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

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.

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

Rogue taxa phenomenon: a biological companion to simulation analysis.

PubMed

Westover, Kristi M; Rusinko, Joseph P; Hoin, Jon; Neal, Matthew

2013-10-01

To provide a baseline biological comparison to simulation study predictions about the frequency of rogue taxa effects, we evaluated the frequency of a rogue taxa effect using viral data sets which differed in diversity. Using a quartet-tree framework, we measured the frequency of a rogue taxa effect in three data sets of increasing genetic variability (within viral serotype, between viral serotype, and between viral family) to test whether the rogue taxa was correlated with the mean sequence diversity of the respective data sets. We found a slight increase in the percentage of rogues as nucleotide diversity increased. Even though the number of rogues increased with diversity, the distribution of the types of rogues (friendly, crazy, or evil) did not depend on the diversity and in the case of the order-level data set the net rogue effect was slightly positive. This study, assessing frequency of the rogue taxa effect using biological data, indicated that simulation studies may over-predict the prevalence of the rogue taxa effect. Further investigations are necessary to understand which types of data sets are susceptible to a negative rogue effect and thus merit the removal of taxa from large phylogenetic reconstructions. Copyright © 2013 Elsevier Inc. All rights reserved.

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...

Human-associated fungi in deep subseafloor sediment?

NASA Astrophysics Data System (ADS)

Fulfer, V. M.; Kirkpatrick, J. B.; D'Hondt, S.

2015-12-01

Recent studies have reported fungi in marine sediment samples from depths as great as 1740 meters below seafloor (mbsf) (Rédou et al., 2014). Such studies have utilized a variety of techniques to identify fungi, including cultivation of isolates, amplicon sequencing, and metagenomics. Six recent studies of marine sediment collectively identify nearly 100 fungal taxa at the genus and species levels (Damare et al., 2006; Lai et al., 2007; Edgcomb et al., 2010; Singh et al., 2010; Orsi et al., 2013; Rédou et al., 2014). Known marine taxa are rarely identified by these studies. For individual studies with more than two taxa, between 16% and 57% of the fungal taxa are human microflora or associated with human environments (e.g., human skin or indoor air). For example, three of the six studies identified Malassezia species that are common skin inhabitants of humans and dogs. Although human-associated taxa have been identified in both shallow and deep sediment, they pose a particularly acute problem for deep subseafloor samples, where claims of a eukaryotic deep biosphere are most striking; depending on the study, 25% to 38% of species identified in sediment taken at depths greater than 40 meters are human-associated. Only one to three species have been reported from each of the four samples taken at depths greater than one km (eight species total; Rédou et al., 2014). Of these eight species, three are human-associated. This ubiquity of human-associated microflora is very problematic for interpretations of an indigenous deep subseafloor fungal community; either human-associated taxa comprise a large fraction of marine sedimentary fungi, or sample and analytical contamination is so widespread that the extent and ubiquity of a deep subseafloor fungal community remains uncertain. This highlights the need for stringent quality control measures throughout coring, sampling, and recovery of marine sediment, and when cultivating, extracting, and/or sequencing fungi from

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

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?

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

Hot spots, indicator taxa, complementarity and optimal networks of taiga.

PubMed Central

Virolainen, K M; Ahlroth, P; Hyvärinen, E; Korkeamäki, E; Mattila, J; Päiivinen, J; Rintala, T; Suomi, T; Suhonen, J

2000-01-01

If hot spots for different taxa coincide, priority-setting surveys in a region could be carried out more cheaply by focusing on indicator taxa. Several previous studies show that hot spots of different taxa rarely coincide. However, in tropical areas indicator taxa may be used in selecting complementary networks to represent biodiversity as a whole. We studied beetles (Coleoptera), Heteroptera, polypores or bracket fungi (Polyporaceae) and vascular plants of old growth boreal taiga forests. Optimal networks for Heteroptera maximized the high overall species richness of beetles and vascular plants, but these networks were least favourable options for polypores. Polypores are an important group indicating the conservation value of old growth taiga forests. Random selection provided a better option. Thus, certain groups may function as good indicators for maximizing the overall species richness of some taxonomic groups, but all taxa should be examined separately. PMID:10885520

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

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.

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

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.

Symbiont acquisition as neoseme: origin of species and higher taxa

NASA Technical Reports Server (NTRS)

Bermudes, D.; Margulis, L.

1987-01-01

We examine the hypothesis that, in the origin of species and higher taxa of eukaryotes, symbiont acquisition followed by partner integration has been equivalent to neoseme appearance leading to speciation. The formation of stable symbiotic associations involves partner-surface recognition, behavioral and metabolic interaction, and, in some cases, gene product (RNA, protein) and genic (RNA, DNA) integration. This analysis is applied here to examples of neosemes that define specific taxa and to neosemes in plants, fungi, and animals that involve the appearance of new types of tissue. If this hypothesis is correct--if the origin of major genetic variation leading to speciation and even higher taxa may occur through symbiont acquisition and integration--then the analysis of "origins of species and higher taxa" becomes analogous to the study of microbial community ecology.

Synonymy of two recently described taxa of Phaneropterinae (Orthoptera, Tettigoniidae).

PubMed

Massa, Bruno

2018-03-14

Specimens of the two taxa Terpnistriella bredoi Massa, 2017 and Pseudogoetia constanti Massa, 2017 from Democratic Republic of Congo were certainly erroneously labeled, because they resulted synonymous with neotropical taxa Vellea cruenta (Burmeister, 1838) and Philophyllia guttulata Stål, 1873.

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.

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.

Eliciting the Functional Taxonomy from protein annotations and taxa

PubMed Central

Falda, Marco; Lavezzo, Enrico; Fontana, Paolo; Bianco, Luca; Berselli, Michele; Formentin, Elide; Toppo, Stefano

2016-01-01

The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules. PMID:27534507

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

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

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

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.

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

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

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.

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

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

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.

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.

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

"Nothing in biology makes sense except in the light of evolution" The historical legacy and relevance of ethnopharmacology in drug discovery is undisputed. Here we connect the parameters influencing the selection of plant derived medicines by human culture with the concept of evolution. In the present contribution we compare global data with local data and try to answer the questions, to what extent are the taxonomic clades included in indigenous pharmacopoeias associated with certain ailment groups, and to what extent can ecology and phylogeny, which we consider a proxy for chemical relatedness and convergence, account for the observed bias? We use an approximated chi-square test (χ(2)) to check for associations between 12 ethnomedical use-categories and 15 taxonomical clades. With cluster analyses we test for correlations between phylogeny and use-categories. We compare the 67 drug-productive families identified by Zhu et al. with the medicinal flora of the Popoluca and the APG database and compare our results with the phylogenetic target classes evidenced by Zhu et al. Furthermore, we compare the medicinal flora of the Popoluca with the world's weeds (cf. Holm et al.) and discuss our results in relation to anthropological rationales for plant selection. The null-hypothesis "species from the 15 taxonomic clades are selected proportionally to their share in the treatment of the twelve organ- and symptom-defined use-categories" is rejected. The cluster dendrogram for the clades shows that the use patterns are to a certain extent associated with Angiosperm phylogeny. With the occurrence of 53 families the 67 drug-productive families are overrepresented in the regional flora of the Popoluca. The importance of these families in terms of their share is even more pronounced with the medicinal flora holding around 70% of all individual Popoluca informant responses. The overall phylogenetic use pattern is influenced by both the inherent pharmacological properties, which

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.

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.

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...

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.

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

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.

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.

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.

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.

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

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

Humanity's Dual Response to Dogs and Wolves.

PubMed

Treves, Adrian; Bonacic, Cristian

2016-07-01

Dogs were first domesticated 31 000-41 000 years ago. Humanity has experienced ecological costs and benefits from interactions with dogs and wolves. We propose that humans inherited a dual response of attraction or aversion that expresses itself independently to domestic and wild canids. The dual response has had far-reaching consequences for the ecology and evolution of all three taxa, including today's global 'ecological paw print' of 1 billion dogs and recent eradications of wolves. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

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.

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

Biogeography of Human Infectious Diseases: A Global Historical Analysis

PubMed Central

Cashdan, Elizabeth

2014-01-01

Objectives Human pathogen richness and prevalence vary widely across the globe, yet we know little about whether global patterns found in other taxa also predict diversity in this important group of organisms. This study (a) assesses the relative importance of temperature, precipitation, habitat diversity, and population density on the global distributions of human pathogens and (b) evaluates the species-area predictions of island biogeography for human pathogen distributions on oceanic islands. Methods Historical data were used in order to minimize the influence of differential access to modern health care on pathogen prevalence. The database includes coded data (pathogen, environmental and cultural) for a worldwide sample of 186 non-industrial cultures, including 37 on islands. Prevalence levels for 10 pathogens were combined into a pathogen prevalence index, and OLS regression was used to model the environmental determinants of the prevalence index and number of pathogens. Results Pathogens (number and prevalence index) showed the expected latitudinal gradient, but predictors varied by latitude. Pathogens increased with temperature in high-latitude zones, while mean annual precipitation was a more important predictor in low-latitude zones. Other environmental factors associated with more pathogens included seasonal dry extremes, frost-free climates, and human population density outside the tropics. Islands showed the expected species-area relationship for all but the smallest islands, and the relationship was not mediated by habitat diversity. Although geographic distributions of free-living and parasitic taxa typically have different determinants, these data show that variables that influence the distribution of free-living organisms also shape the global distribution of human pathogens. Understanding the cause of these distributions is potentially important, since geographical variation in human pathogens has an important influence on global disparities in

Biogeography of human infectious diseases: a global historical analysis.

PubMed

Cashdan, Elizabeth

2014-01-01

Human pathogen richness and prevalence vary widely across the globe, yet we know little about whether global patterns found in other taxa also predict diversity in this important group of organisms. This study (a) assesses the relative importance of temperature, precipitation, habitat diversity, and population density on the global distributions of human pathogens and (b) evaluates the species-area predictions of island biogeography for human pathogen distributions on oceanic islands. Historical data were used in order to minimize the influence of differential access to modern health care on pathogen prevalence. The database includes coded data (pathogen, environmental and cultural) for a worldwide sample of 186 non-industrial cultures, including 37 on islands. Prevalence levels for 10 pathogens were combined into a pathogen prevalence index, and OLS regression was used to model the environmental determinants of the prevalence index and number of pathogens. Pathogens (number and prevalence index) showed the expected latitudinal gradient, but predictors varied by latitude. Pathogens increased with temperature in high-latitude zones, while mean annual precipitation was a more important predictor in low-latitude zones. Other environmental factors associated with more pathogens included seasonal dry extremes, frost-free climates, and human population density outside the tropics. Islands showed the expected species-area relationship for all but the smallest islands, and the relationship was not mediated by habitat diversity. Although geographic distributions of free-living and parasitic taxa typically have different determinants, these data show that variables that influence the distribution of free-living organisms also shape the global distribution of human pathogens. Understanding the cause of these distributions is potentially important, since geographical variation in human pathogens has an important influence on global disparities in human welfare.

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...

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.

The functionality of the gastrointestinal microbiome in non-human animals.

PubMed

Hanning, Irene; Diaz-Sanchez, Sandra

2015-11-10

Due to the significance of the microbiome on human health, much of the current data available regarding microbiome functionality is centered on human medicine. For agriculturally important taxa, the functionality of gastrointestinal bacteria has been studied with the primary goals of improving animal health and production performance. With respect to cattle, the digestive functions of bacteria in cattle are unarguably critical to digestion and positively impact production performance. Conversely, some research suggests that the gastrointestinal microbiome in chickens competes with the host for nutrients and produces toxins that can harm the host resulting in decreased growth efficiency. Concerning many other species including reptiles and cetaceans, some cataloging of fecal bacteria has been conducted, but the functionality within the host remains ambiguous. These taxa could provide interesting gastrointestinal insight into functionality and symbiosis considering the extreme feeding regimes (snakes), highly specialized diets (vampire bats), and living environments (polar bears), which warrants further exploration.

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.

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.

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

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.

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.

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

Comparative cortical bone thickness between the long bones of humans and five common non-human mammal taxa.

PubMed

Croker, Sarah L; Reed, Warren; Donlon, Denise

2016-03-01

The task of identifying fragments of long bone shafts as human or non-human is difficult but necessary, for both forensic and archaeological cases, and a fast simple method is particularly useful. Previous literature suggests there may be differences in the thickness of the cortical bone between these two groups, but this has not been tested thoroughly. The aim of this study was not only to test this suggestion, but also to provide data that could be of practical assistance for future comparisons. The major limb bones (humerus, radius, femur and tibia) of 50 Caucasoid adult skeletons of known age and sex were radiographed, along with corresponding skeletal elements from sheep, pigs, cattle, large dogs and kangaroos. Measurements were taken from the radiographs at five points along the bone shaft, of shaft diameter, cortical bone thickness, and a cortical thickness index (sum of cortices divided by shaft diameter) in both anteroposterior and mediolateral orientations. Each variable for actual cortical bone thickness as well as cortical thickness indices were compared between the human group (split by sex) and each of the non-human groups in turn, using Student's t-tests. Results showed that while significant differences did exist between the human groups and many of the non-human groups, these were not all in the same direction. That is, some variables in the human groups were significantly greater than, and others were significantly less than, the corresponding variable in the non-human groups, depending on the particular non-human group, sex of the human group, or variable under comparison. This was the case for measurements of both actual cortical bone thickness and cortical thickness index. Therefore, for bone shaft fragments for which the skeletal element is unknown, the overlap in cortical bone thickness between different areas of different bones is too great to allow identification using this method alone. However, by providing extensive cortical bone

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.

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

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

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.

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

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.

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.

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

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

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

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.

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.

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

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

cyanobacterial diversity. Although controlling harmful cyanobacterial blooms should preferably include other measures, such as nutrient reductions, our experimental assessment of taxa-specific cyanobacterial responses to large-bodied Daphnia and long-term monitoring data highlights the potential of such biomanipulations to enhance the ecological and societal value of eutrophic water bodies. PMID:27043823

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.

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...

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

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

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).

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...

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.

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

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.

Interspecies difference in placement of developing teeth and its relationship with cross-sectional geometry of the mandibular symphysis in four primate species including modern humans.

PubMed

Fukase, Hitoshi

2012-02-01

The form of the anthropoid mandibular symphysis has recently been addressed in association with spatial requirements for the forming anterior teeth. To evaluate potential relationships between the symphyseal shape and teeth further, the growth patterns of the symphyseal region and the positioning of the tooth crypts were examined using CT data, comparing four primate species (modern humans, chimpanzees, Japanese monkeys, and hamadryas baboons) with varied symphyseal curvature and tooth size. First, results showed that interspecies differences in overall mandibular shape including symphyseal inclination and bicanine width are consistently expressed throughout postnatal ontogeny, although local symphyseal configurations related to the superior transverse torus (STT) tended to change considerably during growth in chimpanzees. Second, the four species were found to exhibit differentiated formation positions of the incisor and canine crypts. In particular, I2 developed between I1 and C in humans with a broad bicanine space and small teeth, whereas it was positioned posterior to I1 and above C in the cercopithecines with an extremely narrow bicanine space. In chimpanzees, despite the large bicanine width, I1 and I2 grew with a large antero-posterior overlap owing to their large size. These results indicate that the dental positioning is determined in concert with the size balance of the available mandibular space and forming teeth. Finally, the positions/contours of I2 crypt were shown to correspond strongly with the STT across the taxa. This suggests that interspecies differences in symphyseal shape should be interpreted partially by the species-specific positional relationships of the developing anterior teeth. Copyright © 2011 Wiley Periodicals, Inc.

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

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.

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

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.

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

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

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

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.

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

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

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

PubMed Central

Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

2015-01-01

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession

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

Human evolution: taxonomy and paleobiology

PubMed Central

WOOD, BERNARD; RICHMOND, BRIAN G.

2000-01-01

This review begins by setting out the context and the scope of human evolution. Several classes of evidence, morphological, molecular, and genetic, support a particularly close relationship between modern humans and the species within the genus Pan, the chimpanzee. Thus human evolution is the study of the lineage, or clade, comprising species more closely related to modern humans than to chimpanzees. Its stem species is the so-called ‘common hominin ancestor’, and its only extant member is Homo sapiens. This clade contains all the species more closely-related to modern humans than to any other living primate. Until recently, these species were all subsumed into a family, Hominidae, but this group is now more usually recognised as a tribe, the Hominini. The rest of the review sets out the formal nomenclature, history of discovery, and information about the characteristic morphology, and its behavioural implications, of the species presently included in the human clade. The taxa are considered within their assigned genera, beginning with the most primitive and finishing with Homo. Within genera, species are presented in order of geological age. The entries conclude with a list of the more important items of fossil evidence, and a summary of relevant taxonomic issues. PMID:10999270

Human evolution: taxonomy and paleobiology.

PubMed

Wood, B; Richmond, B G

2000-07-01

This review begins by setting out the context and the scope of human evolution. Several classes of evidence, morphological, molecular, and genetic, support a particularly close relationship between modern humans and the species within the genus Pan, the chimpanzee. Thus human evolution is the study of the lineage, or clade, comprising species more closely related to modern humans than to chimpanzees. Its stem species is the so-called 'common hominin ancestor', and its only extant member is Homo sapiens. This clade contains all the species more closely-related to modern humans than to any other living primate. Until recently, these species were all subsumed into a family, Hominidae, but this group is now more usually recognised as a tribe, the Hominini. The rest of the review sets out the formal nomenclature, history of discovery, and information about the characteristic morphology, and its behavioural implications, of the species presently included in the human clade. The taxa are considered within their assigned genera, beginning with the most primitive and finishing with Homo. Within genera, species are presented in order of geological age. The entries conclude with a list of the more important items of fossil evidence, and a summary of relevant taxonomic issues.

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.

From cheetahs to chimpanzees: a comparative review of the drivers of human-carnivore conflict and human-primate conflict.

PubMed

Dickman, Amy J

2012-01-01

Human-wildlife conflict is a growing conservation threat, and is increasingly of importance to primate conservationists. Despite this, relatively little work has been done to date on the drivers of human-primate conflict, especially compared to other conflict-causing taxa such as large carnivores. However, the drivers of conflict are often very similar across species, so conflict researchers can learn important lessons from work conducted on other taxa. This paper discusses 8 key factors which are likely to affect how hostile people are towards wildlife and any damage they cause--6 of these are common to both carnivores and primates, while one is much more applicable to carnivores and the other is specific to primates. These conflict drivers involve numerous social and cultural factors, and highlight the importance of truly understanding the local drivers of conflict in order to develop effective mitigation strategies. Copyright © 2013 S. Karger AG, Basel.

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

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

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.

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.

Humpback Dolphin (Genus Sousa) Behavioural Responses to Human Activities.

PubMed

Piwetz, Sarah; Lundquist, David; Würsig, Bernd

2015-01-01

Humpback dolphins (genus Sousa) use shallow, near-shore waters throughout their range. This coastal distribution makes them vulnerable to recreational and commercial disturbances, especially near heavily populated and industrialized areas. Most research focusing on Sousa and human activities has emphasized direct impacts and threats, involving injury and death, with relatively little focus on indirect effects on dolphins, such as changes in behaviour that may lead to deleterious effects. Understanding behaviour is important in resolving human-wildlife conflict and is an important component of conservation. This chapter gives an overview of animal behavioural responses to human activity with examples from diverse taxa; reviews the scientific literature on behavioural responses of humpback dolphins to human activity throughout their range, including marine vessel traffic, dolphin tourism, cetacean-fishery interactions, noise pollution, and habitat alteration; and highlights information and data gaps for future humpback dolphin research to better inform behaviour-based management decisions that contribute to conservation efforts. © 2015 Elsevier Ltd All rights reserved.

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

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.

Human Presence Increases Parasitic Load in Endangered Lion-Tailed Macaques (Macaca silenus) in Its Fragmented Rainforest Habitats in Southern India

PubMed Central

Hussain, Shaik; Ram, Muthuvarmadam Subramanian; Kumar, Ajith; Shivaji, Sisinthy; Umapathy, Govindhaswamy

2013-01-01

Background Understanding changes in the host-parasite relationship due to habitat fragmentation is necessary for better management and conservation of endangered species in fragmented landscapes. Pathogens and parasites can pose severe threat to species in restricted environments such as forest fragments where there is increased contact of wildlife with human and livestock populations. Environmental stress and reduced nutritional level in forest fragments can influence parasite infection and intensity on the native species. In this study, we examine the impact of habitat fragmentation on the prevalence of gastrointestinal parasites in lion-tailed macaques in a fragmented rainforest in Western Ghats. Methods The prevalence of different gastrointestinal parasites was estimated from 91 fecal samples collected from 9 lion-tailed macaque groups in nine forest fragments. The parasites were identified up to genus level on the basis of the morphology and coloration of the egg, larva and cyst. The covariates included forest fragment area, group size and the presence/absence of human settlements and livestock in proximity. We used a linear regression model to identify the covariates that significantly influenced the prevalence of different parasite taxa. Results Nine gastrointestinal parasite taxa were detected in lion-tailed macaque groups. The groups near human settlements had greater prevalence and number of taxa, and these variables also had significant positive correlations with group size. We found that these parameters were also greater in groups near human settlements after controlling for group size. Livestock were present in all five fragments that had human settlements in proximity. Conclusion The present study suggests that high prevalence and species richness of gastrointestinal parasites in lion-tailed macaque groups are directly related to habitat fragmentation, high anthropogenic activities and high host density. The parasite load partially explains the

Human presence increases parasitic load in endangered lion-tailed macaques (Macaca silenus) in its fragmented rainforest habitats in Southern India.

PubMed

Hussain, Shaik; Ram, Muthuvarmadam Subramanian; Kumar, Ajith; Shivaji, Sisinthy; Umapathy, Govindhaswamy

2013-01-01

Understanding changes in the host-parasite relationship due to habitat fragmentation is necessary for better management and conservation of endangered species in fragmented landscapes. Pathogens and parasites can pose severe threat to species in restricted environments such as forest fragments where there is increased contact of wildlife with human and livestock populations. Environmental stress and reduced nutritional level in forest fragments can influence parasite infection and intensity on the native species. In this study, we examine the impact of habitat fragmentation on the prevalence of gastrointestinal parasites in lion-tailed macaques in a fragmented rainforest in Western Ghats. The prevalence of different gastrointestinal parasites was estimated from 91 fecal samples collected from 9 lion-tailed macaque groups in nine forest fragments. The parasites were identified up to genus level on the basis of the morphology and coloration of the egg, larva and cyst. The covariates included forest fragment area, group size and the presence/absence of human settlements and livestock in proximity. We used a linear regression model to identify the covariates that significantly influenced the prevalence of different parasite taxa. Nine gastrointestinal parasite taxa were detected in lion-tailed macaque groups. The groups near human settlements had greater prevalence and number of taxa, and these variables also had significant positive correlations with group size. We found that these parameters were also greater in groups near human settlements after controlling for group size. Livestock were present in all five fragments that had human settlements in proximity. The present study suggests that high prevalence and species richness of gastrointestinal parasites in lion-tailed macaque groups are directly related to habitat fragmentation, high anthropogenic activities and high host density. The parasite load partially explains the reason for the decline in immature survival

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

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

obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial “hubs” and their importance in phyllosphere microbiome structuring has crucial implications for plant–pathogen and microbe–microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via “hub” microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome “keystone” pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes. PMID:26788878

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.

Reconstructing human evolution: Achievements, challenges, and opportunities

PubMed Central

Wood, Bernard

2010-01-01

This contribution reviews the evidence that has resolved the branching structure of the higher primate part of the tree of life and the substantial body of fossil evidence for human evolution. It considers some of the problems faced by those who try to interpret the taxonomy and systematics of the human fossil record. How do you to tell an early human taxon from one in a closely related clade? How do you determine the number of taxa represented in the human clade? How can homoplasy be recognized and factored into attempts to recover phylogeny? PMID:20445105

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

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

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.

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

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...

Revealing the paradox of drug reward in human evolution

PubMed Central

Sullivan, Roger J; Hagen, Edward H; Hammerstein, Peter

2008-01-01

Neurobiological models of drug abuse propose that drug use is initiated and maintained by rewarding feedback mechanisms. However, the most commonly used drugs are plant neurotoxins that evolved to punish, not reward, consumption by animal herbivores. Reward models therefore implicitly assume an evolutionary mismatch between recent drug-profligate environments and a relatively drug-free past in which a reward centre, incidentally vulnerable to neurotoxins, could evolve. By contrast, emerging insights from plant evolutionary ecology and the genetics of hepatic enzymes, particularly cytochrome P450, indicate that animal and hominid taxa have been exposed to plant toxins throughout their evolution. Specifically, evidence of conserved function, stabilizing selection, and population-specific selection of human cytochrome P450 genes indicate recent evolutionary exposure to plant toxins, including those that affect animal nervous systems. Thus, the human propensity to seek out and consume plant neurotoxins is a paradox with far-reaching implications for current drug-reward theory. We sketch some potential resolutions of the paradox, including the possibility that humans may have evolved to counter-exploit plant neurotoxins. Resolving the paradox of drug reward will require a synthesis of ecological and neurobiological perspectives of drug seeking and use. PMID:18353749

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.

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

Human Hunting and Nascent Animal Management at Middle Pre-Pottery Neolithic Yiftah'el, Israel.

PubMed

Sapir-Hen, Lidar; Dayan, Tamar; Khalaily, Hamoudi; Munro, Natalie D

2016-01-01

The current view for the southern Levant is that wild game hunting was replaced by herd management over the course of the Pre-Pottery Neolithic B period, but there is significant debate over the timing, scale and origin of this transition. To date, most relevant studies focus either on wild game exploitation in the periods prior to domestication or on classic markers of domestication of domestic progenitor species over the course of the PPNB. We studied the faunal remains from the 2007-2008 excavations of the Middle PPNB (MPPNB) site of Yiftah'el, Northern Israel. Our analysis included a close examination of the timing and impact of the trade-off between wild game and domestic progenitor taxa that reflects the very beginning of this critical transition in the Mediterranean zone of the southern Levant. Our results reveal a direct trade-off between the intensive hunting of wild ungulates that had been staples for millennia, and domestic progenitor taxa. We suggest that the changes in wild animal use are linked to a region-wide shift in the relationship between humans and domestic progenitor species including goat, pig and cattle.

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.

Toxic equivalency factors (TEFs) for PCBs, PCDDs, PCDFs for humans and wildlife

USGS Publications Warehouse

Van Den, Berg; Birnbaum, L.; Bosveld, A.T.C.; Brunstrom, B.; Cook, P.; Feeley, M.; Giesy, J.P.; Hanberg, A.; Hasegawa, R.; Kennedy, S.W.; Kubiak, T.; Larsen, J.C.; Van Leeuwen, F. X. R.; Liem, A.K.D.; Nolt, C.; Peterson, R.E.; Poellinger, L.; Safe, S.; Schrenk, D.; Tillitt, D.; Tysklind, M.; Younes, M.; Waern, F.; Zacharewski, T.

1998-01-01

An expert meeting was organized by the World Health Organization (WHO) and held in Stockholm on 15-18 June 1997. The objective of this meeting was to derive consensus toxic equivalency factors (TEFs) for polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) and dioxinlike polychlorinated biphenyls (PCBs) for both human, fish, and wildlife risk assessment. Based on existing literature data, TEFs were (re)evaluated and either revised (mammals) or established (fish and birds). A few mammalian WHO-TEFs were revised, including 1,2,3,7,8-pentachlorinated DD, octachlorinated DD, occachlorinated DF, and PCB 77. These mammalian TEFs are also considered applicable for humans and wild mammalian species. Furthermore, it was concluded that there was insufficient in vivo evidence to continue the use of TEFs for some di-ortho PCBs, as suggested earlier by Ahlborg et al. In addition, TEFs for fish and birds were determined. The WHO working group attempted to harmonize TEFs across different taxa to the extent possible. However, total synchronization of TEFs was not feasible, as there were orders of a magnitude difference in TEFs between taxa for some compounds. In this respect, the absent or very low response of fish to mono-ortho PCBs is most noticeable compared to mammals and birds. Uncertainties that could compromise the TEF concept were also reviewed, including nonadditive interactions, differences in shape of the dose-response curve, and species responsiveness. In spite of these uncertainties, it was concluded that the TEF concept is still the most plausible and feasible approach for risk assessment of halogenated aromatic hydrocarbons with dioxinlike properties.

