds, due to the low densities of small taxa (rotifers and copepod juveniles) and big taxa (malacostraceans or insects). Differences is size structure and diversity were also observed between spring and summer, suggesting a higher recruitment of juveniles in spring, and thus, a higher predation pressure upon zooplankton at that moment. Macrophyte cover did not apparently influence those parameters, except for the biomass of ostracods, copepods, and insects. Therefore, predation by fish strongly affected invertebrate biomass, reflecting their selective feeding, and allowing high densities of small taxa. Predation pressure decreased size diversity, by limiting the abundance of vulnerable taxa of specific size. Seasonal changes were likely related to the spring recruitment of fish juveniles. The presence of small fish and invertebrate predator taxa among the macrophytes, restrict their role as refuges for prey invertebrates.

The oral microbiota in patients with pancreatic cancer, patients with IPMNs, and controls: a pilot study.

PubMed

Olson, Sara H; Satagopan, Jaya; Xu, Youming; Ling, Lilan; Leong, Siok; Orlow, Irene; Saldia, Amethyst; Li, Peter; Nunes, Pamela; Madonia, Vincent; Allen, Peter J; O'Reilly, Eileen; Pamer, Eric; Kurtz, Robert C

2017-09-01

Poor oral health appears to be a risk factor for pancreatic cancer, possibly implicating the oral microbiota. In this pilot study, we evaluated the characteristics of the oral microbiota in patients with pancreatic ductal adenocarcinoma (PDAC), intraductal papillary mucinous neoplasms (IPMN), and healthy controls. Forty newly diagnosed PDAC patients, 39 IPMN patients, and 58 controls, excluding current smokers and users of antibiotics, provided saliva samples. Common oral bacterial species were comprehensively surveyed by sequencing of the 16S rRNA microbial genes. We obtained measures of diversity and the mean relative proportions of individual taxa. We explored the degree to which these measures differed according to respondent characteristics based on individual interviews. PDAC cases did not differ in diversity measures from either controls or IPMN cases. PDAC cases had higher mean relative proportions of Firmicutes and related taxa, while controls had higher mean relative proportions of Proteobacteria and related taxa. Results were generally similar when comparing PDAC to IPMN cases. Among IPMNs and controls combined, younger individuals had higher levels of several taxa within the Proteobacteria. The only other variable consistently related to mean relative proportions was mouthwash use, with taxa within Firmicutes more common among users. While there were no differences in diversity of the oral microbiota among these groups, there were differences in the mean relative proportions of some taxa. Characteristics of the oral microbiota are not associated with most measures of oral health.

Comparative anatomy, homologies and evolution of the pectoral and forelimb musculature of tetrapods with special attention to extant limbed amphibians and reptiles

PubMed Central

Abdala, Virginia; Diogo, Rui

2010-01-01

The main aim of the present work is to synthesize the information obtained from our dissections of the pectoral and forelimb muscles of representative members of the major extant taxa of limbed amphibians and reptiles and from our review of the literature, in order to provide an account of the comparative anatomy, homologies and evolution of these muscles in the Tetrapoda. The pectoral and forelimb musculature of all these major taxa conform to a general pattern that seems to have been acquired very early in the evolutionary history of tetrapods. Although some muscles are missing in certain taxa, and a clear departure from this general pattern is obviously present in derived groups such as birds, the same overall configuration is easily distinguishable in these taxa. Among the most notable anatomical differences between the groups, one that seems to have relevant evolutionary and functional implications, concerns the distal insertion points of the forearm musculature. In tetrapods, the muscles of the radial and ulnar complexes of the forearm are pleisomorphically mainly inserted onto the radius/ulna or onto the more proximal carpal bones, but in mammals some of these muscles insert more distally onto bones such as the metacarpals. Interestingly, a similar trend towards a more distal insertion of these muscles is also found in some non-mammalian tetrapod taxa, such as some anurans (e.g. Phyllomedusa). This may be correlated with the acquisition of more subtle digital movement abilities in these latter taxa. PMID:20807270

Arnica (Asteraceae) phylogeny revisited using RPB2: complex patterns and multiple d-paralogues.

PubMed

Ekenäs, Catarina; Heidari, Nahid; Andreasen, Katarina

2012-08-01

The region coding for the second largest subunit of RNA polymerase II (RPB2) was explored for resolving interspecific relationships in Arnica and lower level taxa in general. The region between exons 17 and 23 was cloned and sequenced for 33 accessions of Arnica and four outgroup taxa. Three paralogues of the RPB2-d copy (RPB2-dA, B and C) were detected in Arnica and outgroup taxa, indicating that the duplications must have occurred before the divergence of Arnica. Parsimony and Bayesian analyses of separate alignments of the three copies reveal complex patterns in Arnica, likely reflecting a history of lineage sorting in combination with apomixis, polyploidization, and possibly hybridization. Cloned sequences of some taxa do not form monophyletic clades within paralogues, but form multiple strongly supported clades with sequences of other taxa. Some well supported groups are present in more than one paralogue and many groups are in line with earlier hypotheses regarding interspecific relationships within the genus. Low levels of homoplasy in combination with relatively high sequence variation indicates that the introns of the RPB2 region could be suitable for phylogenetic studies in low level taxonomy. Copyright © 2012. Published by Elsevier Inc.

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.

PubMed

Bacci, Giovanni; Ceccherini, Maria Teresa; Bani, Alessia; Bazzicalupo, Marco; Castaldini, Maurizio; Galardini, Marco; Giovannetti, Luciana; Mocali, Stefano; Pastorelli, Roberta; Pantani, Ottorino Luca; Arfaioli, Paola; Pietramellara, Giacomo; Viti, Carlo; Nannipieri, Paolo; Mengoni, Alessio

2015-03-01

We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

Macroinvertebrate Response to Drought in Undisturbed Headwater Streams of Southwest Georgia.

NASA Astrophysics Data System (ADS)

Winn, R. T.; Griswold, M. W.; Golladay, S. W.; Crisman, T. L.

2005-05-01

Macroinvertebrates were sampled in four headwater streams for two years (2001-2003) to establish baseline conditions for a study evaluating forestry best management practices. The Palmer Drought Severity Index indicated that the study site experienced a prolonged moderate to severe drought prior to study initiation, with year one of the study characterized as a moderate drought, while year two encompassed drought and initial rainfall recovery. Benthic macroinvertebrates were collected in streams during year one (December 2001/February 2002) and year two (December 2002/February 2003) using a multi-habitat sampling procedure. Individuals were identified to the lowest practical taxonomic level (mostly genus), and metrics including abundance, total number of taxa, and Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa were calculated. Repeated measures ANOVA identified differences in macroinvertebrate assemblages due to sampling period, with lower values for December 2001 relative to February 2003. Abundance and EPT taxa showed an increasing relationship with average daily flow in successive samples of the study. Initiation of drought conditions prior to the study adversely affected species composition (low numbers of EPT taxa and long lived taxa) and trophic structure (co-dominance of shredders, collectors, and predators).

A Stream Multimetric Macroinvertebrate Index (MMI) for the Sand Hills Ecoregion of the Southeastern Plains, USA

NASA Astrophysics Data System (ADS)

Kosnicki, Ely; Sefick, Stephen A.; Paller, Michael H.; Jerrell, Miller S.; Prusha, Blair A.; Sterrett, Sean C.; Tuberville, Tracey D.; Feminella, Jack W.

2016-10-01

A macroinvertebrate multimetric index is an effective tool for assessing the biological integrity of streams. However, data collected under a single protocol may not be available for an entire region. We sampled macroinvertebrates from the full extent of the Sand Hills ecoregion Level IV of the Southeastern Plains with a standard protocol during the summers of 2010-2012. We evaluated the performance of 94 metrics through a series of screening criteria and built 48 macroinvertebrate multimetric indexs with combinations of the best performing metrics, representing richness, habit, functional feeding guild, sensitivity, and community composition. A series of narrative-response tests for each macroinvertebrate multimetric index was used to find the best performing macroinvertebrate multimetric index which we called the Sand Hills macroinvertebrate multimetric index. The Sand Hills macroinvertebrate multimetric index consisted of the measures Biotic Index, % Shredder taxa, Clinger taxa2/total taxa, Plecoptera and Trichoptera richness, and Tanytarsini taxa2/Chironomidae taxa. Comparison of the Sand Hills macroinvertebrate multimetric index with existing assessment tools calculated with our data indicated that the Sand Hills macroinvertebrate multimetric index performs at a high level with regard to identifying degraded sites and in its response to stress gradients.