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.

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.

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.

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.

Characteristics of Rare or Recently Described Corynebacterium Species Recovered from Human Clinical Material in Canada

PubMed Central

Bernard, K. A.; Munro, C.; Wiebe, D.; Ongsansoy, E.

2002-01-01

Nineteen new Corynebacterium species or taxa described since 1995 have been associated with human disease. We report the characteristics of 72 strains identified as or most closely resembling 14 of these newer, medically relevant Corynebacterium species or taxa, as well as describe in brief an isolate of Corynebacterium bovis, a rare pathogen for humans. The bacteria studied in this report were nearly all derived from human clinical specimens and were identified by a polyphasic approach. Most were characterized by nearly full 16S rRNA gene sequence analysis. Some isolates were recovered from previously unreported sources and exhibited unusual phenotypes or represented the first isolates found outside Europe. Products of fermentation, with emphasis on the presence or absence of propionic acid, were also studied in order to provide an additional characteristic with which to differentiate among phenotypically similar species. PMID:12409436

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.

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.

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

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

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.

Human and veterinary pharmaceuticals in the marine environment including fish farms in Korea.

PubMed

Kim, Hee-Young; Lee, In-Seok; Oh, Jeong-Eun

2017-02-01

The occurrence trends and effects of 30 human and veterinary pharmaceuticals, including antibiotics, anthelmintics, anti-inflammatory drugs, and β-blockers, in the marine environment, with a focus on seawater, sediment, cultured fish, and their feed collected from coastal and fish farm areas in the southern sea of Korea, were investigated. The concentrations of total pharmaceuticals in coastal area seawater (mean: 533ng/L) were higher than those in fish farm seawater (mean: 300ng/L), while the opposite trend (coastal area: 136ng/gdrywtincluding cultured fish and feed) and the predominance of pharmaceuticals of terrestrial origin (human and livestock) in coastal areas. Pharmaceuticals used as fish drugs, such as sulfadiazine, erythromycin, and trimethoprim, were commonly detected in fish farm media (seawater, sediment, and cultured fish), which might contaminate fish farm media. Copyright © 2016. Published by Elsevier B.V.

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 ...

Does testosterone affect lateralization of brain and behaviour? A meta-analysis in humans and other animal species.

PubMed

Pfannkuche, Kristina A; Bouma, Anke; Groothuis, Ton G G

2009-04-12

Lateralization of brain and behaviour has been the topic of research for many years in neuropsychology, but the factors guiding its development remain elusive. Based on sex differences in human lateralization, four hypotheses have been postulated that suggest a role for androgens, specifically testosterone. With the discovery that lateralization is a fundamental principle in the organization of brain and behaviour among vertebrates, it has now become possible to experimentally test such hypotheses in animal models. The use of different taxa, humans, other mammalian species and birds (with oestradiol and not testosterone involved in sexual differentiation in birds) facilitates to differentiate between the hypotheses. We used meta-analyses for analysing papers that provided sufficient information, and a semi-quantitative approach based on all relevant studies that we extracted from the literature. We tested the predictions of these hypotheses regarding strength and direction of lateralization for motor output, language and visuospatial cognition in these three taxa. We tested for sex differences and early organizational effects of testosterone (both correlative and experimental studies). We found sex differences in the direction of lateralization for non-human mammals (motor biases similar to humans) and in direction and strength in birds (visual cognitive tasks). However, the prediction that prenatal testosterone exposure affects the direction of lateralization was not supported for humans. In birds and non-human mammals, opposite trends were found, with the effect in non-human mammals being opposite to the expectation based on sex differences. None of the four hypotheses was sufficiently supported and more studies, testing a wider array of functions in different taxa while reporting the data more completely are needed.

From fish to modern humans--comparative anatomy, homologies and evolution of the head and neck musculature.

PubMed

Diogo, R; Abdala, V; Lonergan, N; Wood, B A

2008-10-01

In a recent paper Diogo (2008) reported the results of the first part of an investigation of the comparative anatomy, homologies and evolution of the head and neck muscles of osteichthyans (bony fish + tetrapods). That report mainly focused on actinopterygian fish, but also compared these fish with certain non-mammalian sarcopterygians. The present paper focuses mainly on sarcopterygians, and particularly on how the head and neck muscles have evolved during the transitions from sarcopterygian fish and non-mammalian tetrapods to monotreme and therian mammals, including modern humans. The data obtained from our dissections of the head and neck muscles of representative members of sarcopterygian fish, amphibians, reptiles, monotremes and therian mammals, such as rodents, tree-shrews, colugos and primates, including modern humans, are compared with the information available in the literature. Our observations and comparisons indicate that the number of mandibular and true branchial muscles (sensu this work) present in modern humans is smaller than that found in mammals such as tree-shrews, rats and monotremes, as well as in reptiles such as lizards. Regarding the pharyngeal musculature, there is an increase in the number of muscles at the time of the evolutionary transition leading to therian mammals, but there was no significant increase during the transition leading to the emergence of higher primates and modern humans. The number of hypobranchial muscles is relatively constant within the therian mammals we examined, although in this case modern humans have more muscles than other mammals. The number of laryngeal and facial muscles in modern humans is greater than that found in most other therian taxa. Interestingly, modern humans possess peculiar laryngeal and facial muscles that are not present in the majority of the other mammalian taxa; this seems to corroborate the crucial role played by vocal communication and by facial expressions in primate and especially in

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

Inferences on the phylogeography of the fungal pathogen Heterobasidion annosum, including evidence of interspecific horizontal genetic transfer and of human-mediated, long-range dispersal

Treesearch

R.E. Linzer; W.J. Otrosina; P. Gonthier; J. Bruhn; G. Laflamme; G. Bussieres; M. Garbelotto

2008-01-01

Fungi in the basidiomycete species complex Heterobasidion annosum are significant root-rot pathogens of conifers throughout the northern hemisphere. We utilize a multilocus phylogenetic approach to examine hypotheses regarding the evolution and divergence of two Heterobasidion taxa associated with pines: the Eurasian H. ...

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.

Molecular phylogeny of anoplocephalid tapeworms (Cestoda: Anoplocephalidae) infecting humans and non-human primates.

PubMed

Doležalová, Jana; Vallo, Peter; Petrželková, Klára J; Foitová, Ivona; Nurcahyo, Wisnu; Mudakikwa, Antoine; Hashimoto, Chie; Jirků, Milan; Lukeš, Julius; Scholz, Tomáš; Modrý, David

2015-09-01

Anoplocephalid tapeworms of the genus Bertiella Stiles and Hassall, 1902 and Anoplocephala Blanchard, 1848, found in the Asian, African and American non-human primates are presumed to sporadic ape-to-man transmissions. Variable nuclear (5.8S-ITS2; 28S rRNA) and mitochondrial genes (cox1; nad1) of isolates of anoplocephalids originating from different primates (Callicebus oenanthe, Gorilla beringei, Gorilla gorilla, Pan troglodytes and Pongo abelii) and humans from various regions (South America, Africa, South-East Asia) were sequenced. In most analyses, Bertiella formed a monophyletic group within the subfamily Anoplocephalinae, however, the 28S rRNA sequence-based analysis indicated paraphyletic relationship between Bertiella from primates and Australian marsupials and rodents, which should thus be regarded as different taxa. Moreover, isolate determined as Anoplocephala cf. gorillae from mountain gorilla clustered within the Bertiella clade from primates. This either indicates that A. gorillae deserves to be included into the genus Bertiella, or, that an unknown Bertiella species infects also mountain gorillas. The analyses allowed the genetic differentiation of the isolates, albeit with no obvious geographical or host-related patterns. The unexpected genetic diversity of the isolates studied suggests the existence of several Bertiella species in primates and human and calls for revision of the whole group, based both on molecular and morphological data.

Osteonic organization of limb bones in mammals, including humans, and birds: a preliminary study.

PubMed

Castrogiovanni, Paola; Imbesi, Rosa; Fisichella, Marco; Mazzone, Venera

2011-01-01

As it is well known, bone tissue is characterized by a calcified extracellular matrix which makes this tissue suitable to support the body and protect the inner organs. Lamellar bone tissue is organized in lamellae, 3-7 microm in thickness, and arranged concentrically around vascular channels: the basic structure in this type of organization is called Haversian system or osteon and the diameter of osteons depends on the number of lamellae. Shape and regional density of osteons are related to the bone segment and the specific functional requirements to meet. Aim of this study is to correlate the compact bone tissue microstructure in various classes of mammals, including humans, and birds in order to find an adequate identification key. The results of our study show that in bone tissue samples from various classes of mammals, including humans, and birds the osteonic structure shows peculiar features, often depending on the rate of bone remodelling, different in different animal species. We conclude that a careful microscopic analysis of bone tissue and the characterization of distinctive osteonic features could give a major contribution to forensic medicine to obtain a more reliable recognition of bone findings.

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

The Social Studies Should Include More Discussion of International Human Rights.

ERIC Educational Resources Information Center

Torney, Judith V.

1980-01-01

Students need more exposure to the concept of human rights. They need to know The Universal Declaration of Human Rights and the subsequent covenants. Also, they need to know that substantial agreement exists in the international community about what constitutes human rights. (Author/KC)

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.

New taxa, including three new genera show uniqueness of Neotropical Nepticulidae (Lepidoptera)

PubMed Central

van Nieukerken, Erik J.; Doorenweerd, Camiel; Nishida, Kenji; Snyers, Chris

2016-01-01

Abstract After finding distinct clades in a molecular phylogeny for Nepticulidae that could not be placed in any known genera and discovering clear apomorphic characters that define these clades, as well as a number of Neotropical species that could be placed in known genera but were undescribed, three new genera and nine new species are here described from the Neotropics: Stigmella gallicola van Nieukerken & Nishida, sp. n. reared from galls on Hampea appendiculata (Malvaceae) in Costa Rica, representing the first example of a gall making Stigmella; Stigmella schinivora van Nieukerken, sp. n. reared from leafmines on Schinus terebinthifolia (Anacardiaceae) in Argentina, Misiones; Stigmella costaricensis van Nieukerken & Nishida, sp. n. and Stigmella intronia van Nieukerken & Nishida, sp. n. each from a single specimen collected the same night in Costa Rica, Parque Nacional Chirripó; Stigmella molinensis van Nieukerken & Snyers, sp. n. reared from leafmines on Salix humboldtiana, Peru, Lima, the first Neotropical species of the Stigmella salicis group sensu stricto; Ozadelpha van Nieukerken, gen. n. with type species Ozadelpha conostegiae van Nieukerken & Nishida, sp. n., reared from leafmines on Conostegia oerstediana (Melastomataceae) from Costa Rica; Neotrifurcula van Nieukerken, gen. n. with type species Neotrifurcula gielisorum van Nieukerken, sp. n. from Chile; Hesperolyra van Nieukerken, gen. n.. with type species Fomoria diskusi Puplesis & Robinson, 2000; Hesperolyra saopaulensis van Nieukerken, sp. n., reared from an unidentified Myrtaceae, Sao Paulo, Brasil; and Acalyptris janzeni van Nieukerken & Nishida, sp. n. from Costa Rica, Guanacaste. Five new combinations are made: Ozadelpha ovata (Puplesis & Robinson, 2000), comb. n. and Ozadelpha guajavae (Puplesis & Diškus, 2002), comb. n., Hesperolyra diskusi (Puplesis & Robinson, 2000), comb. n., Hesperolyra molybditis (Zeller, 1877), comb. n. and Hesperolyra repanda (Puplesis & Diškus, 2002), comb. n. Three specimens are briefly described, but left unnamed: Ozadelpha specimen EvN4680, Neotrifurcula specimen EvN4504 and Neotrifurcula specimen RH2. PMID:27917037

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.

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.

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.

Mapping allergenic pollen vegetation in UK to study environmental exposure and human health.

PubMed

McInnes, Rachel N; Hemming, Deborah; Burgess, Peter; Lyndsay, Donna; Osborne, Nicholas J; Skjøth, Carsten Ambelas; Thomas, Sam; Vardoulakis, Sotiris

2017-12-01

Allergenic pollen is produced by the flowers of a number of trees, grasses and weeds found throughout the UK. Exposure to such pollen grains can exacerbate pollen-related asthma and allergenic conditions such as allergic rhinitis (hay fever). Maps showing the location of these allergenic taxa have many applications: they can be used to provide advice on risk assessments; combined with health data to inform research on health impacts such as respiratory hospital admissions; combined with weather data to improve pollen forecasting systems; or as inputs to pollen emission models. In this study we present 1km resolution maps of 12 taxa of trees, grass and weeds found in the UK. We have selected the main species recorded by the UK pollen network. The taxa mapped in this study were: Alnus (alder), Fraxinus (ash), Betula (birch), Corylus (hazel), Quercus (oak), Pinus (pine) and Salix (willow), Poaceae (grass), Artemisia (mugwort), Plantago (plantain), Rumex (dock, sorrels) and Urtica (nettle). We also focus on one high population centre and present maps showing local level detail around the city of London. Our results show the different geographical distributions of the 12 taxa of trees, weeds and grass, which can be used to study plants in the UK associated with allergy and allergic asthma. These maps have been produced in order to study environmental exposure and human health, although there are many possible applications. This novel method not only provides maps of many different plant types, but also at high resolution across regions of the UK, and we uniquely present 12 key plant taxa using a consistent methodology. To consider the impact on human health due to exposure of the pollen grains, it is important to consider the timing of pollen release, and its dispersal, as well as the effect on air quality, which is also discussed here. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

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.

Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications.

PubMed

Omenn, Gilbert S; Lane, Lydie; Lundberg, Emma K; Beavis, Ronald C; Overall, Christopher M; Deutsch, Eric W

2016-11-04

The HUPO Human Proteome Project (HPP) has two overall goals: (1) stepwise completion of the protein parts list-the draft human proteome including confidently identifying and characterizing at least one protein product from each protein-coding gene, with increasing emphasis on sequence variants, post-translational modifications (PTMs), and splice isoforms of those proteins; and (2) making proteomics an integrated counterpart to genomics throughout the biomedical and life sciences community. PeptideAtlas and GPMDB reanalyze all major human mass spectrometry data sets available through ProteomeXchange with standardized protocols and stringent quality filters; neXtProt curates and integrates mass spectrometry and other findings to present the most up to date authorative compendium of the human proteome. The HPP Guidelines for Mass Spectrometry Data Interpretation version 2.1 were applied to manuscripts submitted for this 2016 C-HPP-led special issue [ www.thehpp.org/guidelines ]. The Human Proteome presented as neXtProt version 2016-02 has 16,518 confident protein identifications (Protein Existence [PE] Level 1), up from 13,664 at 2012-12, 15,646 at 2013-09, and 16,491 at 2014-10. There are 485 proteins that would have been PE1 under the Guidelines v1.0 from 2012 but now have insufficient evidence due to the agreed-upon more stringent Guidelines v2.0 to reduce false positives. neXtProt and PeptideAtlas now both require two non-nested, uniquely mapping (proteotypic) peptides of at least 9 aa in length. There are 2,949 missing proteins (PE2+3+4) as the baseline for submissions for this fourth annual C-HPP special issue of Journal of Proteome Research. PeptideAtlas has 14,629 canonical (plus 1187 uncertain and 1755 redundant) entries. GPMDB has 16,190 EC4 entries, and the Human Protein Atlas has 10,475 entries with supportive evidence. neXtProt, PeptideAtlas, and GPMDB are rich resources of information about post-translational modifications (PTMs), single amino acid

A Compositional Look at the Human Gastrointestinal Microbiome and Immune Activation Parameters in HIV Infected Subjects

PubMed Central

Mutlu, Ece A.; Keshavarzian, Ali; Losurdo, John; Swanson, Garth; Siewe, Basile; Forsyth, Christopher; French, Audrey; DeMarais, Patricia; Sun, Yan; Koenig, Lars; Cox, Stephen; Engen, Phillip; Chakradeo, Prachi; Abbasi, Rawan; Gorenz, Annika; Burns, Charles; Landay, Alan

2014-01-01

HIV progression is characterized by immune activation and microbial translocation. One factor that may be contributing to HIV progression could be a dysbiotic microbiome. We therefore hypothesized that the GI mucosal microbiome is altered in HIV patients and this alteration correlates with immune activation in HIV. 121 specimens were collected from 21 HIV positive and 22 control human subjects during colonoscopy. The composition of the lower gastrointestinal tract mucosal and luminal bacterial microbiome was characterized using 16S rDNA pyrosequencing and was correlated to clinical parameters as well as immune activation and circulating bacterial products in HIV patients on ART. The composition of the HIV microbiome was significantly different than that of controls; it was less diverse in the right colon and terminal ileum, and was characterized by loss of bacterial taxa that are typically considered commensals. In HIV samples, there was a gain of some pathogenic bacterial taxa. This is the first report characterizing the terminal ileal and colonic mucosal microbiome in HIV patients with next generation sequencing. Limitations include use of HIV-infected subjects on HAART therapy. PMID:24586144

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

Practical uses for ecdysteroids in mammals including humans: an update

PubMed Central

Lafont, R.; Dinan, L.

2003-01-01

Ecdysteroids are widely used as inducers for gene-switch systems based on insect ecdysteroid receptors and genes of interest placed under the control of ecdysteroid-response elements. We review here these systems, which are currently mainly used in vitro with cultured cells in order to analyse the role of a wide array of genes, but which are expected to represent the basis for future gene therapy strategies. Such developments raise several questions, which are addressed in detail. First, the metabolic fate of ecdysteroids in mammals, including humans, is only poorly known, and the rapid catabolism of ecdysteroids may impede their use as in vivo inducers. A second set of questions arose in fact much earlier with the pioneering “heterophylic” studies of Burdette in the early sixties on the pharmacological effects of ecdysteroids on mammals. These and subsequent studies showed a wide range of effects, most of them being beneficial for the organism (e.g. hypoglycaemic, hypocholesterolaemic, anabolic). These effects are reviewed and critically analysed, and some hypotheses are proposed to explain the putative mechanisms involved. All of these pharmacological effects have led to the development of a wide array of ecdysteroid-containing preparations, which are primarily used for their anabolic and/or “adaptogenic” properties on humans (or horses or dogs). In the same way, increasing numbers of patents have been deposited concerning various beneficial effects of ecdysteroids in many medical or cosmetic domains, which make ecdysteroids very attractive candidates for several practical uses. It may be questioned whether all these pharmacological actions are compatible with the development of ecdysteroid-inducible gene switches for gene therapy, and also if ecdysteroids should be classified among doping substances. Abbreviation: 20E 20-hydroxyecdysone 2d20E 2-deoxy-20-hydroxyecdysone 2dE 2-deoxyecdysone BAH bisacylhydrazine BmEcR Bombyx mori EcR CfEcR Choristoneura

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

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

Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae

PubMed Central

2012-01-01

Background Staphylococcus belongs to the Gram-positive low G + C content group of the Firmicutes division of bacteria. Staphylococcus aureus is an important human and veterinary pathogen that causes a broad spectrum of diseases, and has developed important multidrug resistant forms such as methicillin-resistant S. aureus (MRSA). Staphylococcus simiae was isolated from South American squirrel monkeys in 2000, and is a coagulase-negative bacterium, closely related, and possibly the sister group, to S. aureus. Comparative genomic analyses of closely related bacteria with different phenotypes can provide information relevant to understanding adaptation to host environment and mechanisms of pathogenicity. Results We determined a Roche/454 draft genome sequence for S. simiae and included it in comparative genomic analyses with 11 other Staphylococcus species including S. aureus. A genome based phylogeny of the genus confirms that S. simiae is the sister group to S. aureus and indicates that the most basal Staphylococcus lineage is Staphylococcus pseudintermedius, followed by Staphylococcus carnosus. Given the primary niche of these two latter taxa, compared to the other species in the genus, this phylogeny suggests that human adaptation evolved after the split of S. carnosus. The two coagulase-positive species (S. aureus and S. pseudintermedius) are not phylogenetically closest but share many virulence factors exclusively, suggesting that these genes were acquired by horizontal transfer. Enrichment in genes related to mobile elements such as prophage in S. aureus relative to S. simiae suggests that pathogenesis in the S. aureus group has developed by gene gain through horizontal transfer, after the split of S. aureus and S. simiae from their common ancestor. Conclusions Comparative genomic analyses across 12 Staphylococcus species provide hypotheses about lineages in which human adaptation has taken place and contributions of horizontal transfer in pathogenesis. PMID

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...

A model for Huanglongbing spread between citrus plants including delay times and human intervention

NASA Astrophysics Data System (ADS)

Vilamiu, Raphael G. d'A.; Ternes, Sonia; Braga, Guilherme A.; Laranjeira, Francisco F.

2012-09-01

The objective of this work was to present a compartmental deterministic mathematical model for representing the dynamics of HLB disease in a citrus orchard, including delay in the disease's incubation phase in the plants, and a delay period on the nymphal stage of Diaphorina citri, the most important HLB insect vector in Brazil. Numerical simulations were performed to assess the possible impacts of human detection efficiency of symptomatic plants, as well as the influence of a long incubation period of HLB in the plant.

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.

A review of the use of pteridophytes for treating human ailments*

PubMed Central

Baskaran, Xavier-ravi; Geo Vigila, Antony-varuvel; Zhang, Shou-zhou; Feng, Shi-xiu; Liao, Wen-bo

2018-01-01

The aim of this review was to explore the pharmacological activity of early tracheophytes (pteridophytes) as an alternative medicine for treating human ailments. As the first vascular plants, pteridophytes (aka, ferns and fern allies) are an ancient lineage, and human beings have been exploring and using taxa from this lineage for over 2000 years because of their beneficial properties. We have documented the medicinal uses of pteridophytes belonging to thirty different families. The lycophyte Selaginella sp. was shown in earlier studies to have multiple pharmacological activity, such as antioxidant, anti-inflammatory, anti-cancer, antidiabetic, antiviral, antimicrobial, and anti-Alzheimer properties. Among all the pteridophytes examined, taxa from the Pteridaceae, Polypodiaceae, and Adiantaceae exhibited significant medicinal activity. Based on our review, many pteridophytes have properties that could be used in alternative medicine for treatment of various human illnesses. Biotechnological tools can be used to preserve and even improve their bioactive molecules for the preparation of medicines against illness. Even though several studies have reported medicinal uses of ferns, the possible bioactive compounds of several pteridophytes have not been identified. Furthermore, their optimal dosage level and treatment strategies still need to be determined. Finally, the future direction of pteridophyte research is discussed. PMID:29405039

Tool-assisted rhythmic drumming in palm cockatoos shares key elements of human instrumental music

PubMed Central

Heinsohn, Robert; Zdenek, Christina N.; Cunningham, Ross B.; Endler, John A.; Langmore, Naomi E.

2017-01-01

All human societies have music with a rhythmic “beat,” typically produced with percussive instruments such as drums. The set of capacities that allows humans to produce and perceive music appears to be deeply rooted in human biology, but an understanding of its evolutionary origins requires cross-taxa comparisons. We show that drumming by palm cockatoos (Probosciger aterrimus) shares the key rudiments of human instrumental music, including manufacture of a sound tool, performance in a consistent context, regular beat production, repeated components, and individual styles. Over 131 drumming sequences produced by 18 males, the beats occurred at nonrandom, regular intervals, yet individual males differed significantly in the shape parameters describing the distribution of their beat patterns, indicating individual drumming styles. Autocorrelation analyses of the longest drumming sequences further showed that they were highly regular and predictable like human music. These discoveries provide a rare comparative perspective on the evolution of rhythmicity and instrumental music in our own species, and show that a preference for a regular beat can have other origins before being co-opted into group-based music and dance. PMID:28782005

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.

Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA

PubMed Central

Camunas-Soler, Joan; Kertesz, Michael; De Vlaminck, Iwijn; Koh, Winston; Pan, Wenying; Martin, Lance; Neff, Norma F.; Okamoto, Jennifer; Wong, Ronald J.; Kharbanda, Sandhya; El-Sayed, Yasser; Blumenfeld, Yair; Stevenson, David K.; Shaw, Gary M.; Wolfe, Nathan D.; Quake, Stephen R.

2017-01-01

Blood circulates throughout the human body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analyzing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases. The vast majority of these novel contigs possess coding sequences, and we have validated their existence both by finding their presence in independent experiments and by performing direct PCR amplification. When their nearest neighbors are located in the tree of life, many of the organisms represent entirely novel taxa, showing that microbial diversity within the human body is substantially broader than previously appreciated. PMID:28830999

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.

PubMed

Manor, Ohad; Borenstein, Elhanan

2017-02-08

Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Human-computer interface including haptically controlled interactions

DOEpatents

Anderson, Thomas G.

2005-10-11

The present invention provides a method of human-computer interfacing that provides haptic feedback to control interface interactions such as scrolling or zooming within an application. Haptic feedback in the present method allows the user more intuitive control of the interface interactions, and allows the user's visual focus to remain on the application. The method comprises providing a control domain within which the user can control interactions. For example, a haptic boundary can be provided corresponding to scrollable or scalable portions of the application domain. The user can position a cursor near such a boundary, feeling its presence haptically (reducing the requirement for visual attention for control of scrolling of the display). The user can then apply force relative to the boundary, causing the interface to scroll the domain. The rate of scrolling can be related to the magnitude of applied force, providing the user with additional intuitive, non-visual control of scrolling.

Recent origin of low trabecular bone density in modern humans

PubMed Central

Chirchir, Habiba; Kivell, Tracy L.; Ruff, Christopher B.; Hublin, Jean-Jacques; Carlson, Kristian J.; Zipfel, Bernhard; Richmond, Brian G.

2015-01-01

Humans are unique, compared with our closest living relatives (chimpanzees) and early fossil hominins, in having an enlarged body size and lower limb joint surfaces in combination with a relatively gracile skeleton (i.e., lower bone mass for our body size). Some analyses have observed that in at least a few anatomical regions modern humans today appear to have relatively low trabecular density, but little is known about how that density varies throughout the human skeleton and across species or how and when the present trabecular patterns emerged over the course of human evolution. Here, we test the hypotheses that (i) recent modern humans have low trabecular density throughout the upper and lower limbs compared with other primate taxa and (ii) the reduction in trabecular density first occurred in early Homo erectus, consistent with the shift toward a modern human locomotor anatomy, or more recently in concert with diaphyseal gracilization in Holocene humans. We used peripheral quantitative CT and microtomography to measure trabecular bone of limb epiphyses (long bone articular ends) in modern humans and chimpanzees and in fossil hominins attributed to Australopithecus africanus, Paranthropus robustus/early Homo from Swartkrans, Homo neanderthalensis, and early Homo sapiens. Results show that only recent modern humans have low trabecular density throughout the limb joints. Extinct hominins, including pre-Holocene Homo sapiens, retain the high levels seen in nonhuman primates. Thus, the low trabecular density of the recent modern human skeleton evolved late in our evolutionary history, potentially resulting from increased sedentism and reliance on technological and cultural innovations. PMID:25535354

Recent origin of low trabecular bone density in modern humans.

PubMed

Chirchir, Habiba; Kivell, Tracy L; Ruff, Christopher B; Hublin, Jean-Jacques; Carlson, Kristian J; Zipfel, Bernhard; Richmond, Brian G

2015-01-13

Humans are unique, compared with our closest living relatives (chimpanzees) and early fossil hominins, in having an enlarged body size and lower limb joint surfaces in combination with a relatively gracile skeleton (i.e., lower bone mass for our body size). Some analyses have observed that in at least a few anatomical regions modern humans today appear to have relatively low trabecular density, but little is known about how that density varies throughout the human skeleton and across species or how and when the present trabecular patterns emerged over the course of human evolution. Here, we test the hypotheses that (i) recent modern humans have low trabecular density throughout the upper and lower limbs compared with other primate taxa and (ii) the reduction in trabecular density first occurred in early Homo erectus, consistent with the shift toward a modern human locomotor anatomy, or more recently in concert with diaphyseal gracilization in Holocene humans. We used peripheral quantitative CT and microtomography to measure trabecular bone of limb epiphyses (long bone articular ends) in modern humans and chimpanzees and in fossil hominins attributed to Australopithecus africanus, Paranthropus robustus/early Homo from Swartkrans, Homo neanderthalensis, and early Homo sapiens. Results show that only recent modern humans have low trabecular density throughout the limb joints. Extinct hominins, including pre-Holocene Homo sapiens, retain the high levels seen in nonhuman primates. Thus, the low trabecular density of the recent modern human skeleton evolved late in our evolutionary history, potentially resulting from increased sedentism and reliance on technological and cultural innovations.