Growth and element flux at fine taxonomic resolution in natural microbial communities

NASA Astrophysics Data System (ADS)

Hungate, Bruce; Mau, Rebecca; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa; Marks, Jane C.; Morrissey, Ember; Price, Lance B.

2015-04-01

Microorganisms are the engines of global biogeochemical cycles, driving half of all photosynthesis and nearly all decomposition. Yet, quantifying the rates at which uncultured microbial taxa grow and transform elements in intact and highly diverse natural communities in the environment remains among the most pressing challenges in microbial ecology today. Here, we show how shifts in the density of DNA caused by stable isotope incorporation can be used to estimate the growth rates of individual bacterial taxa in intact soil communities. We found that the distribution of growth rates followed the familiar lognormal distribution observed for the abundances, biomasses, and traits of many organisms. Growth rates of most bacterial taxa increased in response to glucose amendment, though the increase in growth observed for many taxa was larger than could be explained by direct utilization of the added glucose for growth, illustrating that glucose addition indirectly stimulated the utilization of other substrates. Variation in growth rates and phylogenetic distances were quantitatively related, connecting evolutionary history and biogeochemical function in intact soil microbial communities. Our approach has the potential to identify biogeochemically significant taxa in the microbial community and quantify their contributions to element transformations and ecosystem processes.

Response of macroinvertebrate communities to remediation-simulating conditions in Pennsylvania streams influenced by acid mine drainage

USGS Publications Warehouse

Ross, R.M.; Long, E.S.; Dropkin, D.S.

2008-01-01

We compared naturally alkaline streams with limestone lithology to freestone streams with and without acid mine drainage (AMD) to predict benthic macroinvertebrate community recovery from AMD in limestone-treated watersheds. Surrogate-recovered (limestone) and, in many cases, freestone systems had significantly higher macroinvertebrate densities; diversity; taxa richness; Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa; EPT/chironomid ratios; scraper/collector - gatherer ratios; herbivores; collector - filterers; and scrapers. AMD-influenced systems had significantly greater numbers of Diptera and collector - gatherers. An entire trophic level (herbivores) was 'restored' in surrogate-recovered streams, which also showed greater trophic specialization. Indicator analysis identified seven taxa (within Crustacea, Diptera, Nematoda, Trichoptera, and Ephemeroptera) as significant indicators of limestone systems and six taxa (within Ephemeroptera, Plecoptera, Tricoptera, Coleoptera, and Mollusca) as significant freestone indicators, all useful as biological indicators of recovery from AMD. ?? Springer Science+Business Media B.V. 2007.

Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

PubMed Central

Reaz, Rezwana; Bayzid, Md. Shamsuzzoha; Rahman, M. Sohel

2014-01-01

Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A ‘quartet’ is an unrooted tree over taxa, hence the quartet-based supertree methods combine many -taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets. PMID:25117474

FISH-mapping of the 5S rDNA locus in chili peppers (Capsicum-Solanaceae).

PubMed

Aguilera, Patricia M; Debat, Humberto J; Scaldaferro, Marisel A; Martí, Dardo A; Grabiele, Mauro

2016-03-01

We present here the physical mapping of the 5S rDNA locus in six wild and five cultivated taxa of Capsicum by means of a genus-specific FISH probe. In all taxa, a single 5S locus per haploid genome that persistently mapped onto the short arm of a unique metacentric chromosome pair at intercalar position, was found. 5S FISH signals of almost the same size and brightness intensity were observed in all the analyzed taxa. This is the first cytological characterization of the 5S in wild taxa of Capsicum by using a genus-derived probe, and the most exhaustive and comprehensive in the chili peppers up to now. The information provided here will aid the cytomolecular characterization of pepper germplasm to evaluate variability and can be instrumental to integrate physical, genetic and genomic maps already generated in the genus.