[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.

Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women

PubMed Central

Carrothers, Janae M; Lackey, Kimberly A; Beatty, Nicola F; York, Mara A; Brooker, Sarah L; Settles, Matthew L; McGuire, Mark A

2017-01-01

Background: The human milk microbiome has been somewhat characterized, but little is known about changes over time and relations with maternal factors such as nutrient intake. Objective: We sought to characterize the human milk microbiome and described associations with maternal nutrient intake, time postpartum, delivery mode, and body mass index (BMI; in kg/m2). Methods: Milk samples (n = 104) and 24-h diet recalls were collected 9 times from 21 healthy lactating women from day 2 to 6 mo postpartum. Women were classified by BMI as healthy weight (<25) or overweight or obese (≥25). Bacterial taxa were characterized with the use of the high-throughput sequencing of the 16S ribosomal RNA gene. Results: The milk microbiome was relatively constant over time, although there were small changes in some of the lesser-abundant genera. Relative abundances of several taxa were associated with BMI, delivery mode, and infant sex. For instance, overweight and obese mothers produced milk with a higher relative abundance of Granulicatella than did healthy-weight women (1.8% ± 0.6% compared with 0.4% ± 0.2%, respectively; P < 0.05). Relative abundances of several bacterial taxa were also associated with variations in maternal dietary intake. For example, intakes of saturated fatty acids (rs = −0.59; P = 0.005) and monounsaturated fatty acids (rs = −0.46; P = 0.036) were inversely associated with the relative abundance of Corynebacterium; total carbohydrates (rs = −0.54; P = 0.011), disaccharides (rs = −0.47; P = 0.031), and lactose (rs = −0.51; P = 0.018) were negatively associated with Firmicutes; and protein consumption was positively correlated with the relative abundance of Gemella (rs = 0.46; P = 0.037). Conclusions: Factors associated with variations in the human milk microbiome are complex and may include maternal nutrient intake, maternal BMI, delivery mode, and infant sex. Future studies designed to investigate the relation between maternal nutrient intake

Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women.

PubMed

Williams, Janet E; Carrothers, Janae M; Lackey, Kimberly A; Beatty, Nicola F; York, Mara A; Brooker, Sarah L; Shafii, Bahman; Price, William J; Settles, Matthew L; McGuire, Mark A; McGuire, Michelle K

2017-09-01

Background: The human milk microbiome has been somewhat characterized, but little is known about changes over time and relations with maternal factors such as nutrient intake. Objective: We sought to characterize the human milk microbiome and described associations with maternal nutrient intake, time postpartum, delivery mode, and body mass index (BMI; in kg/m 2 ). Methods: Milk samples ( n = 104) and 24-h diet recalls were collected 9 times from 21 healthy lactating women from day 2 to 6 mo postpartum. Women were classified by BMI as healthy weight (<25) or overweight or obese (≥25). Bacterial taxa were characterized with the use of the high-throughput sequencing of the 16S ribosomal RNA gene. Results: The milk microbiome was relatively constant over time, although there were small changes in some of the lesser-abundant genera. Relative abundances of several taxa were associated with BMI, delivery mode, and infant sex. For instance, overweight and obese mothers produced milk with a higher relative abundance of Granulicatella than did healthy-weight women (1.8% ± 0.6% compared with 0.4% ± 0.2%, respectively; P < 0.05). Relative abundances of several bacterial taxa were also associated with variations in maternal dietary intake. For example, intakes of saturated fatty acids ( r s = -0.59; P = 0.005) and monounsaturated fatty acids ( r s = -0.46; P = 0.036) were inversely associated with the relative abundance of Corynebacterium ; total carbohydrates ( r s = -0.54; P = 0.011), disaccharides ( r s = -0.47; P = 0.031), and lactose ( r s = -0.51; P = 0.018) were negatively associated with Firmicutes; and protein consumption was positively correlated with the relative abundance of Gemella ( r s = 0.46; P = 0.037). Conclusions: Factors associated with variations in the human milk microbiome are complex and may include maternal nutrient intake, maternal BMI, delivery mode, and infant sex. Future studies designed to investigate the relation between maternal nutrient

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota.

PubMed

de Muinck, Eric J; Lundin, Knut E A; Trosvik, Pål

2017-01-01

The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial

Oligotyping analysis of the human oral microbiome

PubMed Central

Eren, A. Murat; Borisy, Gary G.; Huse, Susan M.; Mark Welch, Jessica L.

2014-01-01

The Human Microbiome Project provided a census of bacterial populations in healthy individuals, but an understanding of the biomedical significance of this census has been hindered by limited taxonomic resolution. A high-resolution method termed oligotyping overcomes this limitation by evaluating individual nucleotide positions using Shannon entropy to identify the most information-rich nucleotide positions, which then define oligotypes. We have applied this method to comprehensively analyze the oral microbiome. Using Human Microbiome Project 16S rRNA gene sequence data for the nine sites in the oral cavity, we identified 493 oligotypes from the V1-V3 data and 360 oligotypes from the V3-V5 data. We associated these oligotypes with species-level taxon names by comparison with the Human Oral Microbiome Database. We discovered closely related oligotypes, differing sometimes by as little as a single nucleotide, that showed dramatically different distributions among oral sites and among individuals. We also detected potentially pathogenic taxa in high abundance in individual samples. Numerous oligotypes were preferentially located in plaque, others in keratinized gingiva or buccal mucosa, and some oligotypes were characteristic of habitat groupings such as throat, tonsils, tongue dorsum, hard palate, and saliva. The differing habitat distributions of closely related oligotypes suggest a level of ecological and functional biodiversity not previously recognized. We conclude that the Shannon entropy approach of oligotyping has the capacity to analyze entire microbiomes, discriminate between closely related but distinct taxa and, in combination with habitat analysis, provide deep insight into the microbial communities in health and disease. PMID:24965363

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.

Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes

PubMed Central

Adams, Rachel I.; Bhangar, Seema; Pasut, Wilmer; Arens, Edward A.; Taylor, John W.; Lindow, Steven E.; Nazaroff, William W.; Bruns, Thomas D.

2015-01-01

Human occupants are an important source of microbes in indoor environments. In this study, we used DNA sequencing of filter samples to assess the fungal and bacterial composition of air in an environmental chamber under different levels of occupancy, activity, and exposed or covered carpeting. In this office-like, mechanically ventilated environment, results showed a strong influence of outdoor-derived particles, with the indoor microbial composition tracking that of outdoor air for the 2-hour sampling periods. The number of occupants and their activity played a significant but smaller role influencing the composition of indoor bioaerosols. Human-associated taxa were observed but were not particularly abundant, except in the case of one fungus that appeared to be transported into the chamber on the clothing of a study participant. Overall, this study revealed a smaller signature of human body-associated taxa than had been expected based on recent studies of indoor microbiomes, suggesting that occupants may not exert a strong influence on bioaerosol microbial composition in a space that, like many offices, is well ventilated with air that is moderately filtered and moderately occupied. PMID:26024222

Fractal dimension of the middle meningeal vessels: variation and evolution in Homo erectus, Neanderthals, and modern humans.

PubMed

Bruner, Emiliano; Mantini, Simone; Perna, Agostino; Maffei, Carlotta; Manzi, Giorgio

2005-01-01

The middle meningeal vascular network leaves its traces on the endocranial surface because of the tight relationship between neurocranial development and brain growth. Analysing the endocast of fossil specimens, it is therefore possible to describe the morphology of these structures, leading inferences on the cerebral physiology and metabolism in extinct human groups. In this paper, general features of the meningeal vascular traces are described for specimens included in the Homo erectus, Homo neanderthalensis, and Homo sapiens hypodigms. The complexity of the arterial network is quantified by its fractal dimension, calculated through the box-counting method. Modern humans show significant differences from the other two taxa because of the anterior vascular dominance and the larger fractal dimension. Neither the fractal dimension nor the anterior development are merely associated with cranial size increase. Considering the differences between Neanderthals and modern humans, these results may be interpreted in terms of phylogeny, cerebral functions, or cranial structural network.

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.

Grandmothering life histories and human pair bonding.

PubMed

Coxworth, James E; Kim, Peter S; McQueen, John S; Hawkes, Kristen

2015-09-22

The evolution of distinctively human life history and social organization is generally attributed to paternal provisioning based on pair bonds. Here we develop an alternative argument that connects the evolution of human pair bonds to the male-biased mating sex ratios that accompanied the evolution of human life history. We simulate an agent-based model of the grandmother hypothesis, compare simulated sex ratios to data on great apes and human hunter-gatherers, and note associations between a preponderance of males and mate guarding across taxa. Then we explore a recent model that highlights the importance of mating sex ratios for differences between birds and mammals and conclude that lessons for human evolution cannot ignore mammalian reproductive constraints. In contradiction to our claim that male-biased sex ratios are characteristically human, female-biased ratios are reported in some populations. We consider the likelihood that fertile men are undercounted and conclude that the mate-guarding hypothesis for human pair bonds gains strength from explicit links with our grandmothering life history.

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.

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

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.

Genome-Wide Association Studies of the Human Gut Microbiota.

PubMed

Davenport, Emily R; Cusanovich, Darren A; Michelini, Katelyn; Barreiro, Luis B; Ober, Carole; Gilad, Yoav

2015-01-01

The bacterial composition of the human fecal microbiome is influenced by many lifestyle factors, notably diet. It is less clear, however, what role host genetics plays in dictating the composition of bacteria living in the gut. In this study, we examined the association of ~200K host genotypes with the relative abundance of fecal bacterial taxa in a founder population, the Hutterites, during two seasons (n = 91 summer, n = 93 winter, n = 57 individuals collected in both). These individuals live and eat communally, minimizing variation due to environmental exposures, including diet, which could potentially mask small genetic effects. Using a GWAS approach that takes into account the relatedness between subjects, we identified at least 8 bacterial taxa whose abundances were associated with single nucleotide polymorphisms in the host genome in each season (at genome-wide FDR of 20%). For example, we identified an association between a taxon known to affect obesity (genus Akkermansia) and a variant near PLD1, a gene previously associated with body mass index. Moreover, we replicate a previously reported association from a quantitative trait locus (QTL) mapping study of fecal microbiome abundance in mice (genus Lactococcus, rs3747113, P = 3.13 x 10-7). Finally, based on the significance distribution of the associated microbiome QTLs in our study with respect to chromatin accessibility profiles, we identified tissues in which host genetic variation may be acting to influence bacterial abundance in the gut.

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.

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

Broader prevalence of Wolbachia in insects including potential human disease vectors.

PubMed

de Oliveira, C D; Gonçalves, D S; Baton, L A; Shimabukuro, P H F; Carvalho, F D; Moreira, L A

2015-06-01

Wolbachia are intracellular, maternally transmitted bacteria considered the most abundant endosymbionts found in arthropods. They reproductively manipulate their host in order to increase their chances of being transmitted to the offspring, and currently are being used as a tool to control vector-borne diseases. Studies on distribution of Wolbachia among its arthropod hosts are important both for better understanding why this bacterium is so common, as well as for its potential use as a biological control agent. Here, we studied the incidence of Wolbachia in a broad range of insect species, collected from different regions of Brazil, using three genetic markers (16S rRNA, wsp and ftsZ), which varied in terms of their sensitivity to detect this bacterium. The overall incidence of Wolbachia among species belonging to 58 families and 14 orders was 61.9%. The most common positive insect orders were Coleoptera, Diptera, Hemiptera and Hymenoptera, with Diptera and Hemiptera having the highest numbers of Wolbachia-positive families. They included potential human disease vectors whose infection status has never been reported before. Our study further shows the importance of using quantitative polymerase chain reaction for high-throughput and sensitive Wolbachia screening.

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...

The Microbiota, Chemical Symbiosis, and Human Disease

PubMed Central

Redinbo, Matthew R.

2014-01-01

Our understanding of mammalian-microbial mutualism has expanded by combing microbial sequencing with evolving molecular and cellular methods, and unique model systems. Here, the recent literature linking the microbiota to diseases of three of the key mammalian mucosal epithelial compartments – nasal, lung and gastrointestinal (GI) tract – is reviewed with a focus on new knowledge about the taxa, species, proteins and chemistry that promote health and impact progression toward disease. The information presented is further organized by specific diseases now associated with the microbiota:, Staphylococcus aureus infection and rhinosinusitis in the nasal-sinus mucosa; cystic fibrosis (CF), chronic obstructive pulmonary disorder (COPD), and asthma in the pulmonary tissues. For the vast and microbially dynamic GI compartment, several disorders are considered, including obesity, atherosclerosis, Crohn’s disease, ulcerative colitis, drug toxicity, and even autism. Our appreciation of the chemical symbiosis ongoing between human systems and the microbiota continues to grow, and suggest new opportunities for modulating this symbiosis using designed interventions. PMID:25305474

Microbial diversity of extreme habitats in human homes.

PubMed

Savage, Amy M; Hills, Justin; Driscoll, Katherine; Fergus, Daniel J; Grunden, Amy M; Dunn, Robert R

2016-01-01

High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.

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...

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.

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.

Heterospecific SNP diversity in humans and rhesus macaque (Macaca mulatta)

PubMed Central

Ng, Jillian; Trask, Jessica Satkoski; Smith, David Glenn; Kanthaswamy, Sree

2018-01-01

Background Conservation of single nucleotide polymorphisms (SNPs) between human and other primates (i.e., heterospecific SNPs) in candidate genes can be used to assess the utility of those organisms as models for human biomedical research. Methods 59,691 heterospecific SNPs in 22 rhesus macaques and 20 humans were analyzed for human trait associations and 4,207 heterospecific SNPs biallelic in both taxa were compared for genetic variation. Results Variation comparisons at the 4,207 SNPs showed that humans were more genetically diverse than rhesus macaques with observed and expected heterozygosities of 0.337 and 0.323 versus 0.119 and 0.102, and minor allele frequencies of 0.239 and 0.063, respectively. 431 of the 59,691 heterospecific SNPs are reportedly associated with human-specific traits. Conclusion While comparisons between human and rhesus macaque genomes are plausible, functional studies of heterospecific SNPs are necessary to determine whether rhesus macaque alleles are associated with the same phenotypes as their corresponding human alleles. PMID:25963897

A concentrated parameter model for the human cardiovascular system including heart valve dynamics and atrioventricular interaction.

PubMed

Korakianitis, Theodosios; Shi, Yubing

2006-09-01

Numerical modeling of the human cardiovascular system has always been an active research direction since the 19th century. In the past, various simulation models of different complexities were proposed for different research purposes. In this paper, an improved numerical model to study the dynamic function of the human circulation system is proposed. In the development of the mathematical model, the heart chambers are described with a variable elastance model. The systemic and pulmonary loops are described based on the resistance-compliance-inertia concept by considering local effects of flow friction, elasticity of blood vessels and inertia of blood in different segments of the blood vessels. As an advancement from previous models, heart valve dynamics and atrioventricular interaction, including atrial contraction and motion of the annulus fibrosus, are specifically modeled. With these improvements the developed model can predict several important features that were missing in previous numerical models, including regurgitant flow on heart valve closure, the value of E/A velocity ratio in mitral flow, the motion of the annulus fibrosus (called the KG diaphragm pumping action), etc. These features have important clinical meaning and their changes are often related to cardiovascular diseases. Successful simulation of these features enhances the accuracy of simulations of cardiovascular dynamics, and helps in clinical studies of cardiac function.

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.

An approach to including protein quality when assessing the net contribution of livestock to human food supply.

PubMed

Ertl, P; Knaus, W; Zollitsch, W

2016-11-01

The production of protein from animal sources is often criticized because of the low efficiency of converting plant protein from feeds into protein in the animal products. However, this critique does not consider the fact that large portions of the plant-based proteins fed to animals may be human-inedible and that the quality of animal proteins is usually superior as compared with plant proteins. The aim of the present study was therefore to assess changes in protein quality in the course of the transformation of potentially human-edible plant proteins into animal products via livestock production; data from 30 Austrian dairy farms were used as a case study. A second aim was to develop an approach for combining these changes with quantitative aspects (e.g. with the human-edible feed conversion efficiency (heFCE), defined as kilogram protein in the animal product divided by kilogram potentially human-edible protein in the feeds). Protein quality of potentially human-edible inputs and outputs was assessed using the protein digestibility-corrected amino acid score and the digestible indispensable amino acid score, two methods proposed by the Food and Agriculture Organization of the United Nations to describe the nutritional value of proteins for humans. Depending on the method used, protein scores were between 1.40 and 1.87 times higher for the animal products than for the potentially human-edible plant protein input on a barn-gate level (=protein quality ratio (PQR)). Combining the PQR of 1.87 with the heFCE for the same farms resulted in heFCE×PQR of 2.15. Thus, considering both quantity and quality, the value of the proteins in the animal products for human consumption (in this case in milk and beef) is 2.15 times higher than that of proteins in the potentially human-edible plant protein inputs. The results of this study emphasize the necessity of including protein quality changes resulting from the transformation of plant proteins to animal proteins when

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.

Quantifying seasonal and diel variation in Anopheline and Culex human biting rates in Southern Ecuador.

PubMed

Ryan, Sadie J; Lippi, Catherine A; Boersch-Supan, Philipp H; Heydari, Naveed; Silva, Mercy; Adrian, Jefferson; Noblecilla, Leonardo F; Ayala, Efraín B; Encalada, Mayling D; Larsen, David A; Krisher, Jesse T; Krisher, Lyndsay; Fregosi, Lauren; Stewart-Ibarra, Anna M

2017-11-22

Quantifying mosquito biting rates for specific locations enables estimation of mosquito-borne disease risk, and can inform intervention efforts. Measuring biting itself is fraught with ethical concerns, so the landing rate of mosquitoes on humans is often used as a proxy measure. Southern coastal Ecuador was historically endemic for malaria (Plasmodium falciparum and Plasmodium vivax), although successful control efforts in the 2000s eliminated autochthonous transmission (since 2011). This study presents an analysis of data collected during the elimination period. Human landing catch (HLC) data for three mosquito taxa: two malaria vectors, Anopheles albimanus and Anopheles punctimacula, and grouped Culex spp. were examined for this study. These data were collected by the National Vector Control Service of the Ministry of Health over a 5-year time span (2007-2012) in five cities in southern coastal Ecuador, at multiple households, in all months of the year, during dusk-dawn (18:00-6:00) hours, often at both indoor and outdoor locations. Hurdle models were used to determine if biting activity was fundamentally different for the three taxa, and to identify spatial and temporal factors influencing bite rate. Due to the many different approaches to studying and quantifying bite rates in the literature, a glossary of terms was created, to facilitate comparative studies in the future. Biting trends varied significantly with species and time. All taxa exhibited exophagic feeding behavior, and outdoor locations increased both the odds and incidence of bites across taxa. Anopheles albimanus was most frequently observed biting, with an average of 4.7 bites/h. The highest and lowest respective months for significant biting activity were March and July for An. albimanus, July and August for An. punctimacula, and February and July for Culex spp. Fine-scale differences in endophagy and exophagy, and temporal differences among months and hours exist in biting patterns among

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

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.

What Is Humane Education and Why It Should Be Included in Modern Education

ERIC Educational Resources Information Center

Jacobs, G. M.

2016-01-01

Humane education has existed since at least the 18th century (Unti & DeRosa, 2003). This brief chapter begins with a brief definition of humane education and examples of how it can be incorporated in linguistics, cross cultural studies and foreign language education. Next, the chapter discusses why humane education constitutes an important…

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.

Human-caused environmental change: Impacts on plant diversity and evolution

PubMed Central

Tilman, David; Lehman, Clarence

2001-01-01

Human-caused environmental changes are creating regional combinations of environmental conditions that, within the next 50 to 100 years, may fall outside the envelope within which many of the terrestrial plants of a region evolved. These environmental modifications might become a greater cause of global species extinction than direct habitat destruction. The environmental constraints undergoing human modification include levels of soil nitrogen, phosphorus, calcium and pH, atmospheric CO2, herbivore, pathogen, and predator densities, disturbance regimes, and climate. Extinction would occur because the physiologies, morphologies, and life histories of plants limit each species to being a superior competitor for a particular combination of environmental constraints. Changes in these constraints would favor a few species that would competitively displace many other species from a region. In the long-term, the “weedy” taxa that became the dominants of the novel conditions imposed by global change should become the progenitors of a series of new species that are progressively less weedy and better adapted to the new conditions. The relative importance of evolutionary versus community ecology responses to global environmental change would depend on the extent of regional and local recruitment limitation, and on whether the suite of human-imposed constraints were novel just regionally or on continental or global scales. PMID:11344290

Influence of the chopped frequency of light on optical transport characteristics of human skin including at acupuncture points

NASA Astrophysics Data System (ADS)

Yang, Hong-qin; Xie, Shu-sen; Liu, Song-hao; Li, Hui; Wang, Yu-hua; Guo, Zhou-yi

2007-11-01

An experimental protocol was established for noninvasively measuring the optical transport characteristics of skin tissue along human meridian direction over body surface including at acupuncture points. The diffuse remittance for 658 nm light radiation along the pericardium meridian and non-meridian directions were measured respectively. The influence of the chopped frequency of light on the detected light signal was investigated. It is shown that the optical transport characteristics of skin tissue accords with the Beer's exponential attenuation law along the meridian including at acupuncture points and non-median directions. However there is an obvious difference between the propagations along the meridian direction and non-meridian direction (P<0.05). Furthermore, the chopped frequency can affect the detected signal. The diffuse remittance signal decreased with the chopped frequency's increase and it was different between the meridian and non-meridian directions. These findings are important and meaningful for interpreting the human meridian phenomena by biomedical optics.

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

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.

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

Novel correlations between microbial taxa and amino acid metabolites in mouse cecal contents

USDA-ARS?s Scientific Manuscript database

Gut microbes share a bi-directional relationship with thousands of metabolites in their environment. Many of these microbes and metabolites are associated with human diseases including obesity, cancer, and inflammatory diseases. Further understanding of how microbes affect metabolite concentration i...

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.

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. 

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.

How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota.

PubMed

Grégory, Dubourg; Chaudet, Hervé; Lagier, Jean-Christophe; Raoult, Didier

2018-03-01

Describing the human hut gut microbiota is one the most exciting challenges of the 21 st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.

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.

Microbiota of human breast tissue.

PubMed

Urbaniak, Camilla; Cummins, Joanne; Brackstone, Muriel; Macklaim, Jean M; Gloor, Gregory B; Baban, Chwanrow K; Scott, Leslie; O'Hanlon, Deidre M; Burton, Jeremy P; Francis, Kevin P; Tangney, Mark; Reid, Gregor

2014-05-01

In recent years, a greater appreciation for the microbes inhabiting human body sites has emerged. In the female mammary gland, milk has been shown to contain bacterial species, ostensibly reaching the ducts from the skin. We decided to investigate whether there is a microbiome within the mammary tissue. Using 16S rRNA sequencing and culture, we analyzed breast tissue from 81 women with and without cancer in Canada and Ireland. A diverse population of bacteria was detected within tissue collected from sites all around the breast in women aged 18 to 90, not all of whom had a history of lactation. The principal phylum was Proteobacteria. The most abundant taxa in the Canadian samples were Bacillus (11.4%), Acinetobacter (10.0%), Enterobacteriaceae (8.3%), Pseudomonas (6.5%), Staphylococcus (6.5%), Propionibacterium (5.8%), Comamonadaceae (5.7%), Gammaproteobacteria (5.0%), and Prevotella (5.0%). In the Irish samples the most abundant taxa were Enterobacteriaceae (30.8%), Staphylococcus (12.7%), Listeria welshimeri (12.1%), Propionibacterium (10.1%), and Pseudomonas (5.3%). None of the subjects had signs or symptoms of infection, but the presence of viable bacteria was confirmed in some samples by culture. The extent to which these organisms play a role in health or disease remains to be determined.

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

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.

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

Inhibition by fenoterol of human eosinophil functions including beta2-adrenoceptor-independent actions.

PubMed

Tachibana, A; Kato, M; Kimura, H; Fujiu, T; Suzuki, M; Morikawa, A

2002-12-01

Agonists at beta2 adrenoceptors are used widely as bronchodilators in treating bronchial asthma. These agents also may have important anti-inflammatory effects on eosinophils in asthma. We examined whether widely prescribed beta2-adrenoceptor agonists differ in ability to suppress stimulus-induced eosinophil effector functions such as superoxide anion (O2-) generation and degranulation. To examine involvement of cellular adhesion in such responses, we also investigated effects of beta2 agonists on cellular adhesion and on CD11b expression by human eosinophils. O2- was measured using chemiluminescence. Eosinophil degranulation and adhesion were assessed by a radioimmunoassay for eosinophil protein X (EPX). CD11b expression was measured by flow cytometry. Fenoterol inhibited platelet-activating factor (PAF)-induced O2- generation by eosinophils significantly more than salbutamol or procaterol. Fenoterol partially inhibited PAF-induced degranulation by eosinophils similarly to salbutamol or procaterol. Fenoterol inhibited phorbol myristate acetate (PMA)-induced O2- generation and degranulation by eosinophils, while salbutamol or procaterol did not. Fenoterol inhibition of PMA-induced O2- generation was not reversed by ICI-118551, a selective beta2-adrenoceptor antagonist. Fenoterol, but not salbutamol or procaterol, significantly inhibited PAF-induced eosinophil adhesion. Fenoterol inhibited O2- generation and degranulation more effectively than salbutamol or procaterol; these effects may include a component involving cellular adhesion. Inhibition also might include a component not mediated via beta2 adrenoceptors.

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

Evolution of the auditory ossicles in extant hominids: metric variation in African apes and humans.

PubMed

Quam, Rolf M; Coleman, Mark N; Martínez, Ignacio

2014-08-01

The auditory ossicles in primates have proven to be a reliable source of phylogenetic information. Nevertheless, to date, very little data have been published on the metric dimensions of the ear ossicles in African apes and humans. The present study relies on the largest samples of African ape ear ossicles studied to date to address questions of taxonomic differences and the evolutionary transformation of the ossicles in gorillas, chimpanzees and humans. Both African ape taxa show a malleus that is characterized by a long and slender manubrium and relatively short corpus, whereas humans show the opposite constellation of a short and thick manubrium and relatively long corpus. These changes in the manubrium are plausibly linked with changes in the size of the tympanic membrane. The main difference between the incus in African apes and humans seems to be related to changes in the functional length. Compared with chimpanzees, human incudes are larger in nearly all dimensions, except articular facet height, and show a more open angle between the axes. The gorilla incus resembles humans more closely in its metric dimensions, including functional length, perhaps as a result of the dramatically larger body size compared with chimpanzees. The differences between the stapedes of humans and African apes are primarily size-related, with humans being larger in nearly all dimensions. Nevertheless, some distinctions between the African apes were found in the obturator foramen and head height. Although correlations between metric variables in different ossicles were generally lower than those between variables in the same bone, variables of the malleus/incus complex appear to be more strongly correlated than those of the incus/stapes complex, perhaps reflecting the different embryological and evolutionary origins of the ossicles. The middle ear lever ratio for the African apes is similar to other haplorhines, but humans show the lowest lever ratio within primates. Very low levels

Evolution of the auditory ossicles in extant hominids: metric variation in African apes and humans

PubMed Central

Quam, Rolf M; Coleman, Mark N; Martínez, Ignacio

2014-01-01

The auditory ossicles in primates have proven to be a reliable source of phylogenetic information. Nevertheless, to date, very little data have been published on the metric dimensions of the ear ossicles in African apes and humans. The present study relies on the largest samples of African ape ear ossicles studied to date to address questions of taxonomic differences and the evolutionary transformation of the ossicles in gorillas, chimpanzees and humans. Both African ape taxa show a malleus that is characterized by a long and slender manubrium and relatively short corpus, whereas humans show the opposite constellation of a short and thick manubrium and relatively long corpus. These changes in the manubrium are plausibly linked with changes in the size of the tympanic membrane. The main difference between the incus in African apes and humans seems to be related to changes in the functional length. Compared with chimpanzees, human incudes are larger in nearly all dimensions, except articular facet height, and show a more open angle between the axes. The gorilla incus resembles humans more closely in its metric dimensions, including functional length, perhaps as a result of the dramatically larger body size compared with chimpanzees. The differences between the stapedes of humans and African apes are primarily size-related, with humans being larger in nearly all dimensions. Nevertheless, some distinctions between the African apes were found in the obturator foramen and head height. Although correlations between metric variables in different ossicles were generally lower than those between variables in the same bone, variables of the malleus/incus complex appear to be more strongly correlated than those of the incus/stapes complex, perhaps reflecting the different embryological and evolutionary origins of the ossicles. The middle ear lever ratio for the African apes is similar to other haplorhines, but humans show the lowest lever ratio within primates. Very low levels

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...

Biodiversity of Total Phenolics, Antioxidant Capacity, and Juice Quality in Apple Cider Taxa

USDA-ARS?s Scientific Manuscript database

Apples are known to contain antioxidants that may play an important role in human health by providing protection against reactive free radicals affecting a wide range of biological molecules including nucleic acids, lipids, and proteins. While fresh apple juice is a main product of processed apples,...

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

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

Chironomids as indicators of natural and human impacts in a 700-yr record from the northern Patagonian Andes

NASA Astrophysics Data System (ADS)

Williams, Natalia; Rieradevall, Maria; Añón Suárez, Diego; Rizzo, Andrea; Daga, Romina; Ribeiro Guevara, Sergio; Arribére, María Angélica

2016-09-01

Chironomid communities were studied in a sediment core collected from Lake Moreno Oeste, located in Nahuel Huapi National Park. A major change in midge assemblages occurred at ∼AD 1760, which was characterized by a decrease of "cold taxa" including Polypedilum sp.2 and Dicrotendipes, and an increase of "warm taxa" including Apsectrotanypus and Polypedilum sp.1. These taxa are likely related to climatic conditions concurrent with the end of a cold period at ∼AD 1500-1700 and the beginning of a drying climate at ∼AD 1740-1900 in northern Patagonia. Coarse tephra layers had low midge diversity; however they did not disrupt the climatic trend as the community recovered rapidly after the event. Since AD 1910, after the increase in suburban housing, fish introduction, and the construction of a road, there was an increase in the relative abundances of taxa typically associated with the littoral zone, such as Parapsectrocladius, Riethia, Apsectrotanypus, and some Tanytarsini morphotypes. The main change in the chironomid community appears to be associated with long-term climate change. At the beginning of the 20th century, other site-specific environmental factors (catchment change and fish introduction) altered the chironomid assemblages, making it more difficult to understand the relative importance of each driver of assemblage change.

[Production of antibacterial substances by resident corynebacteria isolated from human skin].

PubMed

Kwaszewska, Anna; Szewczyk, Eligia M

2007-01-01

Coryneform bacteria, especially lipophilic species, form stable but not dominant population on a human skin. This position is probably controlled by secretion of bacteriocin-like substances, which act directly on coexisting bacteria. Among 118 investigated corynebacteria belonging to seven species/taxa and isolated from human skin, 90% possessed an ability to produce such substances. The spectrum of their activity was restricted to killing gram-positive bacteria, but along with corynebacteria it also covered cocci, with Staphylococcus aureus in this group. This feature was revealed better on low pH media (pH 5.6) and media with 1.5% NaCl for cocci, but on pH 7,4 for corynebacteria.

Prehistoric Human-environment Interactions and Their Impact on Aquatic Ecosystems

NASA Astrophysics Data System (ADS)

Mackay, H.; Henderson, A. C. G.; van Hardenbroek, M.; Cavers, G.; Crone, A.; Davies, K. L.; Fonville, T. R.; Head, K.; Langdon, P. G.; Matton, R.; McCormick, F.; Murray, E.; Whitehouse, N. J.; Brown, A. G.

2017-12-01

One of the first widespread human-environment interactions in Scotland and Ireland occurred 3000 years ago when communities first inhabited wetlands, building artificial islands in lakes called crannogs. The reason behind the development and intermittent occupation of crannogs is unclear. We don't know if they were a response to changes in environment or if they were driven by societal influences. Furthermore, the impact of the construction, settlement and human activities on lake ecosystems is unknown, but is a key example of early anthropogenic signatures on the environment. Our research characterises the prehistoric human-environment interactions associated with crannogs by analysing geochemical and biological signals preserved within the crannog and wetland sediments. Records of anthropogenic activities and environmental change have been produced using lipid biomarkers of faecal matter, sedimentary DNA, and the remains of beetles, aquatic invertebrates (chironomids), siliceous algae (diatoms) and pollen. Results of these analyses reveal settlement occupations occurred in phases from the Iron Age to the Medieval Period. The main effects of occupation on the wetland ecosystems are nutrient-driven increases in productivity and shifts in aquatic species from clear water taxa to those associated with more eutrophic conditions. Crannog abandonment reduces nutrient inputs and therefore levels of aquatic productivity, as evidenced by decreases in the abundance of siliceous algae. Despite returns to pre-settlement nutrient and productivity levels, the lake ecosystems do not recover to their previous ecological state: dominant aquatic invertebrate and siliceous algae taxa shift in response to elevated levels of macrophytes within the lakes. Whilst these phase changes in lake ecosystems highlight their adaptive capacity to environmental change, the temporary human interactions associated with crannogs had persisting environmental impacts that shaped the long

Unraveling the evolution of uniquely human cognition.

PubMed

MacLean, Evan L

2016-06-07

A satisfactory account of human cognitive evolution will explain not only the psychological mechanisms that make our species unique, but also how, when, and why these traits evolved. To date, researchers have made substantial progress toward defining uniquely human aspects of cognition, but considerably less effort has been devoted to questions about the evolutionary processes through which these traits have arisen. In this article, I aim to link these complementary aims by synthesizing recent advances in our understanding of what makes human cognition unique, with theory and data regarding the processes of cognitive evolution. I review evidence that uniquely human cognition depends on synergism between both representational and motivational factors and is unlikely to be accounted for by changes to any singular cognitive system. I argue that, whereas no nonhuman animal possesses the full constellation of traits that define the human mind, homologies and analogies of critical aspects of human psychology can be found in diverse nonhuman taxa. I suggest that phylogenetic approaches to the study of animal cognition-which can address questions about the selective pressures and proximate mechanisms driving cognitive change-have the potential to yield important insights regarding the processes through which the human cognitive phenotype evolved.

Tardigrada of Ireland: a review of records and an updated checklist of species including a new addition to the Irish fauna.

PubMed

DeMilio, Erica; Lawton, Colin; Marley, Nigel J

2016-01-01

The phylum Tardigrada was not recorded in Ireland until the Clare Island Survey of 1909-1911, with only rare subsequent reports on Irish tardigrade species. In recent decades, significant taxonomic revision has occurred within Tardigrada. This has resulted in the need for a review of all known historical records from Ireland and Northern Ireland in order to produce an updated checklist of valid taxa. The new checklist includes fifty-one tardigrade species and subspecies including a new addition to the Irish fauna reported herein, Echiniscus quadrispinosus quadrispinosus Richters, 1902 from Newtown, Ballyvaughan, Co. Clare.

Inhibition by fenoterol of human eosinophil functions including β2-adrenoceptor-independent actions

PubMed Central

TACHIBANA, A; KATO, M; KIMURA, H; FUJIU, T; SUZUKI, M; MORIKAWA, A

2002-01-01

Agonists at β2 adrenoceptors are used widely as bronchodilators in treating bronchial asthma. These agents also may have important anti-inflammatory effects on eosinophils in asthma. We examined whether widely prescribed β2-adrenoceptor agonists differ in ability to suppress stimulus-induced eosinophil effector functions such as superoxide anion (O2−) generation and degranulation. To examine involvement of cellular adhesion in such responses, we also investigated effects of β2 agonists on cellular adhesion and on CD11b expression by human eosinophils. O2− was measured using chemiluminescence. Eosinophil degranulation and adhesion were assessed by a radioimmunoassay for eosinophil protein X (EPX). CD11b expression was measured by flow cytometry. Fenoterol inhibited platelet-activating factor (PAF)-induced O2− generation by eosinophils significantly more than salbutamol or procaterol. Fenoterol partially inhibited PAF-induced degranulation by eosinophils similarly to salbutamol or procaterol. Fenoterol inhibited phorbol myristate acetate (PMA)-induced O2− generation and degranulation by eosinophils, while salbutamol or procaterol did not. Fenoterol inhibition of PMA-induced O2− generation was not reversed by ICI-118551, a selective β2-adrenoceptor antagonist. Fenoterol, but not salbutamol or procaterol, significantly inhibited PAF-induced eosinophil adhesion. Fenoterol inhibited O2− generation and degranulation more effectively than salbutamol or procaterol; these effects may include a component involving cellular adhesion. Inhibition also might include a component not mediated via β2 adrenoceptors. PMID:12452831

Species within the genus Encyonema Ktzing, including two new species Encyonema reimeri sp. nov. and E. nicafei sp. nov. and E. stoermeri nom. nov., stat. nov.

USGS Publications Warehouse

Spaulding, S.A.; Pool, J.R.; Castro, S.I.; Hinz, F.

2010-01-01

We observed six diatom taxa from North American samples and one taxon from China that are considered within the genus Encyonema Ktzing. Two of the taxa are described as new, Encyonema reimeri Spaulding, Pool et Castro sp. nov. and Encyonema nicafei Spaulding sp. nov. A third taxon, Encyonema stoermeri Spaulding, Pool et Castro nom. nov., shat. nov. is assigned a new name and rank. In the past, these taxa have been ascribed to several names, but primarily the names Cymbella muelleri Hustedt and C. muelleri f. ventricosa (Tempre et Peragallo) Reimer have been used, based on their inclusion in the two volumes of "The Diatoms of the United States". We compare the new species with other members of this group of taxa, including Encyonema latum Krammer, E. sinicum Krammer and E. yellowstonianum Krammer. This group of species shares the features of 1) a broad axial area, 2) raphe branches curved with the convex side toward the dorsal valve margin, 3) slightly expanded and dorsally deflected proximal raphe ends, and 4) oval areolae near the axial area, becoming lineolate, or transapically elongate, towards the dorsal margin. We expect that many of the species reported in the U.S. have been identified using names of species from other continents. We also expect that critical microscopy and use of original literature is likely to clarify the geographic distribution of species within Encyonema. This work is important in order to understand, document and protect the species diversity of diatoms and their aquatic habitats.

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.

Effects of Cannabis Use on Human Behavior, Including Cognition, Motivation, and Psychosis: A Review.

PubMed

Volkow, Nora D; Swanson, James M; Evins, A Eden; DeLisi, Lynn E; Meier, Madeline H; Gonzalez, Raul; Bloomfield, Michael A P; Curran, H Valerie; Baler, Ruben

2016-03-01

With a political debate about the potential risks and benefits of cannabis use as a backdrop, the wave of legalization and liberalization initiatives continues to spread. Four states (Colorado, Washington, Oregon, and Alaska) and the District of Columbia have passed laws that legalized cannabis for recreational use by adults, and 23 others plus the District of Columbia now regulate cannabis use for medical purposes. These policy changes could trigger a broad range of unintended consequences, with profound and lasting implications for the health and social systems in our country. Cannabis use is emerging as one among many interacting factors that can affect brain development and mental function. To inform the political discourse with scientific evidence, the literature was reviewed to identify what is known and not known about the effects of cannabis use on human behavior, including cognition, motivation, and psychosis.

Microbial Co-occurrence Relationships in the Human Microbiome

PubMed Central

Izard, Jacques; Segata, Nicola; Gevers, Dirk

2012-01-01

The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

PubMed Central

Chen, Tsute; Yu, Wen-Han; Izard, Jacques; Baranova, Oxana V.; Lakshmanan, Abirami; Dewhirst, Floyd E.

2010-01-01

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD—taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org PMID:20624719

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.

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

PubMed Central

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

2009-01-01

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

Form and Function in Human Song.

PubMed

Mehr, Samuel A; Singh, Manvir; York, Hunter; Glowacki, Luke; Krasnow, Max M

2018-02-05

Humans use music for a variety of social functions: we sing to accompany dance, to soothe babies, to heal illness, to communicate love, and so on. Across animal taxa, vocalization forms are shaped by their functions, including in humans. Here, we show that vocal music exhibits recurrent, distinct, and cross-culturally robust form-function relations that are detectable by listeners across the globe. In Experiment 1, internet users (n = 750) in 60 countries listened to brief excerpts of songs, rating each song's function on six dimensions (e.g., "used to soothe a baby"). Excerpts were drawn from a geographically stratified pseudorandom sample of dance songs, lullabies, healing songs, and love songs recorded in 86 mostly small-scale societies, including hunter-gatherers, pastoralists, and subsistence farmers. Experiment 1 and its analysis plan were pre-registered. Despite participants' unfamiliarity with the societies represented, the random sampling of each excerpt, their very short duration (14 s), and the enormous diversity of this music, the ratings demonstrated accurate and cross-culturally reliable inferences about song functions on the basis of song forms alone. In Experiment 2, internet users (n = 1,000) in the United States and India rated three contextual features (e.g., gender of singer) and seven musical features (e.g., melodic complexity) of each excerpt. The songs' contextual features were predictive of Experiment 1 function ratings, but musical features and the songs' actual functions explained unique variance in function ratings. These findings are consistent with the existence of universal links between form and function in vocal music. Copyright © 2017 Elsevier Ltd. All rights reserved.

Other-regarding preferences in a non-human primate: Common marmosets provision food altruistically

PubMed Central

Burkart, Judith M.; Fehr, Ernst; Efferson, Charles; van Schaik, Carel P.

2007-01-01

Human cooperation is unparalleled in the animal world and rests on an altruistic concern for the welfare of genetically unrelated strangers. The evolutionary roots of human altruism, however, remain poorly understood. Recent evidence suggests a discontinuity between humans and other primates because individual chimpanzees do not spontaneously provide food to other group members, indicating a lack of concern for their welfare. Here, we demonstrate that common marmoset monkeys (Callithrix jacchus) do spontaneously provide food to nonreciprocating and genetically unrelated individuals, indicating that other-regarding preferences are not unique to humans and that their evolution did not require advanced cognitive abilities such as theory of mind. Because humans and marmosets are cooperative breeders and the only two primate taxa in which such unsolicited prosociality has been found, we conclude that these prosocial predispositions may emanate from cooperative breeding. PMID:18077409

Human impacts on the rates of recent, present, and future bird extinctions.

PubMed

Pimm, Stuart; Raven, Peter; Peterson, Alan; Sekercioglu, Cagan H; Ehrlich, Paul R

2006-07-18

Unqualified, the statement that approximately 1.3% of the approximately 10,000 presently known bird species have become extinct since A.D. 1500 yields an estimate of approximately 26 extinctions per million species per year (or 26 E/MSY). This is higher than the benchmark rate of approximately 1 E/MSY before human impacts, but is a serious underestimate. First, Polynesian expansion across the Pacific also exterminated many species well before European explorations. Second, three factors increase the rate: (i) The number of known extinctions before 1800 is increasing as taxonomists describe new species from skeletal remains. (ii) One should calculate extinction rates over the years since taxonomists described the species. Most bird species were described only after 1850. (iii) Some species are probably extinct; there is reluctance to declare them so prematurely. Thus corrected, recent extinction rates are approximately 100 E/MSY. In the last decades, the rate is <50 E/MSY, but would be 150 E/MSY were it not for conservation efforts. Increasing numbers of extinctions are on continents, whereas previously most were on islands. We predict a 21st century rate of approximately 1,000 E/MSY. Extinction threatens 12% of bird species; another 12% have small geographical ranges and live where human actions rapidly destroy their habitats. If present forest losses continue, extinction rates will reach 1,500 E/MSY by the century's end. Invasive species, expanding human technologies, and global change will harm additional species. Birds are poor models for predicting extinction rates for other taxa. Human actions threaten higher fractions of other well known taxa than they do birds. Moreover, people take special efforts to protect birds.

Human impacts on the rates of recent, present, and future bird extinctions

PubMed Central

Pimm, Stuart; Raven, Peter; Peterson, Alan; Şekercioğlu, Çağan H.; Ehrlich, Paul R.

2006-01-01

Unqualified, the statement that ≈1.3% of the ≈10,000 presently known bird species have become extinct since A.D. 1500 yields an estimate of ≈26 extinctions per million species per year (or 26 E/MSY). This is higher than the benchmark rate of ≈1 E/MSY before human impacts, but is a serious underestimate. First, Polynesian expansion across the Pacific also exterminated many species well before European explorations. Second, three factors increase the rate: (i) The number of known extinctions before 1800 is increasing as taxonomists describe new species from skeletal remains. (ii) One should calculate extinction rates over the years since taxonomists described the species. Most bird species were described only after 1850. (iii) Some species are probably extinct; there is reluctance to declare them so prematurely. Thus corrected, recent extinction rates are ≈100 E/MSY. In the last decades, the rate is <50 E/MSY, but would be 150 E/MSY were it not for conservation efforts. Increasing numbers of extinctions are on continents, whereas previously most were on islands. We predict a 21st century rate of ≈1,000 E/MSY. Extinction threatens 12% of bird species; another 12% have small geographical ranges and live where human actions rapidly destroy their habitats. If present forest losses continue, extinction rates will reach 1,500 E/MSY by the century’s end. Invasive species, expanding human technologies, and global change will harm additional species. Birds are poor models for predicting extinction rates for other taxa. Human actions threaten higher fractions of other well known taxa than they do birds. Moreover, people take special efforts to protect birds. PMID:16829570

An accurate bacterial DNA quantification assay for HTS library preparation of human biological samples.

PubMed

Seashols-Williams, Sarah; Green, Raquel; Wohlfahrt, Denise; Brand, Angela; Tan-Torres, Antonio Limjuco; Nogales, Francy; Brooks, J Paul; Singh, Baneshwar

2018-05-17

Sequencing and classification of microbial taxa within forensically relevant biological fluids has the potential for applications in the forensic science and biomedical fields. The quantity of bacterial DNA from human samples is currently estimated based on quantity of total DNA isolated. This method can miscalculate bacterial DNA quantity due to the mixed nature of the sample, and consequently library preparation is often unreliable. We developed an assay that can accurately and specifically quantify bacterial DNA within a mixed sample for reliable 16S ribosomal DNA (16S rDNA) library preparation and high throughput sequencing (HTS). A qPCR method was optimized using universal 16S rDNA primers, and a commercially available bacterial community DNA standard was used to develop a precise standard curve. Following qPCR optimization, 16S rDNA libraries from saliva, vaginal and menstrual secretions, urine, and fecal matter were amplified and evaluated at various DNA concentrations; successful HTS data were generated with as low as 20 pg of bacterial DNA. Changes in bacterial DNA quantity did not impact observed relative abundances of major bacterial taxa, but relative abundance changes of minor taxa were observed. Accurate quantification of microbial DNA resulted in consistent, successful library preparations for HTS analysis. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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...

Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates.

PubMed

Jumas-Bilak, Estelle; Bouvet, Philippe; Allen-Vercoe, Emma; Aujoulat, Fabien; Lawson, Paul A; Jean-Pierre, Hélène; Marchandin, Hélène

2015-11-01

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5-91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).

A Review of the Diagnosis and Treatment of Ochratoxin A Inhalational Exposure Associated with Human Illness and Kidney Disease including Focal Segmental Glomerulosclerosis

PubMed Central

Hope, Janette H.; Hope, Bradley E.

2012-01-01

Ochratoxin A (OTA) exposure via ingestion and inhalation has been described in the literature to cause kidney disease in both animals and humans. This paper reviews Ochratoxin A and its relationship to human health and kidney disease with a focus on a possible association with focal segmental glomerulosclerosis (FSGS) in humans. Prevention and treatment strategies for OTA-induced illness are also discussed, including cholestyramine, a bile-acid-binding resin used as a sequestrant to reduce the enterohepatic recirculation of OTA. PMID:22253638

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.

[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

Pathological alterations typical of human Tay-Sachs disease, in the retina of a deep-sea fish.

PubMed

Fishelson, L; Delarea, Y; Galil, B S

2000-08-01

Micrographs of retinas from the deep-sea fish Cataetyx laticeps revealed visual cells containing membranous whorls in the ellipsoids of the inner segments resulting from stretching and modifications of the mitochondria membranes and their cristae. These pathological structures seem to be homologous to the whorls observed in retinas of human carriers of Tay-Sachs disease. This disease, a genetic disorder, is found in humans and some mammals. Our findings in fish suggest that the gene responsible can be found throughout the vertebrate evolutionary tree, possibly dormant in most taxa.

Diverse taxa of cyanobacteria produce beta-N-methylamino-L-alanine, a neurotoxic amino acid.

PubMed

Cox, Paul Alan; Banack, Sandra Anne; Murch, Susan J; Rasmussen, Ulla; Tien, Georgia; Bidigare, Robert Richard; Metcalf, James S; Morrison, Louise F; Codd, Geoffrey A; Bergman, Birgitta

2005-04-05

Cyanobacteria can generate molecules hazardous to human health, but production of the known cyanotoxins is taxonomically sporadic. For example, members of a few genera produce hepatotoxic microcystins, whereas production of hepatotoxic nodularins appears to be limited to a single genus. Production of known neurotoxins has also been considered phylogenetically unpredictable. We report here that a single neurotoxin, beta-N-methylamino-L-alanine, may be produced by all known groups of cyanobacteria, including cyanobacterial symbionts and free-living cyanobacteria. The ubiquity of cyanobacteria in terrestrial, as well as freshwater, brackish, and marine environments, suggests a potential for wide-spread human exposure.

Diverse taxa of cyanobacteria produce β-N-methylamino-l-alanine, a neurotoxic amino acid

PubMed Central

Cox, Paul Alan; Banack, Sandra Anne; Murch, Susan J.; Rasmussen, Ulla; Tien, Georgia; Bidigare, Robert Richard; Metcalf, James S.; Morrison, Louise F.; Codd, Geoffrey A.; Bergman, Birgitta

2005-01-01

Cyanobacteria can generate molecules hazardous to human health, but production of the known cyanotoxins is taxonomically sporadic. For example, members of a few genera produce hepatotoxic microcystins, whereas production of hepatotoxic nodularins appears to be limited to a single genus. Production of known neurotoxins has also been considered phylogenetically unpredictable. We report here that a single neurotoxin, β-N-methylamino-l-alanine, may be produced by all known groups of cyanobacteria, including cyanobacterial symbionts and free-living cyanobacteria. The ubiquity of cyanobacteria in terrestrial, as well as freshwater, brackish, and marine environments, suggests a potential for wide-spread human exposure. PMID:15809446

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

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

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.

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

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

Tardigrada of Ireland: a review of records and an updated checklist of species including a new addition to the Irish fauna

PubMed Central

DeMilio, Erica; Lawton, Colin; Marley, Nigel J.

2016-01-01

Abstract The phylum Tardigrada was not recorded in Ireland until the Clare Island Survey of 1909–1911, with only rare subsequent reports on Irish tardigrade species. In recent decades, significant taxonomic revision has occurred within Tardigrada. This has resulted in the need for a review of all known historical records from Ireland and Northern Ireland in order to produce an updated checklist of valid taxa. The new checklist includes fifty-one tardigrade species and subspecies including a new addition to the Irish fauna reported herein, Echiniscus quadrispinosus quadrispinosus Richters, 1902 from Newtown, Ballyvaughan, Co. Clare. PMID:27667947

Sequence-specific 1H-NMR assignments for the aromatic region of several biologically active, monomeric insulins including native human insulin.

PubMed

Roy, M; Lee, R W; Kaarsholm, N C; Thøgersen, H; Brange, J; Dunn, M F

1990-06-12

The aromatic region of the 1H-FT-NMR spectrum of the biologically fully-potent, monomeric human insulin mutant, B9 Ser----Asp, B27 Thr----Glu has been investigated in D2O. At 1 to 5 mM concentrations, this mutant insulin is monomeric above pH 7.5. Coupling and amino acid classification of all aromatic signals is established via a combination of homonuclear one- and two-dimensional methods, including COSY, multiple quantum filters, selective spin decoupling and pH titrations. By comparisons with other insulin mutants and with chemically modified native insulins, all resonances in the aromatic region are given sequence-specific assignments without any reliance on the various crystal structures reported for insulin. These comparisons also give the sequence-specific assignments of most of the aromatic resonances of the mutant insulins B16 Tyr----Glu, B27 Thr----Glu and B25 Phe----Asp and the chemically modified species des-(B23-B30) insulin and monoiodo-Tyr A14 insulin. Chemical dispersion of the assigned resonances, ring current perturbations and comparisons at high pH have made possible the assignment of the aromatic resonances of human insulin, and these studies indicate that the major structural features of the human insulin monomer (including those critical to biological function) are also present in the monomeric mutant.

A chronology for late prehistoric Madagascar.

PubMed

Burney, David A; Burney, Lida Pigott; Godfrey, Laurie R; Jungers, William L; Goodman, Steven M; Wright, Henry T; Jull, A J Timothy

2004-01-01

A database has been assembled with 278 age determinations for Madagascar. Materials 14C dated include pretreated sediments and plant macrofossils from cores and excavations throughout the island, and bones, teeth, or eggshells of most of the extinct megafaunal taxa, including the giant lemurs, hippopotami, and ratites. Additional measurements come from uranium-series dates on speleothems and thermoluminescence dating of pottery. Changes documented include late Pleistocene climatic events and, in the late Holocene, the apparently human-caused transformation of the environment. Multiple lines of evidence point to the earliest human presence at ca. 2300 14C yr BP (350 cal yr BC). A decline in megafauna, inferred from a drastic decrease in spores of the coprophilous fungus Sporormiella spp. in sediments at 1720+/-40 14C yr BP (230-410 cal yr AD), is followed by large increases in charcoal particles in sediment cores, beginning in the SW part of the island, and spreading to other coasts and the interior over the next millennium. The record of human occupation is initially sparse, but shows large human populations throughout the island by the beginning of the Second Millennium AD. Dating of the "subfossil" megafauna, including pygmy hippos, elephant birds, giant tortoises, and large lemurs, demonstrates that most if not all the extinct taxa were still present on the island when humans arrived. Many taxa overlapped chronologically with humans for a millennium or more. The extinct lemurs Hadropithecus stenognathus, Pachylemur insignis, Mesopropithecus pithecoides, and Daubentonia robusta, and the elephant birds Aepyornis spp. and Mullerornis spp., were still present near the end of the First Millennium AD. Palaeopropithecus ingens, Megaladapis edwardsi, and Archaeolemur sp. (cf. edwardsi) may have survived until the middle of the Second Millennium A.D. One specimen of Hippopotamus of unknown provenance dates to the period of European colonization.

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

Integron, Plasmid and Host Strain Characteristics of Escherichia coli from Humans and Food Included in the Norwegian Antimicrobial Resistance Monitoring Programs.