Concept relationship editor: a visual interface to support the assertion of synonymy relationships between taxonomic classifications

NASA Astrophysics Data System (ADS)

Craig, Paul; Kennedy, Jessie

2008-01-01

An increasingly common approach being taken by taxonomists to define the relationships between taxa in alternative hierarchical classifications is to use a set-based notation which states relationship between two taxa from alternative classifications. Textual recording of these relationships is cumbersome and difficult for taxonomists to manage. While text based GUI tools are beginning to appear which ease the process, these have several limitations. Interactive visual tools offer greater potential to allow taxonomists to explore the taxa in these hierarchies and specify such relationships. This paper describes the Concept Relationship Editor, an interactive visualisation tool designed to support the assertion of relationships between taxonomic classifications. The tool operates using an interactive space-filling adjacency layout which allows users to expand multiple lists of taxa with common parents so they can explore and assert relationships between two classifications.

STUDIES ON RARE AND POORLY KNOWN LEECHES (ANNELIDA: HIRUDINEA: GLOSSIPHONIIDAE) IN EASTERN NORTH AMERICA

EPA Science Inventory

Three taxa within the leech family Glossiphoniidae, Actinobdella inequiannulata, Placobdella hollensis, and Theromyzon spp., though widespread in eastern North America, remain poorly known with respect to their biology and systematics. All three taxa have been collected in New E...

In memory of I. K. Lopatin

USDA-ARS?s Scientific Manuscript database

Life and works of one of the most prominent leaf beetle systematist, I. K. Lopatin, is described. Complete list of his publications is provided along with list of taxa that he described and taxa that were named after him....

Distributions of Bacterial Generalists among the Guts of Birds, Fish, and Mammals - abstract

EPA Science Inventory

Complex distributions of bacterial taxa within diverse animal microbiomes have inspired ecological and biogeographical approaches to revealing the functions of taxa that may be most important for host health. Of particular interest are bacteria that find many diverse habitats sui...

Algal Assemblages for Large River Monitoring: Comparison Among Biovolume, Absolute and Relative Abundance Metrics

EPA Science Inventory

Periphyton and phytoplankton samples were collected and analyzed from 393 locations in three mid-continent (US) great rivers: the Upper Mississippi, Missouri and Ohio rivers. From the 410 taxa identified, 303 taxa were common enough for multivariate analyses. Algae assemblages we...

Aquatic macroinvertebrates collected at Ravenna Army Ammunition Plant, Portage and Trumbull Counties, Ohio, 1998

USGS Publications Warehouse

Tertuliani, John S.

1999-01-01

The results of a survey of macroinvertebrate communities in the Ravenna Army Ammunition Plant, were used as an indicator of disturbance in streams flowing through or near the training areas at the Plant. The data were interpreted using the Invertebrate Community Index (ICI), a multiple-metric index developed by the Ohio Environmental Protection Agency and based on the structural and functional characteristics of the macroinvertebrate community. Quantitative samples of the macroinvertebrate were collected for ICI determination from three streams South Fork Eagle Creek, Sand Creek, and Hinkley Creek flowing through the study area. These samples were collected using Hester-Dendy type artificial substrate samplers, which were placed in the streams during a 6-week sampling period, June 2 through July 15, 1998. A qualitative- dipnet sample from the natural substrates also was collected at each station on July 15, 1998, the last day of the sampling period. The macroinvertebrate communities at all three stations met the criterion designated for warmwater habitat aquatic life use, and communities at two of the three stations exceeded the criterion. The ICI scores were 42 at South Fork Eagle Creek, 50 at Sand Creek, and 48 at Hinkley Creek. The density of macroinvertebrates at South Fork Eagle Creek was 1,245 per square foot and represented 38 distinct taxa. The density at Sand Creek was 246 per square foot and represented 29 distinct taxa. The density at Hinkley Creek was 864 per square foot and represented 36 distinct taxa. Qualitative samples were also collected at 21 other sites using a D-framed dipnet. The qualitative sites encompassed three main environments: stream, pond, and swamp-wetland. All available habitat types in each environment were sampled until no new taxa were evident during coarse examination. The highest number of taxa were collected from the streams. The total number of taxa collected in streams ranged from 25 to 76; the mean was 60 and median 64. The

Validating DNA barcodes: A non-destructive extraction protocol enables simultaneous vouchering of DNA and morphological vouchers

USDA-ARS?s Scientific Manuscript database

Morphology-based keys support accurate identification of many taxa. However, identification can be difficult for taxa that are not well studied, very small, members of cryptic species complexes, or represented by immature stages. For such cases, DNA barcodes may provide diagnostic characters. Ecolog...