PubMed

Sunde, Marianne; Simonsen, Gunnar Skov; Slettemeås, Jannice Schau; Böckerman, Inger; Norström, Madelaine

2015-01-01

Antimicrobial resistant Escherichia coli (n=331) isolates from humans with bloodstream infections were investigated for the presence of class 1 and class 2 integrons. The integron cassettes arrays were characterized and the findings were compared with data from similar investigations on resistant E. coli from meat and meat products (n=241) produced during the same time period. All isolates were obtained from the Norwegian monitoring programs for antimicrobial resistance in human pathogens and in the veterinary sector. Methods used included PCR, sequencing, conjugation experiments, plasmid replicon typing and subtyping, pulsed-field-gel-electrophoresis and serotyping. Integrons of class 1 and 2 occurred significantly more frequently among human isolates; 45.4% (95% CI: 39.9-50.9) than among isolates from meat; 18% (95% CI: 13.2 -23.3), (p<0.01, Chi-square test). Identical cassette arrays including dfrA1-aadA1, aadA1, dfrA12-orfF-aadA2, oxa-30-aadA1 (class 1 integrons) and dfrA1-sat1-aadA1 (class 2 integrons) were detected from both humans and meat. However, the most prevalent cassette array in human isolates, dfrA17-aadA5, did not occur in isolates from meat, suggesting a possible linkage between this class 1 integron and a subpopulation of E. coli adapted to a human host. The drfA1-aadA1 and aadA1 class 1 integrons were found frequently in both human and meat isolates. These isolates were subjected to further studies to investigate similarities with regard to transferability, plasmid and host strain characteristics. We detected incF plasmids with pMLST profile F24:A-:B1 carrying drfA1-aadA1 integrons in isolates from pork and in a more distantly related E. coli strain from a human with septicaemia. Furthermore, we showed that most of the class 1 integrons with aadA1 were located on incF plasmids with pMLST profile F51:A-:B10 in human isolates. The plasmid was present in unrelated as well as closely related host strains, demonstrating that dissemination of this

Effect of changes in human ecology and behavior on patterns of sexually transmitted diseases, including human immunodeficiency virus infection.

PubMed Central

Wasserheit, J N

1994-01-01

The last 20 years have witnessed six striking changes in patterns of sexually transmitted diseases (STDs): emergence of new STD organisms and etiologies, reemergence of old STDs, shifts in the populations in which STDs are concentrated, shifts in the etiological spectra of STD syndromes, alterations in the incidence of STD complications, and increases in antimicrobial resistance. For example, human immunodeficiency virus (HIV) emerged to devastate the United States with a fatal pandemic involving at least 1 million people. The incidence of syphilis rose progressively after 1956 to reach a 40-year peak by 1990. In both cases, disease patterns shifted from homosexual men to include minority heterosexuals. Over the last decade, gonorrhea became increasingly concentrated among adolescents, and several new types of antimicrobial resistance appeared. Three interrelated types of environments affect STD patterns. The microbiologic, hormonal, and immunologic microenvironments most directly influence susceptibility, infectiousness, and development of sequelae. These microenvironments are shaped, in part, by the personal environments created by an individual's sexual, substance-use, and health-related behaviors. The personal environments are also important determinants of acquisition of infection and development of sequelae but, in addition, they mediate risk of exposure to infection. These are, therefore, the environments that most directly affect changing disease patterns. Finally, individuals' personal environments are, in turn, molded by powerful macroenvironmental forces, including socioeconomic, demographic, geographic, political, epidemiologic, and technological factors. Over the past 20 years, the profound changes that have occurred in many aspects of the personal environment and the macroenvironment have been reflected in new STD patterns. PMID:8146135

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

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.

Dynamic microbial populations along the Cuyahoga River

PubMed Central

Craine, Joseph; Hester, James; Shalkhauser, Amanda; Chan, Ernest R.; Logue, Kyle; Small, Scott; Serre, David

2017-01-01

The study of the microbial communities has gained traction in recent years with the advent of next-generation sequencing with, or without, PCR-based amplification of the 16S ribosomal RNA region. Such studies have been applied to topics as diverse as human health and environmental ecology. Fewer studies have investigated taxa outside of bacteria, however. We present here data demonstrating the utility of studying taxa outside of bacteria including algae, diatoms, archaea and fungi. Here, we show how location along the Cuyahoga River as well as a transient rainfall event heavily influence the microbial composition. Our data reveal how individual OTUs vary between samples and how the patterns of OTU abundance can accurately predict sampling location. The clustering of samples reveals that these taxa are all sensitive to water conditions in unique ways and demonstrate that, for our dataset, algae was most distinctive between sample groups, surpassing bacteria. Diversity between sampling sites could allow studies investigating pollution or water quality to identify marker OTUs or patterns of OTU abundance as indicators to assess environmental conditions or the impact of human activity. We also directly compare data derived from primers amplifying distinct taxa and show that taxa besides bacteria are excellent indicators of water condition. PMID:29049324

The skull roof tracks the brain during the evolution and development of reptiles including birds.

PubMed

Fabbri, Matteo; Mongiardino Koch, Nicolás; Pritchard, Adam C; Hanson, Michael; Hoffman, Eva; Bever, Gabriel S; Balanoff, Amy M; Morris, Zachary S; Field, Daniel J; Camacho, Jasmin; Rowe, Timothy B; Norell, Mark A; Smith, Roger M; Abzhanov, Arhat; Bhullar, Bhart-Anjan S

2017-10-01

Major transformations in brain size and proportions, such as the enlargement of the brain during the evolution of birds, are accompanied by profound modifications to the skull roof. However, the hypothesis of concerted evolution of shape between brain and skull roof over major phylogenetic transitions, and in particular of an ontogenetic relationship between specific regions of the brain and the skull roof, has never been formally tested. We performed 3D morphometric analyses to examine the deep history of brain and skull-roof morphology in Reptilia, focusing on changes during the well-documented transition from early reptiles through archosauromorphs, including nonavian dinosaurs, to birds. Non-avialan taxa cluster tightly together in morphospace, whereas Archaeopteryx and crown birds occupy a separate region. There is a one-to-one correspondence between the forebrain and frontal bone and the midbrain and parietal bone. Furthermore, the position of the forebrain-midbrain boundary correlates significantly with the position of the frontoparietal suture across the phylogenetic breadth of Reptilia and during the ontogeny of individual taxa. Conservation of position and identity in the skull roof is apparent, and there is no support for previous hypotheses that the avian parietal is a transformed postparietal. The correlation and apparent developmental link between regions of the brain and bony skull elements are likely to be ancestral to Tetrapoda and may be fundamental to all of Osteichthyes, coeval with the origin of the dermatocranium.

Using populations of human and microbial genomes for organism detection in metagenomes

DOE PAGES

Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; ...

2015-04-29

Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-freemore » human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.« less

Using populations of human and microbial genomes for organism detection in metagenomes

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

Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel

Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-freemore » human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.« less

Human age and skin physiology shape diversity and abundance of Archaea on skin

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

Moissl-Eichinger, Christine; Probst, Alexander J.; Birarda, Giovanni

The human skin microbiome acts as an important barrier protecting our body from pathogens and other environmental influences. Recent investigations have provided evidence that Archaea are a constant but highly variable component of the human skin microbiome, yet factors that determine their abundance changes are unknown. Here, we tested the hypothesis that the abundance of archaea on human skin is influenced by human age and skin physiology by quantitative PCR of 51 different skin samples taken from human subjects of various age. Our results reveal that archaea are more abundant in human subjects either older than 60 years or youngermore » than 12 years as compared to middle-aged human subjects. These results, together with results obtained from spectroscopy analysis, allowed us gain first insights into a potential link of lower sebum levels and lipid content and thus reduced skin moisture with an increase in archaeal signatures. In conclusion, amplicon sequencing of selected samples revealed the prevalence of specific eury- and mainly thaumarchaeal taxa, represented by a core archaeome of the human skin.« less

Human age and skin physiology shape diversity and abundance of Archaea on skin

DOE PAGES

Moissl-Eichinger, Christine; Probst, Alexander J.; Birarda, Giovanni; ...

2017-06-22

The human skin microbiome acts as an important barrier protecting our body from pathogens and other environmental influences. Recent investigations have provided evidence that Archaea are a constant but highly variable component of the human skin microbiome, yet factors that determine their abundance changes are unknown. Here, we tested the hypothesis that the abundance of archaea on human skin is influenced by human age and skin physiology by quantitative PCR of 51 different skin samples taken from human subjects of various age. Our results reveal that archaea are more abundant in human subjects either older than 60 years or youngermore » than 12 years as compared to middle-aged human subjects. These results, together with results obtained from spectroscopy analysis, allowed us gain first insights into a potential link of lower sebum levels and lipid content and thus reduced skin moisture with an increase in archaeal signatures. In conclusion, amplicon sequencing of selected samples revealed the prevalence of specific eury- and mainly thaumarchaeal taxa, represented by a core archaeome of the human skin.« less

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

PubMed Central

Fisher, Jenny C.; Eren, A. Murat; Green, Hyatt C.; Shanks, Orin C.; Morrison, Hilary G.; Vineis, Joseph H.; Sogin, Mitchell L.

2015-01-01

Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts. PMID:26231648

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

Development of the nervus terminalis in mammals including toothed whales and humans.

PubMed

Oelschläger, H A; Buhl, E H; Dann, J F

1987-01-01

The early ontogenesis and topography of the mammalian terminalis system was investigated in 43 microslide series of toothed whale and human embryos and fetuses. In early embryonal stages the development of the nasal pit, the olfacto-terminalis placode, and the olfactory bulb anlage is rather similar in toothed whales and humans. However, toothed whales do not show any trace of the vomeronasalis complex. In early fetal stages the olfactory bulb anlage in toothed whales is reduced and leaves the isolated future terminalis ganglion (ganglia) which contains the greatest number of cells within Mammalia. The ganglion is connected with the nasal mucosa via peripheral fiber bundles and with the telencephalon via central terminalis rootlets. The functional implications of the terminalis system in mammals and its evolution in toothed whales are discussed. Obviously, the autonomic component has been enlarged in the course of perfect adaptation to an aquatic environment.

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

Linking brains and brawn: exercise and the evolution of human neurobiology.

PubMed

Raichlen, David A; Polk, John D

2013-01-07

The hunting and gathering lifestyle adopted by human ancestors around 2 Ma required a large increase in aerobic activity. High levels of physical activity altered the shape of the human body, enabling access to new food resources (e.g. animal protein) in a changing environment. Recent experimental work provides strong evidence that both acute bouts of exercise and long-term exercise training increase the size of brain components and improve cognitive performance in humans and other taxa. However, to date, researchers have not explored the possibility that the increases in aerobic capacity and physical activity that occurred during human evolution directly influenced the human brain. Here, we hypothesize that proximate mechanisms linking physical activity and neurobiology in living species may help to explain changes in brain size and cognitive function during human evolution. We review evidence that selection acting on endurance increased baseline neurotrophin and growth factor signalling (compounds responsible for both brain growth and for metabolic regulation during exercise) in some mammals, which in turn led to increased overall brain growth and development. This hypothesis suggests that a significant portion of human neurobiology evolved due to selection acting on features unrelated to cognitive performance.

Recognition of Potentially Novel Human Disease-Associated Pathogens by Implementation of Systematic 16S rRNA Gene Sequencing in the Diagnostic Laboratory▿ †

PubMed Central

Keller, Peter M.; Rampini, Silvana K.; Büchler, Andrea C.; Eich, Gerhard; Wanner, Roger M.; Speck, Roberto F.; Böttger, Erik C.; Bloemberg, Guido V.

2010-01-01

Clinical isolates that are difficult to identify by conventional means form a valuable source of novel human pathogens. We report on a 5-year study based on systematic 16S rRNA gene sequence analysis. We found 60 previously unknown 16S rRNA sequences corresponding to potentially novel bacterial taxa. For 30 of 60 isolates, clinical relevance was evaluated; 18 of the 30 isolates analyzed were considered to be associated with human disease. PMID:20631113

Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces

PubMed Central

Gibbons, Sean M.; Schwartz, Tara; Fouquier, Jennifer; Mitchell, Michelle; Sangwan, Naseer; Kelley, Scott T.

2014-01-01

Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in four public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late-successional community developed within 5 to 8 h on restroom floors and showed remarkable stability over weeks to months. Despite late-successional dominance by skin- and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivable community, even after several hours of human exclusion. Methicillin-resistant Staphylococcus aureus (MRSA)-associated virulence genes were found on floors but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophages, human papilloma virus, and herpesviruses, were significantly correlated with bacterial abundances and showed an unexpectedly low virus-to-bacterium ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces. PMID:25398865

Ecological succession and viability of human-associated microbiota on restroom surfaces

DOE PAGES

Gibbons, Sean M.; Schwartz, Tara; Fouquier, Jennifer; ...

2014-11-14

Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in four public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late-successional community developed within 5 to 8 h on restroom floors and showed remarkable stability over weeks to months. Despite late-successional dominance by skin- and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivablemore » community, even after several hours of human exclusion. Methicillin-resistant Staphylococcus aureus (MRSA)-associated virulence genes were found on floors but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophages, human papilloma virus, and herpesviruses, were significantly correlated with bacterial abundances and showed an unexpectedly low virus-to-bacterium ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces.« less

Ecological succession and viability of human-associated microbiota on restroom surfaces

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

Gibbons, Sean M.; Schwartz, Tara; Fouquier, Jennifer

Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in four public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late-successional community developed within 5 to 8 h on restroom floors and showed remarkable stability over weeks to months. Despite late-successional dominance by skin- and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivablemore » community, even after several hours of human exclusion. Methicillin-resistant Staphylococcus aureus (MRSA)-associated virulence genes were found on floors but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophages, human papilloma virus, and herpesviruses, were significantly correlated with bacterial abundances and showed an unexpectedly low virus-to-bacterium ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces.« less

Last glacial megafaunal death assemblage and early human occupation at Lake Menindee, southeastern Australia

NASA Astrophysics Data System (ADS)

Cupper, Matthew L.; Duncan, Jacqui

2006-09-01

The Tedford subfossil locality at Lake Menindee preserves a diverse assemblage of marsupials, monotremes and placental rodents. Of the 38 mammal taxa recorded at the site, almost a third are of extinct megafauna. Some of the bones are articulated or semi-articulated and include almost complete skeletons, indicating that aeolian sediments rapidly buried the animals following death. New optical ages show the site dates to the early part of the last glacial (55,700 ± 1300 yr weighted mean age). This is close to the 51,200-39,800 yr Australia-wide extinction age for megafauna suggested by Roberts et al. [2001, Science 292:1888-1892], but like all previous researchers, we cannot conclusively determine whether humans were implicated in the deaths of the animals. Although an intrusive hearth at the site dating to 45,100 ± 1400 yr ago is the oldest evidence of human occupation of the Darling River, no artifacts were identified in situ within the sub-fossil-bearing unit. Non-anthropogenic causes, such as natural senescence or ecosystem stress due to climatic aridity, probably explain the mortality of the faunal assemblage at Lake Menindee.

Human Dispersals Along the African Rift Valley in the Late Quaternary

NASA Astrophysics Data System (ADS)

Tryon, C. A.; Faith, J. T.; Peppe, D. J.

2014-12-01

Climate- and tectonic-driven environmental dynamics of the East African Rift System (EARS) during the Quaternary played an important role in the demographic history of early Homo sapiens, including expansions of modern humans across and out of Africa. Human forager population size, geographic range, and behaviors such as hunting strategies and residential mobility likely varied in response to changes in the local and regional environment. Throughout the Quaternary, floral and faunal change was linked at least in part to variations in moisture availability, temperature, and atmospheric CO2, which in addition to uplift and faulting, contributed to the expansion and contraction of a number of large lakes that served as biogeographic barriers to many taxa. This is particularly clear for the Lake Victoria basin, where biogeographic, geological, and paleontological evidence documents repeated expansion and contraction of the ranges of species in response to lake level and vegetation change. Across much of eastern Africa, the topography of the rift facilitated north-south dispersals, the timing of which may have depended in part on the expansion and contraction of the equatorial forest belt. Dispersal potential likely increased during the more arid periods of the late Quaternary, when the roles of lakes and forests as dispersal barriers was reduced and the extent of low net primary productivity dry grasslands increased, the latter requiring large home ranges for human foragers, conditions suitable for range expansions within H. sapiens.

Fungi in the healthy human gastrointestinal tract

PubMed Central

Hallen-Adams, Heather E.; Suhr, Mallory J.

2017-01-01

ABSTRACT Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are common on fermented foods but cannot grow at human body temperature), while still others have dietary or environmental sources (Saccharomyces cerevisiae, a fermentation agent and sometime probiotic; Aspergillus species, ubiquitous molds) yet are likely to impact gut ecology. The gut mycobiome appears less stable than the bacterial microbiome, and is likely subject to environmental factors. PMID:27736307

Fungi in the healthy human gastrointestinal tract.

PubMed

Hallen-Adams, Heather E; Suhr, Mallory J

2017-04-03

Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are common on fermented foods but cannot grow at human body temperature), while still others have dietary or environmental sources (Saccharomyces cerevisiae, a fermentation agent and sometime probiotic; Aspergillus species, ubiquitous molds) yet are likely to impact gut ecology. The gut mycobiome appears less stable than the bacterial microbiome, and is likely subject to environmental factors.

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

The facial skeleton of the chimpanzee-human last common ancestor

PubMed Central

Cobb, Samuel N

2008-01-01

This review uses the current morphological evidence to evaluate the facial morphology of the hypothetical last common ancestor (LCA) of the chimpanzee/bonobo (panin) and human (hominin) lineages. Some of the problems involved in reconstructing ancestral morphologies so close to the formation of a lineage are discussed. These include the prevalence of homoplasy and poor phylogenetic resolution due to a lack of defining derived features. Consequently the list of hypothetical features expected in the face of the LCA is very limited beyond its hypothesized similarity to extant Pan. It is not possible to determine with any confidence whether the facial morphology of any of the current candidate LCA taxa (Ardipithecus kadabba, Ardipithecus ramidus, Orrorin tugenensis and Sahelanthropus tchadensis) is representative of the LCA, or a stem hominin, or a stem panin or, in some cases, a hominid predating the emergence of the hominin lineage. The major evolutionary trends in the hominin lineage subsequent to the LCA are discussed in relation to the dental arcade and dentition, subnasal morphology and the size, position and prognathism of the facial skeleton. PMID:18380866

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...

Spatiotemporal dynamics of urban green spaces and human-wildlife conflicts in Tokyo

NASA Astrophysics Data System (ADS)

Hosaka, Tetsuro; Numata, Shinya

2016-08-01

Although urban green spaces are increasingly important both for humans and wildlife, an increase in urban green spaces may also increase human-wildlife conflicts in urban areas. However, few studies have examined the relationship between the size of green spaces and the level of conflicts with wildlife in multiple taxa, including invertebrates and vertebrates. To better understand current pest statistics and predict changes that will occur as the area of green spaces increases, we analysed a dataset compiling the number of pest consultations in 53 metropolitan districts in Tokyo over a 20-year period and its relationships with the area of green space. Stinging insects (e.g., wasps) made up over 50% of pest consultations, followed (in order) by rats and other nuisance animals (e.g., snakes). The number of consultations per unit population did not correlate, or was even negatively correlated, with the proportions of green spaces (mainly forest) for many indoor pests, but did positively correlate for some outdoor pests, such as wasps and snakes. Therefore, wasps and snakes can increase when urban green spaces increase. Because even minor nuisances are relevant for urban lifestyles, considerations of ways to minimise conflicts with wildlife are critical for urban green space management.

Early-Middle Pleistocene environmental changes and human evolution in the Italian peninsula

NASA Astrophysics Data System (ADS)

Manzi, Giorgio; Magri, Donatella; Palombo, Maria Rita

2011-06-01

This paper is aimed to elucidate the ecological scenario in Italy in the Early to Middle Pleistocene, when species of the genus Homo are known to spread across Europe in two distinct waves: earlier than 1.2 Ma and at about 600 ka, respectively. This topic represents both (1) a fundamental aspect for a better understanding of the factors that allowed humans to colonize the middle latitudes of Eurasia, and (2) a reasonable frontier for current Quaternary palaeobiology, thanks to increasing knowledge of regional and local patterns. As for Italy, a combination of palaeobotanical and palaeontological data sets shows on the one hand a general complexity in both space and time, and on the other hand changes of considerable importance within and among the biological communities. These changes had a major importance during the worldwide change in the Earth climatic system known as "Middle Pleistocene Revolution", which according to our data culminates with crucial effects of the extreme conditions of MIS 16. Subsequently, during great part of the Middle Pleistocene, the peculiar features of the Italian territory may have favoured isolation and a local persistence of plant populations and possibly mammal taxa, humans included, as for instance suggested by the corrected chronology of the Ceprano calvarium.

Investigation into the role of phosphodiesterase IV in bronchorelaxation, including studies with human bronchus.

PubMed Central

Cortijo, J.; Bou, J.; Beleta, J.; Cardelús, I.; Llenas, J.; Morcillo, E.; Gristwood, R. W.

1993-01-01

1. We have investigated the role of cyclic nucleotide phosphodiesterase IV (PDE IV) in the relaxation of human bronchus and guinea-pig trachea in vitro and in guinea-pigs in vivo. 2. Functional studies showed that the selective PDE IV inhibitors, rolipram and denbufylline, relaxed human and guinea-pig preparations in vitro. 3. Two clinically used xanthine non-selective PDE inhibitors, theophylline and pentoxifylline, were also effective in these preparations, but were much less potent than the selective agents used. 4. The rank order of potency for the four PDE inhibitors in both species was similar. 5. Biochemical studies indicated that PDE IV was the major PDE isoform present in the human bronchial tissue. PDEs I, II and V were also identified. 6. Theophylline and pentoxifylline were, as expected, non-selective inhibitors of the human enzymes, but there was a good correlation between PDE IV inhibitory and bronchorelaxation potencies, suggesting that PDE IV inhibition is important for the clinical bronchodilator activities of the two xanthine compounds. 7. We have confirmed the ability of selective PDE IV inhibitors to cause bronchodilatation in guinea-pigs in vivo. 8. We conclude that our study has provided further evidence that selective PDE IV inhibitors could act as bronchodilators in the clinic. PMID:8383567

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.

Climate change and evolving human diversity in Europe during the last glacial.

PubMed Central

Gamble, Clive; Davies, William; Pettitt, Paul; Richards, Martin

2004-01-01

A link between climate change and human evolution during the Pleistocene has often been assumed but rarely tested. At the macro-evolutionary level Foley showed for hominids that extinction, rather than speciation, correlates with environmental change as recorded in the deep sea record. Our aim is to examine this finding at a smaller scale and with high-resolution environmental and archaeological archives. Our interest is in changing patterns of human dispersal under shifting Pleistocene climates during the last glacial period in Europe. Selecting this time frame and region allows us to observe how two hominid taxa, Neanderthals and Crô-Magnons, adapted to climatic conditions during oxygen isotope stage 3. These taxa are representative of two hominid adaptive radiations, termed terrestrial and aquatic, which exhibited different habitat preferences but similar tolerances to climatic factors. Their response to changing ecological conditions was predicated upon their ability to extend their societies in space and time. We examine this difference further using a database of all available radiocarbon determinations from western Europe in the late glacial. These data act as proxies for population history, and in particular the expansion and contraction of regional populations as climate changed rapidly. Independent assessment of these processes is obtained from the genetic history of Europeans. The results indicate that climate affects population contraction rather than expansion. We discuss the consequences for genetic and cultural diversity which led to the legacy of the Ice Age: a single hominid species, globally distributed. PMID:15101580

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

3D geometric morphometric analysis of the proximal epiphysis of the hominoid humerus

PubMed Central

Arias-Martorell, Julia; Potau, Josep Maria; Bello-Hellegouarch, Gaëlle; Pastor, Juan Francisco; Pérez-Pérez, Alejandro

2012-01-01

In this study we perform a three-dimensional geometric morphometric (3D GM) analysis of the proximal epiphysis of the humerus in extant great apes, including humans, in order to accurately describe the functional anatomical differences between these taxa. In addition, a fossil hominin specimen of Australopithecus afarensis was included in a multivariate GM analysis in order to test the potential of this methodological approach for making locomotor inferences from fossil remains. The results obtained show significant differences in proximal humeral morphology among the taxa studied, which had thus far largely remained unnoticed. Based on morphofunctional considerations, these anatomical differences can be correlated to differences in the locomotor repertoires of the taxa, thus confirming that the proximal humerus is suitable for constructing paleobiological inferences about locomotion. Modern humans display markedly divergent features, which set them apart from both the extant great apes and the fossil hominin A. afarensis. The morphology of the proximal epiphysis of the humerus of the latter more closely resembles that of the orangutans, thus suggesting that despite hindlimb adaptations to bipedalism, the forelimb of this taxon was still functionally involved in arboreal behaviors, such as climbing or suspension. PMID:22946496

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

Using populations of human and microbial genomes for organism detection in metagenomes.

PubMed

Ames, Sasha K; Gardner, Shea N; Marti, Jose Manuel; Slezak, Tom R; Gokhale, Maya B; Allen, Jonathan E

2015-07-01

Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected. © 2015 Ames et al.; Published by Cold Spring Harbor Laboratory Press.

A multi-scale study of Orthoptera species richness and human population size controlling for sampling effort

NASA Astrophysics Data System (ADS)

Cantarello, Elena; Steck, Claude E.; Fontana, Paolo; Fontaneto, Diego; Marini, Lorenzo; Pautasso, Marco

2010-03-01

Recent large-scale studies have shown that biodiversity-rich regions also tend to be densely populated areas. The most obvious explanation is that biodiversity and human beings tend to match the distribution of energy availability, environmental stability and/or habitat heterogeneity. However, the species-people correlation can also be an artefact, as more populated regions could show more species because of a more thorough sampling. Few studies have tested this sampling bias hypothesis. Using a newly collated dataset, we studied whether Orthoptera species richness is related to human population size in Italy’s regions (average area 15,000 km2) and provinces (2,900 km2). As expected, the observed number of species increases significantly with increasing human population size for both grain sizes, although the proportion of variance explained is minimal at the provincial level. However, variations in observed Orthoptera species richness are primarily associated with the available number of records, which is in turn well correlated with human population size (at least at the regional level). Estimated Orthoptera species richness (Chao2 and Jackknife) also increases with human population size both for regions and provinces. Both for regions and provinces, this increase is not significant when controlling for variation in area and number of records. Our study confirms the hypothesis that broad-scale human population-biodiversity correlations can in some cases be artefactual. More systematic sampling of less studied taxa such as invertebrates is necessary to ascertain whether biogeographical patterns persist when sampling effort is kept constant or included in models.

Oxytocin- and arginine vasopressin-containing fibers in the cortex of humans, chimpanzees, and rhesus macaques.

PubMed

Rogers, Christina N; Ross, Amy P; Sahu, Shweta P; Siegel, Ethan R; Dooyema, Jeromy M; Cree, Mary Ann; Stopa, Edward G; Young, Larry J; Rilling, James K; Albers, H Elliott; Preuss, Todd M

2018-05-24

Oxytocin (OT) and arginine-vasopressin (AVP) are involved in the regulation of complex social behaviors across a wide range of taxa. Despite this, little is known about the neuroanatomy of the OT and AVP systems in most non-human primates, and less in humans. The effects of OT and AVP on social behavior, including aggression, mating, and parental behavior, may be mediated primarily by the extensive connections of OT- and AVP-producing neurons located in the hypothalamus with the basal forebrain and amygdala, as well as with the hypothalamus itself. However, OT and AVP also influence social cognition, including effects on social recognition, cooperation, communication, and in-group altruism, which suggests connectivity with cortical structures. While OT and AVP V1a receptors have been demonstrated in the cortex of rodents and primates, and intranasal administration of OT and AVP has been shown to modulate cortical activity, there is to date little evidence that OT-and AVP-containing neurons project into the cortex. Here, we demonstrate the existence of OT- and AVP-containing fibers in cortical regions relevant to social cognition using immunohistochemistry in humans, chimpanzees, and rhesus macaques. OT-immunoreactive fibers were found in the straight gyrus of the orbitofrontal cortex as well as the anterior cingulate gyrus in human and chimpanzee brains, while no OT-immunoreactive fibers were found in macaque cortex. AVP-immunoreactive fibers were observed in the anterior cingulate gyrus in all species, as well as in the insular cortex in humans, and in a more restricted distribution in chimpanzees. This is the first report of OT and AVP fibers in the cortex in human and non-human primates. Our findings provide a potential mechanism by which OT and AVP might exert effects on brain regions far from their production site in the hypothalamus, as well as potential species differences in the behavioral functions of these target regions. © 2018 Wiley Periodicals, Inc.

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.

Detection of bacterial pathogens including potential new species in human head lice from Mali.

PubMed

Amanzougaghene, Nadia; Fenollar, Florence; Sangaré, Abdoul Karim; Sissoko, Mahamadou S; Doumbo, Ogobara K; Raoult, Didier; Mediannikov, Oleg

2017-01-01

In poor African countries, where no medical and biological facilities are available, the identification of potential emerging pathogens of concern at an early stage is challenging. Head lice, Pediculus humanus capitis, have a short life, feed only on human blood and do not transmit pathogens to their progeny. They are, therefore, a perfect tool for the xenodiagnosis of current or recent human infection. This study assessed the occurrence of bacterial pathogens from head lice collected in two rural villages from Mali, where a high frequency of head lice infestation had previously been reported, using molecular methods. Results show that all 600 head lice, collected from 117 individuals, belonged to clade E, specific to West Africa. Bartonella quintana, the causative agent of trench fever, was identified in three of the 600 (0.5%) head lice studied. Our study also shows, for the first time, the presence of the DNA of two pathogenic bacteria, namely Coxiella burnetii (5.1%) and Rickettsia aeschlimannii (0.6%), detected in human head lice, as well as the DNA of potential new species from the Anaplasma and Ehrlichia genera of unknown pathogenicity. The finding of several Malian head lice infected with B. quintana, C. burnetii, R. aeschlimannii, Anaplasma and Ehrlichia is alarming and highlights the need for active survey programs to define the public health consequences of the detection of these emerging bacterial pathogens in human head lice.

The evolution of laughter in great apes and humans

PubMed Central

Owren, Michael J; Zimmermann, Elke

2010-01-01

It has long been claimed that human emotional expressions, such as laughter, have evolved from nonhuman displays. The aim of the current study was to test this prediction by conducting acoustic and phylogenetic analyses based on the acoustics of tickle-induced vocalizations of orangutans, gorillas, chimpanzees, bonobos and humans. Results revealed both important similarities and differences among the various species’ vocalizations, with the phylogenetic tree reconstructed based on these acoustic data matching the well-established genetic relationships of great apes and humans. These outcomes provide evidence of a common phylogenetic origin of tickle-induced vocalizations in these taxa, which can therefore be termed “laughter” across all five species. Results are consistent with the claims of phylogenetic continuity of emotional expressions. Together with observations made on the use of laughter in great apes and humans, findings of this study further indicate that there were two main periods of selection-driven evolutionary change in laughter within the Hominidae, to a smaller degree, among the great apes and, most distinctively, after the separation of hominins from the last common ancestor with chimpanzees and bonobos. PMID:20585520

Human-mediated dispersal of aquatic invertebrates with waterproof footwear.

PubMed

Valls, Luis; Castillo-Escrivà, Andreu; Mesquita-Joanes, Francesc; Armengol, Xavier

2016-02-01

Human-mediated dispersal has rarely been considered in wetland conservation strategies at regional scales, yet high concern exists about this aspect for (inter-)national management considering invasive species in other aquatic systems. In this context, we aim at understanding the role of human-mediated dispersal by footwear in protected wetlands with high conservation value. Zooplankton and zoobenthos were sampled in 13 shallow lakes in central Spain and, at the same time, mud attached to waders was collected and later cultured in deionized water under laboratory conditions for 4 weeks. Two-hundred and four individuals belonging to 19 invertebrate taxa were recovered after hatching; Ostracoda (84 %), Cladocera (53 %), Copepoda (30 %), Anostraca (30 %), and Notostraca (7 %) were the most frequent groups among the hatched crustaceans. NMDS and PERMANOVA analyses showed significant differences between the dispersed (via footwear) and the source active metacommunity, suggesting different dispersal abilities among the species found. Human vectors facilitate dispersal among protected lakes, which could eventuality lead to biotic homogenization and faster spread of non-indigenous species. Preservation strategies and education campaigns associated to target humans in close contact with water bodies should be imperative in conservation management of protected lakes.

Changing Patterns of Emerging Zoonotic Diseases in Wildlife, Domestic Animals, and Humans Linked to Biodiversity Loss and Globalization.

PubMed

Aguirre, A Alonso

2017-12-15

The fundamental human threats to biodiversity including habitat destruction, globalization, and species loss have led to ecosystem disruptions altering infectious disease transmission patterns, the accumulation of toxic pollutants, and the invasion of alien species and pathogens. To top it all, the profound role of climate change on many ecological processes has affected the inability of many species to adapt to these relatively rapid changes. This special issue, "Zoonotic Disease Ecology: Effects on Humans, Domestic Animals and Wildlife," explores the complex interactions of emerging infectious diseases across taxa linked to many of these anthropogenic and environmental drivers. Selected emerging zoonoses including RNA viruses, Rift Valley fever, trypanosomiasis, Hanta virus infection, and other vector-borne diseases are discussed in detail. Also, coprophagous beetles are proposed as important vectors in the transmission and maintenance of infectious pathogens. An overview of the impacts of climate change in emerging disease ecology within the context of Brazil as a case study is provided. Animal Care and Use Committee requirements were investigated, concluding that ecology journals have low rates of explicit statements regarding the welfare and wellbing of wildlife during experimental studies. Most of the solutions to protect biodiversity and predicting and preventing the next epidemic in humans originating from wildlife are oriented towards the developed world and are less useful for biodiverse, low-income economies. We need the development of regional policies to address these issues at the local level.

The human genome and sport, including epigenetics, gene doping, and athleticogenomics.

PubMed

Sharp, N C Craig

2010-03-01

Hugh Montgomery's discovery of the first of more than 239 fitness genes together with rapid advances in human gene therapy have created a prospect of using genes, genetic elements, and cells that have the capacity to enhance athletic performance (to paraphrase the World Anti-Doping Agency's definition of gene doping). This brief overview covers the main areas of interface between genetics and sport, attempts to provide a context against which gene doping may be viewed, and predicts a futuristic legitimate use of genomic (and possibly epigenetic) information in sport. Copyright 2010 Elsevier Inc. All rights reserved.

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City.

PubMed

Bik, Holly M; Maritz, Julia M; Luong, Albert; Shin, Hakdong; Dominguez-Bello, Maria Gloria; Carlton, Jane M

2016-01-01

In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. Downstream analysis was carried out in the QIIME pipeline, in conjunction with neighborhood metadata (ethnicity, population, age groups) from the NYC Open Data portal. Neither the 16S nor 18S rRNA datasets showed any clustering patterns related to geography or neighborhood demographics. Bacterial assemblages on ATM keypads were dominated by taxonomic groups known to be associated with human skin communities ( Actinobacteria , Bacteroides , Firmicutes , and Proteobacteria ), although SourceTracker analysis was unable to identify the source habitat for the majority of taxa. Eukaryotic assemblages were dominated by fungal taxa as well as by a low-diversity protist community containing both free-living and potentially pathogenic taxa ( Toxoplasma , Trichomonas ). Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes. IMPORTANCE Automated teller machine (ATM) keypads represent

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City

PubMed Central

Maritz, Julia M.; Luong, Albert

2016-01-01

ABSTRACT In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the “urban microbiome” may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. Downstream analysis was carried out in the QIIME pipeline, in conjunction with neighborhood metadata (ethnicity, population, age groups) from the NYC Open Data portal. Neither the 16S nor 18S rRNA datasets showed any clustering patterns related to geography or neighborhood demographics. Bacterial assemblages on ATM keypads were dominated by taxonomic groups known to be associated with human skin communities (Actinobacteria, Bacteroides, Firmicutes, and Proteobacteria), although SourceTracker analysis was unable to identify the source habitat for the majority of taxa. Eukaryotic assemblages were dominated by fungal taxa as well as by a low-diversity protist community containing both free-living and potentially pathogenic taxa (Toxoplasma, Trichomonas). Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes. IMPORTANCE Automated teller machine (ATM) keypads

Occurance of Staphylococcus nepalensis strains in different sources including human clinical material.

PubMed

Nováková, Dana; Pantůcek, Roman; Petrás, Petr; Koukalová, Dagmar; Sedlácek, Ivo

2006-10-01

Five isolates of coagulase-negative staphylococci were obtained from human urine, the gastrointestinal tract of squirrel monkeys, pig skin and from the environment. All key biochemical characteristics of the tested strains corresponded with the description of Staphylococcus xylosus species. However, partial 16S rRNA gene sequences obtained from analysed strains corresponded with those of Staphylococcus nepalensis reference strains, except for two strains which differed in one residue. Ribotyping with EcoRI and HindIII restriction enzymes, whole cell protein profile analysis performed by SDS-PAGE and SmaI macrorestriction analysis were used for more precise characterization and identification of the analysed strains. Obtained results showed that EcoRI and HindIII ribotyping and whole cell protein fingerprinting are suitable and reliable methods for the differentiation of S. nepalensis strains from the other novobiocin resistant staphylococci, whereas macrorestriction analysis was found to be a good tool for strain typing. The isolation of S. nepalensis is sporadic, and according to our best knowledge this study is the first report of the occurrence of this species in human clinical material as well as in other sources.

Detection of bacterial pathogens including potential new species in human head lice from Mali

PubMed Central

Amanzougaghene, Nadia; Fenollar, Florence; Sangaré, Abdoul Karim; Sissoko, Mahamadou S.; Doumbo, Ogobara K.; Raoult, Didier

2017-01-01

In poor African countries, where no medical and biological facilities are available, the identification of potential emerging pathogens of concern at an early stage is challenging. Head lice, Pediculus humanus capitis, have a short life, feed only on human blood and do not transmit pathogens to their progeny. They are, therefore, a perfect tool for the xenodiagnosis of current or recent human infection. This study assessed the occurrence of bacterial pathogens from head lice collected in two rural villages from Mali, where a high frequency of head lice infestation had previously been reported, using molecular methods. Results show that all 600 head lice, collected from 117 individuals, belonged to clade E, specific to West Africa. Bartonella quintana, the causative agent of trench fever, was identified in three of the 600 (0.5%) head lice studied. Our study also shows, for the first time, the presence of the DNA of two pathogenic bacteria, namely Coxiella burnetii (5.1%) and Rickettsia aeschlimannii (0.6%), detected in human head lice, as well as the DNA of potential new species from the Anaplasma and Ehrlichia genera of unknown pathogenicity. The finding of several Malian head lice infected with B. quintana, C. burnetii, R. aeschlimannii, Anaplasma and Ehrlichia is alarming and highlights the need for active survey programs to define the public health consequences of the detection of these emerging bacterial pathogens in human head lice. PMID:28931077

Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science.

PubMed

Tridico, Silvana R; Murray, Dáithí C; Addison, Jayne; Kirkbride, Kenneth P; Bunce, Michael

2014-01-01

Mammalian hairs are one of the most ubiquitous types of trace evidence collected in the course of forensic investigations. However, hairs that are naturally shed or that lack roots are problematic substrates for DNA profiling; these hair types often contain insufficient nuclear DNA to yield short tandem repeat (STR) profiles. Whilst there have been a number of initial investigations evaluating the value of metagenomics analyses for forensic applications (e.g. examination of computer keyboards), there have been no metagenomic evaluations of human hairs-a substrate commonly encountered during forensic practice. This present study attempts to address this forensic capability gap, by conducting a qualitative assessment into the applicability of metagenomic analyses of human scalp and pubic hair. Forty-two DNA extracts obtained from human scalp and pubic hairs generated a total of 79,766 reads, yielding 39,814 reads post control and abundance filtering. The results revealed the presence of unique combinations of microbial taxa that can enable discrimination between individuals and signature taxa indigenous to female pubic hairs. Microbial data from a single co-habiting couple added an extra dimension to the study by suggesting that metagenomic analyses might be of evidentiary value in sexual assault cases when other associative evidence is not present. Of all the data generated in this study, the next-generation sequencing (NGS) data generated from pubic hair held the most potential for forensic applications. Metagenomic analyses of human hairs may provide independent data to augment other forensic results and possibly provide association between victims of sexual assault and offender when other associative evidence is absent. Based on results garnered in the present study, we believe that with further development, bacterial profiling of hair will become a valuable addition to the forensic toolkit.

Application of Adverse Outcome Pathways (AOPs) in Human ...

EPA Pesticide Factsheets

The adverse outcome pathway (AOP) framework was developed to help organize and disseminate existing knowledge concerning the means through which specific perturbations of biological pathways can lead to adverse outcomes considered relevant to risk-based regulatory decision-making. Because many fundamental molecular and cellular pathways are conserved across taxa, data from assays that screen chemicals for their ability to interact with specific biomolecular targets can often be credibly applied to a broad range of species, even if the apical outcomes of those perturbations may differ. Information concerning the different trajectories of adversity that molecular initiating events may take in different taxa, life stages, and sexes of organisms can be captured in the form of an AOP network. As an example, AOPs documenting divergent consequences of thyroid peroxidase (TPO) and deiodinase (DIO) inhibition in mammals, amphibians, and fish have been developed. These AOPs provide the foundation for using data from common in vitro assays for TPO or DIO activity to inform both human health and ecological risk assessments. They also provide the foundation for an integrated approach to testing and assessment, where available information and biological understanding can be integrated in order to formulate plausible and testable hypotheses which can be used to target in vivo testing on the endpoints of greatest concern. Application of this AOP knowledge in several different r

Application of adverse outcome pathways (AOPs) in human ...

EPA Pesticide Factsheets

The adverse outcome pathway (AOP) framework was developed to help organize and disseminate existing knowledge concerning the means through which specific perturbations of biological pathways can lead to adverse outcomes considered relevant to risk-based regulatory decision-making. Because many fundamental molecular and cellular pathways are conserved across taxa, data from assays that screen chemicals for their ability to interact with specific biomolecular targets can often be credibly applied to a broad range of species, even if the apical outcomes of those perturbations may differ. Information concerning the different trajectories of adversity that molecular initiating events may take in different taxa, life stages, and sexes of organisms can be captured in the form of an AOP network. As an example, AOPs documenting divergent consequences of thyroid peroxidase (TPO) and deiodinase (DIO) inhibition in mammals, amphibians, and fish have been developed. These AOPs provide the foundation for using data from common in vitro assays for TPO or DIO activity to inform both human health and ecological risk assessments. They also provide the foundation for an integrated approach to testing and assessment, where available information and biological understanding can be integrated in order to formulate plausible and testable hypotheses which can be used to target in vivo testing on the endpoints of greatest concern. Application of this AOP knowledge in several different r

42 CFR 410.100 - Included services.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 2 2011-10-01 2011-10-01 false Included services. 410.100 Section 410.100 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES MEDICARE PROGRAM SUPPLEMENTARY MEDICAL INSURANCE (SMI) BENEFITS Comprehensive Outpatient Rehabilitation Facility (CORF) Services...

Genetic heterogeneity and phylogeny of Trichuris spp. from captive non-human primates based on ribosomal DNA sequence data.

PubMed

Cavallero, Serena; De Liberato, Claudio; Friedrich, Klaus G; Di Cave, David; Masella, Valentina; D'Amelio, Stefano; Berrilli, Federica

2015-08-01

Nematodes of the genus Trichuris, known as whipworms, are recognized to infect numerous mammalian species including humans and non-human primates. Several Trichuris spp. have been described and species designation/identification is traditionally based on host-affiliation, although cross-infection and hybridization events may complicate species boundaries. The main aims of the present study were to genetically characterize adult Trichuris specimens from captive Japanese macaques (Macaca fuscata) and grivets (Chlorocebus aethiops), using the ribosomal DNA (ITS) as molecular marker and to investigate the phylogeny and the extent of genetic variation also by comparison with data on isolates from other humans, non-human primates and other hosts. The phylogenetic analysis of Trichuris sequences from M. fuscata and C. aethiops provided evidences of distinct clades and subclades thus advocating the existence of additional separated taxa. Neighbor Joining and Bayesian trees suggest that specimens from M. fuscata may be distinct from, but related to Trichuris trichiura, while a close relationship is suggested between the subclade formed by the specimens from C. aethiops and the subclade formed by T. suis. The tendency to associate Trichuris sp. to host species can lead to misleading taxonomic interpretations (i.e. whipworms found in primates are identified as T. trichiura). The results here obtained confirm previous evidences suggesting the existence of Trichuris spp. other than T. trichiura infecting non-human living primates. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluating morphometric body mass prediction equations with a juvenile human test sample: accuracy and applicability to small-bodied hominins.

PubMed

Walker, Christopher S; Yapuncich, Gabriel S; Sridhar, Shilpa; Cameron, Noël; Churchill, Steven E

2018-02-01

Body mass is an ecologically and biomechanically important variable in the study of hominin biology. Regression equations derived from recent human samples allow for the reasonable prediction of body mass of later, more human-like, and generally larger hominins from hip joint dimensions, but potential differences in hip biomechanics across hominin taxa render their use questionable with some earlier taxa (i.e., Australopithecus spp.). Morphometric prediction equations using stature and bi-iliac breadth avoid this problem, but their applicability to early hominins, some of which differ in both size and proportions from modern adult humans, has not been demonstrated. Here we use mean stature, bi-iliac breadth, and body mass from a global sample of human juveniles ranging in age from 6 to 12 years (n = 530 age- and sex-specific group annual means from 33 countries/regions) to evaluate the accuracy of several published morphometric prediction equations when applied to small humans. Though the body proportions of modern human juveniles likely differ from those of small-bodied early hominins, human juveniles (like fossil hominins) often differ in size and proportions from adult human reference samples and, accordingly, serve as a useful model for assessing the robustness of morphometric prediction equations. Morphometric equations based on adults systematically underpredict body mass in the youngest age groups and moderately overpredict body mass in the older groups, which fall in the body size range of adult Australopithecus (∼26-46 kg). Differences in body proportions, notably the ratio of lower limb length to stature, influence predictive accuracy. Ontogenetic changes in these body proportions likely influence the shift in prediction error (from under- to overprediction). However, because morphometric equations are reasonably accurate when applied to this juvenile test sample, we argue these equations may be used to predict body mass in small-bodied hominins

Demonstrating an Approach for Including Pesticide Use in Life Cycle Assessment: Estimating Human and Ecosystem Toxicity of Pesticide Use in Midwest Corn Farming

EPA Science Inventory

Purpose This study demonstrates an approach to assess human health and ecotoxicity impacts of pesticide use by including multiple environmental pathways and various exposure routes using the case of corn grown for bio-based fuel or chemical production in US Midwestern states.Meth...

Demonstrating an approach for including pesticide use in life-cycle assessment: Estimating human and ecosystem toxicity of pesticide use in Midwest corn farming

EPA Science Inventory

PurposeThis study demonstrates an approach to assess human health and ecotoxicity impacts of pesticide use by including multiple environmental pathways and various exposure routes using the case of corn grown for bio-based fuel or chemical production in US Midwestern states.Metho...

42 CFR 441.520 - Included services.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 4 2014-10-01 2014-10-01 false Included services. 441.520 Section 441.520 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED... the following services: (1) Assistance with ADLs, IADLs, and health-related tasks through hands-on...

42 CFR 441.520 - Included services.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 4 2012-10-01 2012-10-01 false Included services. 441.520 Section 441.520 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED... the following services: (1) Assistance with ADLs, IADLs, and health-related tasks through hands-on...

42 CFR 441.520 - Included services.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 4 2013-10-01 2013-10-01 false Included services. 441.520 Section 441.520 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED... the following services: (1) Assistance with ADLs, IADLs, and health-related tasks through hands-on...

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.

Vegetation changes and human impact inferred from an oxbow lake in southwestern Amazonia, Brazil since the 19th century

NASA Astrophysics Data System (ADS)

Rodríguez-Zorro, Paula A.; Enters, Dirk; Hermanowski, Barbara; da Costa, Marcondes Lima; Behling, Hermann

2015-10-01

Pollen and X-ray fluorescence spectrometry (XRF) analyses from a 272 cm-long sediment core of Lago Amapá, an oxbow lake in western Amazonia, reveal the first palaeoecological investigation of late Holocene sediments in Acre state, Brazil. Radiocarbon dating of older sediments failed due to re-deposition of organic material but a historical map suggests that lacustrine deposition started at 1900 AD. We detected two periods of changes in sediment and vegetation, dominated by pioneer taxa especially Cecropia. The first period around 1900 AD is documenting an initial oxbow lake, with regular fluvial input (high Ti) and low accumulation of organic matter (low inc/coh ratio). During that period Andean pollen taxa originating from Peruvian Andean headwaters were deposited. A fully lacustrine phase started about 1950 AD and is characterized by prolonged periods of stagnant water (low Fe/Mn ratio). The increase of pioneer taxa, sedimentation rates and a reduction of most of the XRF element counts point to a period during which Lago Amapá was a more isolated lake which was flooded only during exceptional severe flood events and is catching mainly anthropogenic disturbances. The extensive human influence during this period was assumed by 1) the high occurrence of pioneer taxa and the absence of charcoal which could indicate changes in vegetation possibly as a result of logging, 2) the Ca and Ti/K ratio which reflect changes to a local sediment source, and 3) comparison of Landsat images from the last 30 years which shows broad changes in vegetation cover and land transformation in the peripheral areas of the oxbow lake.

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

Taxonomic synopsis of invasive and native Spartina (Poaceae, Chloridoideae) in the Pacific Northwest (British Columbia, Washington and Oregon), including the first report of Spartina ×townsendii for British Columbia, Canada

PubMed Central

Saarela, Jeffery M.

2012-01-01

Abstract Five species of the grass genus Spartina are invading salt marshes along the Pacific coast of North America, of which three have been documented in British Columbia, Canada, in only the last decade. A taxonomic synopsis of the two native (Spartina gracilis, Spartina pectinata) and five introduced Spartina taxa (Spartina anglica, Spartina alterniflora, Spartina densiflora, Spartina patens, Spartina ×townsendii) in the Pacific Northwest is presented to facilitate their identification, including nomenclature, a new taxonomic key, new descriptions for a subset of taxa, and representative specimens. Spartina ×townsendii is newly reported for the flora of British Columbia. The non-coastal species Spartina pectinata is reported from an urban site in British Columbia, the first confirmed report of the taxon for the province. Lectotypes are newly designated for Spartina anglica C.E. Hubb., Spartina maritima subvar. fallax St.-Yves, and Spartina cynosuroides f. major St.-Yves. PMID:22461730

Human T-cell leukemia virus type I Tax genotype analysis in Okinawa, the southernmost and remotest islands of Japan: Different distributions compared with mainland Japan and the potential value for the prognosis of aggressive adult T-cell leukemia/lymphoma.

PubMed

Sakihama, Shugo; Saito, Mineki; Kuba-Miyara, Megumi; Tomoyose, Takeaki; Taira, Naoya; Miyagi, Takashi; Hayashi, Masaki; Kinjo, Shigeko; Nakachi, Sawako; Tedokon, Iori; Nishi, Yukiko; Tamaki, Keita; Morichika, Kazuho; Uchihara, Jun-Nosuke; Morishima, Satoko; Karube, Ken-Nosuke; Tanaka, Yuetsu; Masuzaki, Hiroaki; Fukushima, Takuya

2017-10-01

Okinawa, comprising remote islands off the mainland of Japan, is an endemic area of human T-cell leukemia virus type I (HTLV-1), the causative virus of adult T-cell leukemia-lymphoma (ATL) and HTLV-1-associated myelopathy (HAM). We investigated the tax genotype of HTLV-1 among 29 HTLV-1 carriers, 74 ATL patients, and 33 HAM patients in Okinawa. The genotype distribution-60 (44%) taxA cases and 76 (56%) taxB cases-differed from that of a previous report from Kagoshima Prefecture in mainland Japan (taxA, 10%; taxB, 90%). A comparison of the clinical outcomes of 45 patients (taxA, 14; taxB, 31) with aggressive ATL revealed that the overall response and 1-year overall survival rates for taxA (50% and 35%, respectively) were lower than those for taxB (71% and 49%, respectively). In a multivariate analysis of two prognostic indices for aggressive ATL, Japan Clinical Oncology Group-Prognostic Index and Prognostic Index for acute and lymphoma ATL, with respect to age, performance status, corrected calcium, soluble interleukin-2 receptor, and tax genotype, the estimated hazard ratio of taxA compared with taxB was 2.68 (95% confidence interval, 0.87-8.25; P=0.086). Our results suggest that the tax genotype has clinical value as a prognostic factor for aggressive ATL. Copyright © 2017 Elsevier Ltd. All rights reserved.

Human dispersal into interior Alaska: antecedent conditions, mode of colonization, and adaptations

NASA Astrophysics Data System (ADS)

Yesner, David R.

2001-01-01

In spite of more than a half-century of exploration, no definitive evidence has yet come to light for human occupation in eastern Beringia preceding 12,000 yr BP. The oldest dates — between 11,500 and 12,000 yr BP — are from sites in interior and northern Alaska. Archaeological sites dating to this time period, such as the Broken Mammoth site in the central Tanana River Valley, have yielded evidence of pioneer colonization by groups with relatively little knowledge of lithic resources. Three possibly older cave sites — Bluefish Caves, Lime Hills Caves, and Trail Creek Caves — have stratigraphic and taphonomic problems that are not easily resolved. No sites in the glaciated coastal zone of southern Alaska are Pleistocene in date, and numerous objections can be raised to the viability of the coastal migration hypothesis, particularly in the western Gulf of Alaska region. For northern and interior Alaska, the earliest colonization appears to have been a "push-pull" phenomenon, linked to the dissolution of the Bering Land Bridge through a combination of rising sea levels and ameliorating climate. The climate of the "Birch-Poplar" rise in the terminal Pleistocene may have forced the extinction of obligate grazers such as mammoth and horse, but it seems to have favored other taxa such as bison and elk, at least until 9000 yr BP. Faunal data from the Broken Mammoth site in the central Tanana valley, with good organic preservation, demonstrate the utilization of a wide diversity of taxa, including small game, waterfowl, and fish. Faunal and sedimentological data give slight support to a Younger Dryas reversal, but this was dwarfed by the mid-Holocene period of dry, windy conditions during which interior Alaska may have been largely abandoned.

7 CFR 1437.303 - Aquaculture, including ornamental fish.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 10 2013-01-01 2013-01-01 false Aquaculture, including ornamental fish. 1437.303... ASSISTANCE PROGRAM Determining Coverage Using Value § 1437.303 Aquaculture, including ornamental fish. (a... human consumption as determined by CCC. (2) Fish raised as feed for other fish that are consumed by...

7 CFR 1437.303 - Aquaculture, including ornamental fish.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 10 2012-01-01 2012-01-01 false Aquaculture, including ornamental fish. 1437.303... ASSISTANCE PROGRAM Determining Coverage Using Value § 1437.303 Aquaculture, including ornamental fish. (a... human consumption as determined by CCC. (2) Fish raised as feed for other fish that are consumed by...

The biogeography of threatened insular iguanas and opportunities for invasive vertebrate management

USGS Publications Warehouse

Tershy, Bernie R.; Newton, Kelly M.; Spatz, Dena R.; Swinnerton, Kirsty; Iverson, John B.; Fisher, Robert N.; Harlow, Peter S.; Holmes, Nick D.; Croll, Donald A.; Iverson, J.B.; Grant, T. D.; Knapp, C. R.; Pasachnik, S. A.

2016-01-01

Iguanas are a particularly threatened group of reptiles, with 61% of species at risk of extinction. Primary threats to iguanas include habitat loss, direct and indirect impacts by invasive vertebrates, overexploitation, and human disturbance. As conspicuous, charismatic vertebrates, iguanas also represent excellent flagships for biodiversity conservation. To assist planning for invasive vertebrate management and thus benefit threatened iguana recovery, we identified all islands with known extant or extirpated populations of Critically Endangered and Endangered insular iguana taxa as recognized by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. For each island, we determined total area, sovereignty, the presence of invasive alien vertebrates, and human population. For the 23 taxa of threatened insular iguanas we identified 230 populations, of which iguanas were extant on 185 islands and extirpated from 45 islands. Twenty-one iguana taxa (91% of all threatened insular iguana taxa) occurred on at least one island with invasive vertebrates present; 16 taxa had 100% of their population(s) on islands with invasive vertebrates present. Rodents, cats, ungulates, and dogs were the most common invasive vertebrates. We discuss biosecurity, eradication, and control of invasive vertebrates to benefit iguana recovery: (1) on islands already free of invasive vertebrates; (2) on islands with high iguana endemicity; and (3) for species and subspecies with small total populations occurring across multiple small islands. Our analyses provide an important first step toward understanding how invasive vertebrate management can be planned effectively to benefit threatened insular iguanas.

Survey of hatching spines of bee larvae including those of apis mellifera (Hymenoptera: Apoidea)

USDA-ARS?s Scientific Manuscript database

This paper explores the occurrence of hatching spines among bee taxa and how these structures enable a larva on hatching to extricate itself from the egg chorion. These spines, arranged in a linear sequence along the sides of the first instar just dorsad to the spiracles, have been observed and reco...

Insights into the human oral microbiome.

PubMed

Verma, Digvijay; Garg, Pankaj Kumar; Dubey, Ashok Kumar

2018-05-01

Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.

Distinctions Among Circulating Antibody Secreting Cell Populations, Including B-1 Cells, in Human Adult Peripheral Blood1

PubMed Central

Quách, Tâm D.; Rodríguez-Zhurbenko, Nely; Hopkins, Thomas J.; Guo, Xiaoti; Vázquez, Ana María Hernández; Li, Wentian; Rothstein, Thomas L.

2015-01-01

Human antibody secreting cell (ASC) populations in circulation are not well studied. In addition to B-1 (CD20+CD27+CD38lo/intCD43+) cell and the conventional plasmablast (CD20-CD27hiCD38hi) cell populations, here we identified a novel B cell population termed 20+38hi B cells (CD20+CD27hiCD38hi) that spontaneously secretes antibody. At steady state, 20+38hi B cells are distinct from plasmablasts on the basis of CD20 expression, amount of antibody production, frequency of mutation, and diversity of B cell receptor repertoire. However, cytokine treatment of 20+38hi B cells induces loss of CD20 and acquisition of CD138, suggesting that 20+38hi B cells are precursors to plasmablasts, or pre-plasmablasts. We then evaluated similarities and differences between CD20+CD27+CD38lo/intCD43+ B-1 cells, CD20+CD27hiCD38hi 20+38hi B cells, CD20-CD27hiCD38hi plasmablasts, and CD20+CD27+CD38lo/intCD43- memory B cells. We found that B-1 cells differ from 20+38hi B cells and plasmablasts in numbers of ways, including antigen expression, morphological appearance, transcriptional profiling, antibody skewing, antibody repertoire, and secretory response to stimulation. In terms of gene expression, B-1 cells align more closely with memory B cells than with 20+38hi B cells or plasmablasts, but differ in that memory B cells do not express antibody secretion related genes. We found that, B-1 cell antibodies utilize Vh4-34, which is often associated with autoreactivity, 3 to 6-fold more often than other B cell populations. Along with selective production of IgM anti-PC, this data suggests that human B-1 cells might be preferentially selected for autoreactivity/natural-specificity. In sum, our results indicate that human healthy adult peripheral blood at steady state consists of 3 distinct ASC populations. PMID:26740107

Factors that contribute to biomarker responses in humans including a study in individuals taking Vitamin C supplementation.

PubMed

Anderson, D

2001-09-01

It is possible in many situations to identify humans exposed to potentially toxic materials in the workplace and in the environment. As in most human studies, there tends to be a high degree of interindividual variability in response to chemical insults. Some non-exposed control individuals exhibit as high a level of damage as some exposed individuals and some of these have levels of damage as low as many of the controls. Thus, it is only the mean values of the groups that can substantiate an exposure-related problem; the data on an individual basis are still of limited use. While human lymphocytes remain the most popular cell type for monitoring purposes, sperm, buccal, nasal, epithelial and placental cells are also used. However, for interpretation of responses, the issue of confounding factors must be addressed. There are endogenous confounding factors, such as age, gender, and genetic make-up and exogenous ones, including lifestyle habits (smoking, drinking, etc.) There are biomarkers of exposure, effect/response and susceptibility and the last may be influenced by the genotype and polymorphism genes existing in a population. From our own studies, confounding effects on cytogenetic damage and ras oncoproteins will be considered in relation to workers exposed to vinyl chloride and petroleum emissions and to volunteers taking Vitamin C supplementation. Smoking history, exposure and duration of employment affected the worker studies. For petroleum emissions, so did gender and season of exposure. For the non-smoking volunteer Vitamin C supplementation study, cholesterol levels, plasma Vitamin C levels, lipid peroxidation products and DNA damage in the Comet assay were also measured. Gender affected differences in Vitamin C levels, antioxidant capacity and the number of chromosome aberrations induced by bleomycin challenge in vitro. The results were the same for both high and low cholesterol subjects. The relationship between biomarkers and the various factors which

PXR (NR1I2): splice variants in human tissues, including brain, and identification of neurosteroids and nicotine as PXR activators.

PubMed

Lamba, Vishal; Yasuda, Kazuto; Lamba, Jatinder K; Assem, Mahfoud; Davila, Julio; Strom, Stephen; Schuetz, Erin G

2004-09-15

To gain insight on the expression of pregnane X receptor (PXR), we analyzed PXR.1 and PXR alternatively spliced transcripts in a panel of 36 human tissues. PXR.1 was expressed in many more tissues than previously determined, including human bone marrow and select regions of the human brain. In each of these tissues, we observed alternative splicing of various exons of PXR that generated multiple distinct PXR isoforms. The most abundant PXR alternative mRNA transcripts lacked 111 nucleotides, deleting 37 amino acids from the PXR LBD (PXR.2), or lacked 123 nt, deleting 41 amino acids from the PXR LBD (PXR.3). CYP3A4, a gene transcriptionally regulated by PXR, showed incomplete overlap with PXR in its tissue distribution. Quantitation of PXR mRNAs in human liver demonstrated that PXR.2 and PXR.3 represented 6.7% and 0.32% of total PXR mRNA transcripts. Brain expression of PXR prompted analysis of whether some brain acting chemicals were PXR ligands. The neurosteroids allopregnanolone and pregnanolone activated PXR and induced transcription of a CYP3A4-luciferase reporter. Nicotine, the psychoactive and addictive chemical in cigarettes, and a known inducer of brain CYP2B6, was an efficacious activator of PXR and inducer of CYP3A4 transcription. Because nicotine activation of PXR will enhance metabolism of nicotine to the non-psychoactive cotinine, these results provide one molecular mechanism for the development of tolerance to nicotine. Moreover, the identification of PXR in many human tissues, such as brain, and activation by tissue specific ligands (such as neurosteroids) suggests additional biological roles for this receptor in these tissues.

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.

Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data.

PubMed

Matzke, Nicholas J; Irmis, Randall B

2018-01-01

Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, only shared derived characters (synapomorphies) provide grouping information, so many character matrices have an ascertainment bias: they omit autapomorphies (unique derived character states), which are considered uninformative. There has been no study of the effect of this ascertainment bias in tip-dating, but autapomorphies can be informative in model-based inference. We expected that excluding autapomorphies would shorten the morphological branchlengths of terminal branches, and thus bias downwards the time branchlengths inferred in tip-dating. We tested for this effect using a matrix for Carboniferous-Permian eureptiles where all autapomorphies had been deliberately coded. Surprisingly, date estimates are virtually unchanged when autapomorphies are excluded, although we find large changes in morphological rate estimates and small effects on topological and dating confidence. We hypothesized that the puzzling lack of effect on dating was caused by the non-clock nature of the eureptile data. We confirm this explanation by simulating strict clock and non-clock datasets, showing that autapomorphy exclusion biases dating only for the clocklike case. A theoretical solution to ascertainment bias is computing the ascertainment bias correction (M k parsinf ), but we explore this correction in detail, and show that it is computationally impractical for typical datasets with many character states and taxa. Therefore we recommend that palaeontologists collect autapomorphies whenever possible when assembling character matrices.

Can Chimpanzee Biology Highlight Human Origin and Evolution?

PubMed Central

Roffman, Itai; Nevo, Eviatar

2010-01-01

The closest living relatives of humans are their chimpanzee/bonobo (Pan) sister species, members of the same subfamily “Homininae”. This classification is supported by over 50 years of research in the fields of chimpanzee cultural diversity, language competency, genomics, anatomy, high cognition, psychology, society, self-consciousness and relation to others, tool use/production, as well as Homo level emotions, symbolic competency, memory recollection, complex multifaceted problem-solving capabilities, and interspecies communication. Language competence and symbolism can be continuously bridged from chimpanzee to man. Emotions, intercommunity aggression, body language, gestures, facial expressions, and vocalization of intonations seem to parallel between the sister taxa Homo and Pan. The shared suite of traits between Pan and Homo genus demonstrated in this article integrates old and new information on human–chimpanzee evolution, bilateral informational and cross-cultural exchange, promoting the urgent need for Pan cultures in the wild to be protected, as they are part of the cultural heritage of mankind. Also, we suggest that bonobos, Pan paniscus, based on shared traits with Australopithecus, need to be included in Australopithecine’s subgenus, and may even represent living-fossil Australopithecines. Unfolding bonobo and chimpanzee biology highlights our common genetic and cultural evolutionary origins. PMID:23908781

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.

Evolutionary diversity of bile salts in reptiles and mammals, including analysis of ancient human and extinct giant ground sloth coprolites

PubMed Central

2010-01-01

Background Bile salts are the major end-metabolites of cholesterol and are also important in lipid and protein digestion and in influencing the intestinal microflora. We greatly extend prior surveys of bile salt diversity in both reptiles and mammals, including analysis of 8,000 year old human coprolites and coprolites from the extinct Shasta ground sloth (Nothrotherium shastense). Results While there is significant variation of bile salts across species, bile salt profiles are generally stable within families and often within orders of reptiles and mammals, and do not directly correlate with differences in diet. The variation of bile salts generally accords with current molecular phylogenies of reptiles and mammals, including more recent groupings of squamate reptiles. For mammals, the most unusual finding was that the Paenungulates (elephants, manatees, and the rock hyrax) have a very different bile salt profile from the Rufous sengi and South American aardvark, two other mammals classified with Paenungulates in the cohort Afrotheria in molecular phylogenies. Analyses of the approximately 8,000 year old human coprolites yielded a bile salt profile very similar to that found in modern human feces. Analysis of the Shasta ground sloth coprolites (approximately 12,000 years old) showed the predominant presence of glycine-conjugated bile acids, similar to analyses of bile and feces of living sloths, in addition to a complex mixture of plant sterols and stanols expected from an herbivorous diet. Conclusions The bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution, with some bile salt modifications only found within single groups such as marsupials. Analysis of the evolution of bile salt structures in different species provides a potentially rich model system for the evolution of a complex biochemical pathway in vertebrates. Our results also demonstrate the stability of bile salts in coprolites preserved in arid climates

Risk Factors for Breast Cancer, Including Occupational Exposures

PubMed Central

Meo, Margrethe; Vainio, Harri

2011-01-01

The knowledge on the etiology of breast cancer has advanced substantially in recent years, and several etiological factors are now firmly established. However, very few new discoveries have been made in relation to occupational risk factors. The International Agency for Research on Cancer has evaluated over 900 different exposures or agents to-date to determine whether they are carcinogenic to humans. These evaluations are published as a series of Monographs (www.iarc.fr). For breast cancer the following substances have been classified as "carcinogenic to humans" (Group 1): alcoholic beverages, exposure to diethylstilbestrol, estrogen-progestogen contraceptives, estrogen-progestogen hormone replacement therapy and exposure to X-radiation and gamma-radiation (in special populations such as atomic bomb survivors, medical patients, and in-utero exposure). Ethylene oxide is also classified as a Group 1 carcinogen, although the evidence for carcinogenicity in epidemiologic studies, and specifically for the human breast, is limited. The classification "probably carcinogenic to humans" (Group 2A) includes estrogen hormone replacement therapy, tobacco smoking, and shift work involving circadian disruption, including work as a flight attendant. If the association between shift work and breast cancer, the most common female cancer, is confirmed, shift work could become the leading cause of occupational cancer in women. PMID:22953181

Pathogen Transmission from Humans to Great Apes is a Growing Threat to Primate Conservation.

PubMed

Dunay, Emily; Apakupakul, Kathleen; Leard, Stephen; Palmer, Jamie L; Deem, Sharon L

2018-01-23

All six great ape species are listed as endangered or critically endangered by the IUCN and experiencing decreasing population trends. One of the threats to these non-human primates is the transmission of pathogens from humans. We conducted a literature review on occurrences of pathogen transmission from humans to great apes to highlight this often underappreciated issue. In total, we found 33 individual occurrences of probable or confirmed pathogen transmission from humans to great apes: 23 involved both pathogen and disease transmission, 7 pathogen transmission only, 2 positive antibody titers to zoonotic pathogens, and 1 pathogen transmission with probable disease. Great ape populations were categorized into captive, semi-free-living, and free-living conditions. The majority of occurrences involved chimpanzees (Pan troglodytes) (n = 23) or mountain gorillas (Gorilla beringei beringei) (n = 8). These findings have implications for conservation efforts and management of endangered great ape populations. Future efforts should focus on monitoring and addressing zoonotic pathogen and disease transmission between humans, great ape species, and other taxa to ensure the health of humans, wild and domestic animals, and the ecosystems we share.

40 CFR 262.102 - What special definitions are included in this subpart?

Code of Federal Regulations, 2011 CFR

2011-07-01

... implementation of the Environmental Management Plan as measured against policy, objectives and targets... potential hazards to human health or the environment and which must include RCRA “P” wastes, and may include... work practices that both protect human health and the environment from the hazards presented by...

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

Disentangling the relative effects of bushmeat availability on human nutrition in central Africa.

PubMed

Fa, John E; Olivero, Jesús; Real, Raimundo; Farfán, Miguel A; Márquez, Ana L; Vargas, J Mario; Ziegler, Stefan; Wegmann, Martin; Brown, David; Margetts, Barrie; Nasi, Robert

2015-02-02

We studied links between human malnutrition and wild meat availability within the Rainforest Biotic Zone in central Africa. We distinguished two distinct hunted mammalian diversity distributions, one in the rainforest areas (Deep Rainforest Diversity, DRD) containing taxa of lower hunting sustainability, the other in the northern rainforest-savanna mosaic, with species of greater hunting potential (Marginal Rainforest Diversity, MRD). Wild meat availability, assessed by standing crop mammalian biomass, was greater in MRD than in DRD areas. Predicted bushmeat extraction was also higher in MRD areas. Despite this, stunting of children, a measure of human malnutrition, was greater in MRD areas. Structural equation modeling identified that, in MRD areas, mammal diversity fell away from urban areas, but proximity to these positively influenced higher stunting incidence. In DRD areas, remoteness and distance from dense human settlements and infrastructures explained lower stunting levels. Moreover, stunting was higher away from protected areas. Our results suggest that in MRD areas, forest wildlife rational use for better human nutrition is possible. By contrast, the relatively low human populations in DRD areas currently offer abundant opportunities for the continued protection of more vulnerable mammals and allow dietary needs of local populations to be met.

Disentangling the relative effects of bushmeat availability on human nutrition in central Africa

NASA Astrophysics Data System (ADS)

Fa, John E.; Olivero, Jesús; Real, Raimundo; Farfán, Miguel A.; Márquez, Ana L.; Vargas, J. Mario; Ziegler, Stefan; Wegmann, Martin; Brown, David; Margetts, Barrie; Nasi, Robert

2015-02-01

We studied links between human malnutrition and wild meat availability within the Rainforest Biotic Zone in central Africa. We distinguished two distinct hunted mammalian diversity distributions, one in the rainforest areas (Deep Rainforest Diversity, DRD) containing taxa of lower hunting sustainability, the other in the northern rainforest-savanna mosaic, with species of greater hunting potential (Marginal Rainforest Diversity, MRD). Wild meat availability, assessed by standing crop mammalian biomass, was greater in MRD than in DRD areas. Predicted bushmeat extraction was also higher in MRD areas. Despite this, stunting of children, a measure of human malnutrition, was greater in MRD areas. Structural equation modeling identified that, in MRD areas, mammal diversity fell away from urban areas, but proximity to these positively influenced higher stunting incidence. In DRD areas, remoteness and distance from dense human settlements and infrastructures explained lower stunting levels. Moreover, stunting was higher away from protected areas. Our results suggest that in MRD areas, forest wildlife rational use for better human nutrition is possible. By contrast, the relatively low human populations in DRD areas currently offer abundant opportunities for the continued protection of more vulnerable mammals and allow dietary needs of local populations to be met.

45 CFR 1308.11 - Eligibility criteria: Hearing impairment including deafness.

Code of Federal Regulations, 2010 CFR

2010-10-01

... hearing loss can include impaired listening skills, delayed language development, and articulation... OF HUMAN DEVELOPMENT SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES THE ADMINISTRATION FOR... frequently, and receive speech, language or hearing services as indicated by the IEPs. As soon as special...

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

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.

Monkeys perform as well as apes and humans in a size discrimination task.

PubMed

Schmitt, Vanessa; Kröger, Iris; Zinner, Dietmar; Call, Josep; Fischer, Julia

2013-09-01

Whether the cognitive competences of monkeys and apes are rather similar or whether the larger-brained apes outperform monkeys in cognitive experiments is a highly debated topic. Direct comparative analyses are therefore essential to examine similarities and differences among species. We here compared six primate species, including humans, chimpanzees, bonobos, gorillas (great apes), olive baboons, and long-tailed macaques (Old World monkeys) in a task on fine-grained size discrimination. Except for gorillas, subjects of all taxa (i.e. humans, apes, and monkeys) were able to discriminate three-dimensional cubes with a volume difference of only 10 % (i.e. cubes of 50 and 48 mm side length) and performed only slightly worse when the cubes were presented successively. The minimal size discriminated declined further with increasing time delay between presentations of the cubes, highlighting the difficulty to memorize exact size differences. The results suggest that differences in brain size, as a proxy for general cognitive abilities, did not account for variation in performance, but that differential socio-ecological pressures may better explain species differences. Our study highlights the fact that differences in cognitive abilities do not always map neatly onto phylogenetic relationships and that in a number of cognitive experiments monkeys do not fare significantly worse than apes, casting doubt on the assumption that larger brains per se confer an advantage in such kinds of tests.

Intraspecific eye color variability in birds and mammals: a recent evolutionary event exclusive to humans and domestic animals.

PubMed

Negro, Juan J; Carmen Blázquez, M; Galván, Ismael

2017-01-01

Human populations and breeds of domestic animals are composed of individuals with a multiplicity of eye (= iris) colorations. Some wild birds and mammals may have intraspecific eye color variability, but this variation seems to be due to the developmental stage of the individual, its breeding status, and/or sexual dimorphism. In other words, eye colour tends to be a species-specific trait in wild animals, and the exceptions are species in which individuals of the same age group or gender all develop the same eye colour. Domestic animals, by definition, include bird and mammal species artificially selected by humans in the last few thousand years. Humans themselves may have acquired a diverse palette of eye colors, likewise in recent evolutionary time, in the Mesolithic or in the Upper Paleolithic. We posit two previously unrecognized hypotheses regarding eye color variation: 1) eye coloration in wild animals of every species tends to be a fixed trait. 2) Humans and domestic animal populations, on the contrary, have eyes of multiple colors. Sexual selection has been invoked for eye color variation in humans, but this selection mode does not easily apply in domestic animals, where matings are controlled by the human breeder. Eye coloration is polygenic in humans. We wish to investigate the genetics of eye color in other animals, as well as the ecological correlates. Investigating the origin and function of eye colors will shed light on the reason why some species may have either light-colored irises (e.g., white, yellow or light blue) or dark ones (dark red, brown or black). The causes behind the vast array of eye colors across taxa have never been thoroughly investigated, but it may well be that all Darwinian selection processes are at work: sexual selection in humans, artificial selection for domestic animals, and natural selection (mainly) for wild animals.

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.

Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans.

PubMed

Sanapareddy, Nina; Legge, Ryan M; Jovov, Biljana; McCoy, Amber; Burcal, Lauren; Araujo-Perez, Felix; Randall, Thomas A; Galanko, Joseph; Benson, Andrew; Sandler, Robert S; Rawls, John F; Abdo, Zaid; Fodor, Anthony A; Keku, Temitope O

2012-10-01

Differences in the composition of the gut microbial community have been associated with diseases such as obesity, Crohn's disease, ulcerative colitis and colorectal cancer (CRC). We used 454 titanium pyrosequencing of the V1-V2 region of the 16S rRNA gene to characterize adherent bacterial communities in mucosal biopsy samples from 33 subjects with adenomas and 38 subjects without adenomas (controls). Biopsy samples from subjects with adenomas had greater numbers of bacteria from 87 taxa than controls; only 5 taxa were more abundant in control samples. The magnitude of the differences in the distal gut microbiota between patients with adenomas and controls was more pronounced than that of any other clinical parameters including obesity, diet or family history of CRC. This suggests that sequence analysis of the microbiota could be used to identify patients at risk for developing adenomas.

NATO Human View Architecture and Human Networks

NASA Technical Reports Server (NTRS)

Handley, Holly A. H.; Houston, Nancy P.

2010-01-01

The NATO Human View is a system architectural viewpoint that focuses on the human as part of a system. Its purpose is to capture the human requirements and to inform on how the human impacts the system design. The viewpoint contains seven static models that include different aspects of the human element, such as roles, tasks, constraints, training and metrics. It also includes a Human Dynamics component to perform simulations of the human system under design. One of the static models, termed Human Networks, focuses on the human-to-human communication patterns that occur as a result of ad hoc or deliberate team formation, especially teams distributed across space and time. Parameters of human teams that effect system performance can be captured in this model. Human centered aspects of networks, such as differences in operational tempo (sense of urgency), priorities (common goal), and team history (knowledge of the other team members), can be incorporated. The information captured in the Human Network static model can then be included in the Human Dynamics component so that the impact of distributed teams is represented in the simulation. As the NATO militaries transform to a more networked force, the Human View architecture is an important tool that can be used to make recommendations on the proper mix of technological innovations and human interactions.

DNA barcoding of human-biting black flies (Diptera: Simuliidae) in Thailand.

PubMed

Pramual, Pairot; Thaijarern, Jiraporn; Wongpakam, Komgrit

2016-12-01

Black flies (Diptera: Simuliidae) are important insect vectors and pests of humans and animals. Accurate identification, therefore, is important for control and management. In this study, we used mitochondrial cytochrome oxidase I (COI) barcoding sequences to test the efficiency of species identification for the human-biting black flies in Thailand. We used human-biting specimens because they enabled us to link information with previous studies involving the immature stages. Three black fly taxa, Simulium nodosum, S. nigrogilvum and S. doipuiense complex, were collected. The S. doipuiense complex was confirmed for the first time as having human-biting habits. The COI sequences revealed considerable genetic diversity in all three species. Comparisons to a COI sequence library of black flies in Thailand and in a public database indicated a high efficiency for specimen identification for S. nodosum and S. nigrogilvum, but this method was not successful for the S. doipuiense complex. Phylogenetic analyses revealed two divergent lineages in the S. doipuiense complex. Human-biting specimens formed a separate clade from other members of this complex. The results are consistent with the Barcoding Index Number System (BINs) analysis that found six BINs in the S. doipuiense complex. Further taxonomic work is needed to clarify the species status of these human-biting specimens. Copyright © 2016 Elsevier B.V. All rights reserved.

Human population, grasshopper and plant species richness in European countries

NASA Astrophysics Data System (ADS)

Steck, Claude E.; Pautasso, Marco

2008-11-01

Surprisingly, several studies over large scales have reported a positive spatial correlation of people and biodiversity. This pattern has important implications for conservation and has been documented for well studied taxa such as plants, amphibians, reptiles, birds and mammals. However, it is unknown whether the pattern applies also to invertebrates other than butterflies and more work is needed to establish whether the species-people relationship is explained by both variables correlating with other environmental factors. We studied whether grasshopper species richness (Orthoptera, suborder Caelifera) is related to human population size in European countries. As expected, the number of Caelifera species increases significantly with increasing human population size. But this is not the case when controlling for country area, latitude and number of plant species. Variations in Caelifera species richness are primarily associated with variations in plant species richness. Caelifera species richness also increases with decreasing mean annual precipitation, Gross Domestic Product per capita (used as an indicator for economic development) and net fertility rate of the human population. Our analysis confirms the hypothesis that the broad-scale human population-biodiversity correlations can be explained by concurrent variations in factors other than human population size such as plant species richness, environmental productivity, or habitat heterogeneity. Nonetheless, more populated countries in Europe still have more Caelifera species than less populated countries and this poses a particular challenge for conservation.

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.

Microsatellite polymorphisms associated with human behavioural and psychological phenotypes including a gene-environment interaction.

PubMed

Bagshaw, Andrew T M; Horwood, L John; Fergusson, David M; Gemmell, Neil J; Kennedy, Martin A

2017-02-03

The genetic and environmental influences on human personality and behaviour are a complex matter of ongoing debate. Accumulating evidence indicates that short tandem repeats (STRs) in regulatory regions are good candidates to explain heritability not accessed by genome-wide association studies. We tested for associations between the genotypes of four selected repeats and 18 traits relating to personality, behaviour, cognitive ability and mental health in a well-studied longitudinal birth cohort (n = 458-589) using one way analysis of variance. The repeats were a highly conserved poly-AC microsatellite in the upstream promoter region of the T-box brain 1 (TBR1) gene and three previously studied STRs in the activating enhancer-binding protein 2-beta (AP2-β) and androgen receptor (AR) genes. Where significance was found we used multiple regression to assess the influence of confounding factors. Carriers of the shorter, most common, allele of the AR gene's GGN microsatellite polymorphism had fewer anxiety-related symptoms, which was consistent with previous studies, but in our study this was not significant following Bonferroni correction. No associations with two repeats in the AP2-β gene withstood this correction. A novel finding was that carriers of the minor allele of the TBR1 AC microsatellite were at higher risk of conduct problems in childhood at age 7-9 (p = 0.0007, which did pass Bonferroni correction). Including maternal smoking during pregnancy (MSDP) in models controlling for potentially confounding influences showed that an interaction between TBR1 genotype and MSDP was a significant predictor of conduct problems in childhood and adolescence (p < 0.001), and of self-reported criminal behaviour up to age 25 years (p ≤ 0.02). This interaction remained significant after controlling for possible confounders including maternal age at birth, socio-economic status and education, and offspring birth weight. The potential functional importance

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.

Actinomyces and related organisms in human infections.

PubMed

Könönen, Eija; Wade, William G

2015-04-01

Actinomyces israelii has long been recognized as a causative agent of actinomycosis. During the past 3 decades, a large number of novel Actinomyces species have been described. Their detection and identification in clinical microbiology laboratories and recognition as pathogens in clinical settings can be challenging. With the introduction of advanced molecular methods, knowledge about their clinical relevance is gradually increasing, and the spectrum of diseases associated with Actinomyces and Actinomyces-like organisms is widening accordingly; for example, Actinomyces meyeri, Actinomyces neuii, and Actinomyces turicensis as well as Actinotignum (formerly Actinobaculum) schaalii are emerging as important causes of specific infections at various body sites. In the present review, we have gathered this information to provide a comprehensive and microbiologically consistent overview of the significance of Actinomyces and some closely related taxa in human infections. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Actinomyces and Related Organisms in Human Infections

PubMed Central

Wade, William G.

2015-01-01

SUMMARY Actinomyces israelii has long been recognized as a causative agent of actinomycosis. During the past 3 decades, a large number of novel Actinomyces species have been described. Their detection and identification in clinical microbiology laboratories and recognition as pathogens in clinical settings can be challenging. With the introduction of advanced molecular methods, knowledge about their clinical relevance is gradually increasing, and the spectrum of diseases associated with Actinomyces and Actinomyces-like organisms is widening accordingly; for example, Actinomyces meyeri, Actinomyces neuii, and Actinomyces turicensis as well as Actinotignum (formerly Actinobaculum) schaalii are emerging as important causes of specific infections at various body sites. In the present review, we have gathered this information to provide a comprehensive and microbiologically consistent overview of the significance of Actinomyces and some closely related taxa in human infections. PMID:25788515

Neandertal versus Modern Human Dietary Responses to Climatic Fluctuations

PubMed Central

El Zaatari, Sireen; Grine, Frederick E.; Ungar, Peter S.; Hublin, Jean-Jacques

2016-01-01

The Neandertal lineage developed successfully throughout western Eurasia and effectively survived the harsh and severely changing environments of the alternating glacial/interglacial cycles from the middle of the Pleistocene until Marine Isotope Stage 3. Yet, towards the end of this stage, at the time of deteriorating climatic conditions that eventually led to the Last Glacial Maximum, and soon after modern humans entered western Eurasia, the Neandertals disappeared. Western Eurasia was by then exclusively occupied by modern humans. We use occlusal molar microwear texture analysis to examine aspects of diet in western Eurasian Paleolithic hominins in relation to fluctuations in food supplies that resulted from the oscillating climatic conditions of the Pleistocene. There is demonstrable evidence for differences in behavior that distinguish Upper Paleolithic humans from members of the Neandertal lineage. Specifically, whereas the Neandertals altered their diets in response to changing paleoecological conditions, the diets of Upper Paleolithic humans seem to have been less affected by slight changes in vegetation/climatic conditions but were linked to changes in their technological complexes. The results of this study also indicate differences in resource exploitation strategies between these two hominin groups. We argue that these differences in subsistence strategies, if they had already been established at the time of the first contact between these two hominin taxa, may have given modern humans an advantage over the Neandertals, and may have contributed to the persistence of our species despite habitat-related changes in food availabilities associated with climate fluctuations. PMID:27119336

Neandertal versus Modern Human Dietary Responses to Climatic Fluctuations.

PubMed

El Zaatari, Sireen; Grine, Frederick E; Ungar, Peter S; Hublin, Jean-Jacques

2016-01-01

The Neandertal lineage developed successfully throughout western Eurasia and effectively survived the harsh and severely changing environments of the alternating glacial/interglacial cycles from the middle of the Pleistocene until Marine Isotope Stage 3. Yet, towards the end of this stage, at the time of deteriorating climatic conditions that eventually led to the Last Glacial Maximum, and soon after modern humans entered western Eurasia, the Neandertals disappeared. Western Eurasia was by then exclusively occupied by modern humans. We use occlusal molar microwear texture analysis to examine aspects of diet in western Eurasian Paleolithic hominins in relation to fluctuations in food supplies that resulted from the oscillating climatic conditions of the Pleistocene. There is demonstrable evidence for differences in behavior that distinguish Upper Paleolithic humans from members of the Neandertal lineage. Specifically, whereas the Neandertals altered their diets in response to changing paleoecological conditions, the diets of Upper Paleolithic humans seem to have been less affected by slight changes in vegetation/climatic conditions but were linked to changes in their technological complexes. The results of this study also indicate differences in resource exploitation strategies between these two hominin groups. We argue that these differences in subsistence strategies, if they had already been established at the time of the first contact between these two hominin taxa, may have given modern humans an advantage over the Neandertals, and may have contributed to the persistence of our species despite habitat-related changes in food availabilities associated with climate fluctuations.

Species of Phaeoacremonium Associated with Infections in Humans and Environmental Reservoirs in Infected Woody Plants

PubMed Central

Mostert, Lizel; Groenewald, Johannes Z.; Summerbell, Richard C.; Robert, Vincent; Sutton, Deanna A.; Padhye, Arvind A.; Crous, Pedro W.

2005-01-01

To date, three species of Phaeoacremonium have been associated with phaeohyphomycosis. These are P. parasiticum (formerly Phialophora parasitica), P. inflatipes, and P. rubrigenum. Numerous unknown isolates resembling Phaeoacremonium spp. have in recent years been isolated from human patients as well as from woody plants that appear to be the main environmental source of these fungi. Nine new Phaeoacremonium species, of which six were obtained as etiologic agents of human opportunistic infection, are reported. They can be identified based on their cultural and morphological characters, and the identifications are strongly supported in phylogenetic analyses of partial sequences of the actin, β-tubulin, and calmodulin genes. A multiple-entry electronic key based on morphological, cultural, and β-tubulin sequence data was developed to facilitate routine species identification. Reexamination of all isolates of P. inflatipes associated with human disease showed them to be misidentified and to belong to the new taxa described here. PMID:15814996

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

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.

Value of the small cohort study including a physical examination for minor structural defects in identifying new human teratogens.

PubMed

Chambers, Christina D

2011-03-01

Most known human teratogens are associated with a unique or characteristic pattern of major and minor malformations and this pattern helps to establish the causal link between the teratogenic exposure and the outcome. Although traditional case-control and cohort study designs can help identify potential teratogens, there is an important role for small cohort studies that include a dysmorphological examination of exposed and unexposed infants for minor structural defects. In combination with other study design approaches, the small cohort study with a specialized physical examination fulfills a necessary function in screening for new potential teratogens and can help to better delineate the spectrum and magnitude of risk for known teratogens. © 2011 The Author. Congenital Anomalies © 2011 Japanese Teratology Society.

A wide diversity of bacteria from the human gut produces and degrades biogenic amines.

PubMed

Pugin, Benoit; Barcik, Weronika; Westermann, Patrick; Heider, Anja; Wawrzyniak, Marcin; Hellings, Peter; Akdis, Cezmi A; O'Mahony, Liam

2017-01-01

Background : Biogenic amines (BAs) are metabolites produced by the decarboxylation of amino acids with significant physiological functions in eukaryotic and prokaryotic cells. BAs can be produced by bacteria in fermented foods, but little is known concerning the potential for microbes within the human gut microbiota to produce or degrade BAs. Objective : To isolate and identify BA-producing and BA-degrading microbes from the human gastrointestinal tract. Design : Fecal samples from human volunteers were screened on multiple growth media, under multiple growth conditions. Bacterial species were identified using 16S rRNA sequencing and BA production or degradation was assessed using ultra-performance liquid chromatography. Results : In total, 74 BA-producing or BA-degrading strains were isolated from the human gut. These isolates belong to the genera Bifidobacterium , Clostridium , Enterococcus , Lactobacillus , Pediococcus , Streptococcus , Enterobacter , Escherichia , Klebsiella , Morganella and Proteus . While differences in production or degradation of specific BAs were observed at the strain level, our results suggest that these metabolic activities are widely spread across different taxa present within the human gut microbiota. Conclusions : The isolation and identification of microbes from the human gut with BA-producing and BA-degrading metabolic activity is an important first step in developing a better understanding of how these metabolites influence health and disease.

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.

Human milk: mother nature's prototypical probiotic food?

PubMed

McGuire, Michelle K; McGuire, Mark A

2015-01-01

The concept of "probiotic" is generally attributed to Dr. Ilya Mechnikov, who hypothesized that longevity could be enhanced by manipulating gastrointestinal microbes using naturally fermented foods. In 2001, a report of the FAO and WHO (2001 Oct, http://www.who.int/foodsafety/publications/fs_-management/en/probiotics.pdf) proposed a more restrictive definition of probiotic, as follows: "a live micro-organism which, when administered in adequate amounts, confers a health benefit on the host." As such, answering the fundamental question posed here-"Is human milk a probiotic?"-requires first grappling with the concept and meaning of the term probiotic. Nonetheless, one must also be convinced that human milk contains bacteria. Indeed, there are scores of publications providing evidence of a paradigm shift in this regard. Variation in the human-milk microbiome may be associated with maternal weight, mode of delivery, lactation state, gestation age, antibiotic use, and maternal health. Milk constituents (e.g., fatty acids and complex carbohydrates) might also be related to the abundance of specific bacterial taxa in milk. Whether these bacteria affect infant health is likely, but more studies are needed to test this hypothesis. In summary, a growing literature suggests that human milk, like all other fluids produced by the body, indeed contains viable bacteria. As such, and recognizing the extensive literature relating breastfeeding to optimal infant health, we propose that human milk should be considered a probiotic food. Determining factors that influence which bacteria are present in milk and if and how they influence the mother's and/or the recipient infant's health remain basic science and public health realms in which almost nothing is known. © 2015 American Society for Nutrition.

Cultivable Anaerobic Microbiota of Severe Early Childhood Caries▿¶

PubMed Central

Tanner, A. C. R.; Mathney, J. M. J.; Kent, R. L.; Chalmers, N. I.; Hughes, C. V.; Loo, C. Y.; Pradhan, N.; Kanasi, E.; Hwang, J.; Dahlan, M. A.; Papadopolou, E.; Dewhirst, F. E.

2011-01-01

Severe early childhood caries (ECC), while strongly associated with Streptococcus mutans using selective detection (culture, PCR), has also been associated with a widely diverse microbiota using molecular cloning approaches. The aim of this study was to evaluate the microbiota of severe ECC using anaerobic culture. The microbial composition of dental plaque from 42 severe ECC children was compared with that of 40 caries-free children. Bacterial samples were cultured anaerobically on blood and acid (pH 5) agars. Isolates were purified, and partial sequences for the 16S rRNA gene were obtained from 5,608 isolates. Sequence-based analysis of the 16S rRNA isolate libraries from blood and acid agars of severe ECC and caries-free children had >90% population coverage, with greater diversity occurring in the blood isolate library. Isolate sequences were compared with taxon sequences in the Human Oral Microbiome Database (HOMD), and 198 HOMD taxa were identified, including 45 previously uncultivated taxa, 29 extended HOMD taxa, and 45 potential novel groups. The major species associated with severe ECC included Streptococcus mutans, Scardovia wiggsiae, Veillonella parvula, Streptococcus cristatus, and Actinomyces gerensceriae. S. wiggsiae was significantly associated with severe ECC children in the presence and absence of S. mutans detection. We conclude that anaerobic culture detected as wide a diversity of species in ECC as that observed using cloning approaches. Culture coupled with 16S rRNA identification identified over 74 isolates for human oral taxa without previously cultivated representatives. The major caries-associated species were S. mutans and S. wiggsiae, the latter of which is a candidate as a newly recognized caries pathogen. PMID:21289150

77 FR 55788 - Endangered and Threatened Wildlife and Plants; Designation of Revised Critical Habitat for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-11

... (16 U.S.C. 1531 et seq.), including whether there are threats to the species from human activity, the... within the geographical area occupied by the taxa at the time of listing that contain physical or... activities in the subject areas and their possible impacts on proposed critical habitat. (4) Information on...

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

PubMed Central

Li, Kelvin; Bihan, Monika; Methé, Barbara A.

2013-01-01

Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa (“core”), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat’s microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of “minor” oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region. PMID

Impact of a vegan diet on the human salivary microbiota.

PubMed

Hansen, Tue H; Kern, Timo; Bak, Emilie G; Kashani, Alireza; Allin, Kristine H; Nielsen, Trine; Hansen, Torben; Pedersen, Oluf

2018-04-11

Little is known about the effect of long-term diet patterns on the composition and functional potential of the human salivary microbiota. In the present study, we sought to contribute to the ongoing elucidation of dietary effects on the oral microbial community by examining the diversity, composition and functional potential of the salivary microbiota in 160 healthy vegans and omnivores using 16S rRNA gene amplicon sequencing. We further sought to identify bacterial taxa in saliva associated with host inflammatory markers. We show that compositional differences in the salivary microbiota of vegans and omnivores is present at all taxonomic levels below phylum level and includes upper respiratory tract commensals (e.g. Neisseria subflava, Haemophilus parainfluenzae, and Rothia mucilaginosa) and species associated with periodontal disease (e.g. Campylobacter rectus and Porphyromonas endodontalis). Dietary intake of medium chain fatty acids, piscine mono- and polyunsaturated fatty acids, and dietary fibre was associated with bacterial diversity, community structure, as well as relative abundance of several species-level operational taxonomic units. Analysis of imputed genomic potential revealed several metabolic pathways differentially abundant in vegans and omnivores indicating possible effects of macro- and micro-nutrient intake. We also show that certain oral bacteria are associated with the systemic inflammatory state of the host.

Character complexity and redundancy in writing systems over human history.

PubMed

Changizi, Mark A; Shimojo, Shinsuke

2005-02-07

A writing system is a visual notation system wherein a repertoire of marks, or strokes, is used to build a repertoire of characters. Are there any commonalities across writing systems concerning the rules governing how strokes combine into characters; commonalities that might help us identify selection pressures on the development of written language? In an effort to answer this question we examined how strokes combine to make characters in more than 100 writing systems over human history, ranging from about 10 to 200 characters,and including numerals, abjads, abugidas, alphabets and syllabaries from five major taxa: Ancient Near-Eastern, European, Middle Eastern, South Asian, Southeast Asian. We discovered underlying similarities in two fundamental respects. (i) The number of strokes per characters is approximately three, independent of the number of characters in the writing system; numeral systems are the exception, having on average only two strokes per character. (ii) Characters are ca. 50% redundant, independent of writing system size; intuitively, this means that acharacter's identity can be determined even when half of its strokes are removed. Because writing systems are under selective pressure to have characters that are easy for the visual system to recognize and for the motor system to write, these fundamental commonalities may be a fingerprint of mechanisms underlying the visuo-motor system.

How Are Gender Equality and Human Rights Interventions Included in Sexual and Reproductive Health Programmes and Policies: A Systematic Review of Existing Research Foci and Gaps.

PubMed

Hartmann, Miriam; Khosla, Rajat; Krishnan, Suneeta; George, Asha; Gruskin, Sofia; Amin, Avni

2016-01-01

The importance of promoting gender equality and human rights in sexual and reproductive health (SRH) programmes and policies has been affirmed in numerous international and regional agreements, most recently the 2030 Agenda for Sustainable Development. Given the critical role of research to determine what works, we aimed to identify research gaps as part of a broader priority setting exercise on integrating gender equality and human rights approaches in SRH programmes and policies. A systematic literature review of reviews was conducted to examine the question: what do we know about how research in the context of SRH programmes and policies has addressed gender equality and human rights and what are the current gaps in research. We searched three databases for reviews that addressed the research question, were published between 1994-2014, and met methodological standards for systematic reviews, qualitative meta-syntheses and other reviews of relevance to the research question. Additional grey literature was identified based on expert input. Articles were appraised by the primary author and examined by an expert panel. An abstraction and thematic analysis process was used to synthesize findings. Of the 3,073 abstracts identified, 56 articles were reviewed in full and 23 were included along with 10 from the grey literature. The majority focused on interventions addressing gender inequalities; very few reviews explicitly included human rights based interventions. Across both topics, weak study designs and use of intermediate outcome measures limited evidence quality. Further, there was limited evidence on interventions that addressed marginalized groups. Better quality studies, longer-term indicators, and measurement of unintended consequences are needed to better understand the impact of these types of interventions on SRH outcomes. Further efforts are needed to cover research on gender equality and human rights issues as they pertain to a broader set of SRH topics

How Are Gender Equality and Human Rights Interventions Included in Sexual and Reproductive Health Programmes and Policies: A Systematic Review of Existing Research Foci and Gaps

PubMed Central

Khosla, Rajat; Krishnan, Suneeta; George, Asha; Gruskin, Sofia; Amin, Avni

2016-01-01

The importance of promoting gender equality and human rights in sexual and reproductive health (SRH) programmes and policies has been affirmed in numerous international and regional agreements, most recently the 2030 Agenda for Sustainable Development. Given the critical role of research to determine what works, we aimed to identify research gaps as part of a broader priority setting exercise on integrating gender equality and human rights approaches in SRH programmes and policies. A systematic literature review of reviews was conducted to examine the question: what do we know about how research in the context of SRH programmes and policies has addressed gender equality and human rights and what are the current gaps in research. We searched three databases for reviews that addressed the research question, were published between 1994–2014, and met methodological standards for systematic reviews, qualitative meta-syntheses and other reviews of relevance to the research question. Additional grey literature was identified based on expert input. Articles were appraised by the primary author and examined by an expert panel. An abstraction and thematic analysis process was used to synthesize findings. Of the 3,073 abstracts identified, 56 articles were reviewed in full and 23 were included along with 10 from the grey literature. The majority focused on interventions addressing gender inequalities; very few reviews explicitly included human rights based interventions. Across both topics, weak study designs and use of intermediate outcome measures limited evidence quality. Further, there was limited evidence on interventions that addressed marginalized groups. Better quality studies, longer-term indicators, and measurement of unintended consequences are needed to better understand the impact of these types of interventions on SRH outcomes. Further efforts are needed to cover research on gender equality and human rights issues as they pertain to a broader set of SRH topics

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

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.

Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges.

PubMed

Deng, Ping; Swanson, Kelly S

2015-01-01

High-throughput DNA sequencing techniques allow for the identification and characterisation of microbes and their genes (microbiome). Using these new techniques, microbial populations in several niches of the human body, including the oral and nasal cavities, skin, urogenital tract and gastrointestinal tract, have been described recently. Very little data on the microbiome of companion animals exist, and most of the data have been derived from the analysis of the faeces of healthy laboratory animals. High-throughput assays provide opportunities to study the complex and dense populations of the gut microbiota, including bacteria, archaea, fungi, protozoa and viruses. Our laboratory and others have recently described the predominant microbial taxa and genes of healthy dogs and cats and how these respond to dietary interventions. In general, faecal microbial phylogeny (e.g. predominance of Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria) and functional capacity (e.g. major functional groups related to carbohydrate, protein, DNA and vitamin metabolism; virulence factors; and cell wall and capsule) of the canine and feline gut are similar to those of the human gut. Initial sequencing projects have provided a glimpse of the microbial super-organism that exists within the canine and feline gut, but leaves much to be explored and discovered. As DNA provides information only about potential functions, studies that focus on the microbial transcriptome, metabolite profiles, and how microbiome changes affect host physiology and health are clearly required. Future studies must determine how diet composition, antibiotics and other drug therapies, breed and disease affect or are affected by the gut microbiome and how this information may be used to improve diets, identify disease biomarkers and develop targeted disease therapies.

A neuronal morphologic type unique to humans and great apes

PubMed Central

Nimchinsky, Esther A.; Gilissen, Emmanuel; Allman, John M.; Perl, Daniel P.; Erwin, Joseph M.; Hof, Patrick R.

1999-01-01

We report the existence and distribution of an unusual type of projection neuron, a large, spindle-shaped cell, in layer Vb of the anterior cingulate cortex of pongids and hominids. These spindle cells were not observed in any other primate species or any other mammalian taxa, and their volume was correlated with brain volume residuals, a measure of encephalization in higher primates. These observations are of particular interest when considering primate neocortical evolution, as they reveal possible adaptive changes and functional modifications over the last 15–20 million years in the anterior cingulate cortex, a region that plays a major role in the regulation of many aspects of autonomic function and of certain cognitive processes. That in humans these unique neurons have been shown previously to be severely affected in the degenerative process of Alzheimer’s disease suggests that some of the differential neuronal susceptibility that occurs in the human brain in the course of age-related dementing illnesses may have appeared only recently during primate evolution. PMID:10220455

Intra-individual metameric variation expressed at the enamel-dentine junction of lower post-canine dentition of South African fossil hominins and modern humans.

PubMed

Pan, Lei; Thackeray, John Francis; Dumoncel, Jean; Zanolli, Clément; Oettlé, Anna; de Beer, Frikkie; Hoffman, Jakobus; Duployer, Benjamin; Tenailleau, Christophe; Braga, José

2017-08-01

The aim of this study is to compare the degree and patterning of inter- and intra-individual metameric variation in South African australopiths, early Homo and modern humans. Metameric variation likely reflects developmental and taxonomical issues, and could also be used to infer ecological and functional adaptations. However, its patterning along the early hominin postcanine dentition, particularly among South African fossil hominins, remains unexplored. Using microfocus X-ray computed tomography (µXCT) and geometric morphometric tools, we studied the enamel-dentine junction (EDJ) morphology and we investigated the intra- and inter-individual EDJ metameric variation among eight australopiths and two early Homo specimens from South Africa, as well as 32 modern humans. Along post-canine dentition, shape changes between metameres represented by relative positions and height of dentine horns, outlines of the EDJ occlusal table are reported in modern and fossil taxa. Comparisons of EDJ mean shapes and multivariate analyses reveal substantial variation in the direction and magnitude of metameric shape changes among taxa, but some common trends can be found. In modern humans, both the direction and magnitude of metameric shape change show increased variability in M 2 -M 3 compared to M 1 -M 2 . Fossil specimens are clustered together showing similar magnitudes of shape change. Along M 2 -M 3 , the lengths of their metameric vectors are not as variable as those of modern humans, but they display considerable variability in the direction of shape change. The distalward increase of metameric variation along the modern human molar row is consistent with the odontogenetic models of molar row structure (inhibitory cascade model). Though much remains to be tested, the variable trends and magnitudes in metamerism in fossil hominins reported here, together with differences in the scale of shape change between modern humans and fossil hominins may provide valuable information

Wildlife Trade and Human Health in Lao PDR: An Assessment of the Zoonotic Disease Risk in Markets.

PubMed

Greatorex, Zoe F; Olson, Sarah H; Singhalath, Sinpakone; Silithammavong, Soubanh; Khammavong, Kongsy; Fine, Amanda E; Weisman, Wendy; Douangngeun, Bounlom; Theppangna, Watthana; Keatts, Lucy; Gilbert, Martin; Karesh, William B; Hansel, Troy; Zimicki, Susan; O'Rourke, Kathleen; Joly, Damien O; Mazet, Jonna A K

2016-01-01

Although the majority of emerging infectious diseases can be linked to wildlife sources, most pathogen spillover events to people could likely be avoided if transmission was better understood and practices adjusted to mitigate risk. Wildlife trade can facilitate zoonotic disease transmission and represents a threat to human health and economies in Asia, highlighted by the 2003 SARS coronavirus outbreak, where a Chinese wildlife market facilitated pathogen transmission. Additionally, wildlife trade poses a serious threat to biodiversity. Therefore, the combined impacts of Asian wildlife trade, sometimes termed bush meat trade, on public health and biodiversity need assessing. From 2010 to 2013, observational data were collected in Lao PDR from markets selling wildlife, including information on volume, form, species and price of wildlife; market biosafety and visitor origin. The potential for traded wildlife to host zoonotic diseases that pose a serious threat to human health was then evaluated at seven markets identified as having high volumes of trade. At the seven markets, during 21 observational surveys, 1,937 alive or fresh dead mammals (approximately 1,009 kg) were observed for sale, including mammals from 12 taxonomic families previously documented to be capable of hosting 36 zoonotic pathogens. In these seven markets, the combination of high wildlife volumes, high risk taxa for zoonoses and poor biosafety increases the potential for pathogen presence and transmission. To examine the potential conservation impact of trade in markets, we assessed the status of 33,752 animals observed during 375 visits to 93 markets, under the Lao PDR Wildlife and Aquatic Law. We observed 6,452 animals listed by Lao PDR as near extinct or threatened with extinction. The combined risks of wildlife trade in Lao PDR to human health and biodiversity highlight the need for a multi-sector approach to effectively protect public health, economic interests and biodiversity.

Wildlife Trade and Human Health in Lao PDR: An Assessment of the Zoonotic Disease Risk in Markets

PubMed Central

Singhalath, Sinpakone; Silithammavong, Soubanh; Khammavong, Kongsy; Fine, Amanda E.; Weisman, Wendy; Douangngeun, Bounlom; Theppangna, Watthana; Keatts, Lucy; Gilbert, Martin; Karesh, William B.; Hansel, Troy; Zimicki, Susan; O’Rourke, Kathleen; Joly, Damien O.; Mazet, Jonna A. K.

2016-01-01

Although the majority of emerging infectious diseases can be linked to wildlife sources, most pathogen spillover events to people could likely be avoided if transmission was better understood and practices adjusted to mitigate risk. Wildlife trade can facilitate zoonotic disease transmission and represents a threat to human health and economies in Asia, highlighted by the 2003 SARS coronavirus outbreak, where a Chinese wildlife market facilitated pathogen transmission. Additionally, wildlife trade poses a serious threat to biodiversity. Therefore, the combined impacts of Asian wildlife trade, sometimes termed bush meat trade, on public health and biodiversity need assessing. From 2010 to 2013, observational data were collected in Lao PDR from markets selling wildlife, including information on volume, form, species and price of wildlife; market biosafety and visitor origin. The potential for traded wildlife to host zoonotic diseases that pose a serious threat to human health was then evaluated at seven markets identified as having high volumes of trade. At the seven markets, during 21 observational surveys, 1,937 alive or fresh dead mammals (approximately 1,009 kg) were observed for sale, including mammals from 12 taxonomic families previously documented to be capable of hosting 36 zoonotic pathogens. In these seven markets, the combination of high wildlife volumes, high risk taxa for zoonoses and poor biosafety increases the potential for pathogen presence and transmission. To examine the potential conservation impact of trade in markets, we assessed the status of 33,752 animals observed during 375 visits to 93 markets, under the Lao PDR Wildlife and Aquatic Law. We observed 6,452 animals listed by Lao PDR as near extinct or threatened with extinction. The combined risks of wildlife trade in Lao PDR to human health and biodiversity highlight the need for a multi-sector approach to effectively protect public health, economic interests and biodiversity. PMID:27008628

Imitation of novel conspecific and human speech sounds in the killer whale (Orcinus orca).

PubMed

Abramson, José Z; Hernández-Lloreda, Mª Victoria; García, Lino; Colmenares, Fernando; Aboitiz, Francisco; Call, Josep

2018-01-31

Vocal imitation is a hallmark of human spoken language, which, along with other advanced cognitive skills, has fuelled the evolution of human culture. Comparative evidence has revealed that although the ability to copy sounds from conspecifics is mostly uniquely human among primates, a few distantly related taxa of birds and mammals have also independently evolved this capacity. Remarkably, field observations of killer whales have documented the existence of group-differentiated vocal dialects that are often referred to as traditions or cultures and are hypothesized to be acquired non-genetically. Here we use a do-as-I-do paradigm to study the abilities of a killer whale to imitate novel sounds uttered by conspecific (vocal imitative learning) and human models (vocal mimicry). We found that the subject made recognizable copies of all familiar and novel conspecific and human sounds tested and did so relatively quickly (most during the first 10 trials and three in the first attempt). Our results lend support to the hypothesis that the vocal variants observed in natural populations of this species can be socially learned by imitation. The capacity for vocal imitation shown in this study may scaffold the natural vocal traditions of killer whales in the wild. © 2018 The Author(s).

Comparison of the Distal Gut Microbiota from People and Animals in Africa

PubMed Central

Ellis, Richard J.; Bruce, Kenneth D.; Jenkins, Claire; Stothard, J. Russell; Ajarova, Lilly; Mugisha, Lawrence; Viney, Mark E.

2013-01-01

The gut microbiota plays a key role in the maintenance of healthy gut function as well as many other aspects of health. High-throughput sequence analyses have revealed the composition of the gut microbiota, showing that there is a core signature to the human gut microbiota, as well as variation in its composition between people. The gut microbiota of animals is also being investigated. We are interested in the relationship between bacterial taxa of the human gut microbiota and those in the gut microbiota of domestic and semi-wild animals. While it is clear that some human gut bacterial pathogens come from animals (showing that human – animal transmission occurs), the extent to which the usually non-pathogenic commensal taxa are shared between humans and animals has not been explored. To investigate this we compared the distal gut microbiota of humans, cattle and semi-captive chimpanzees in communities that are geographically sympatric in Uganda. The gut microbiotas of these three host species could be distinguished by the different proportions of bacterial taxa present. We defined multiple operational taxonomic units (OTUs) by sequence similarity and found evidence that some OTUs were common between human, cattle and chimpanzees, with the largest number of shared OTUs occurring between chimpanzees and humans, as might be expected with their close physiological similarity. These results show the potential for the sharing of usually commensal bacterial taxa between humans and other animals. This suggests that further investigation of this phenomenon is needed to fully understand how it drives the composition of human and animal gut microbiotas. PMID:23355898

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

Genetic diversity and conservation of Mexican forest trees

Treesearch

C. Wehenkel; S. Mariscal-Lucero; J.P. Jaramillo-Correa; C.A. López-Sánchez; J.J. Vargas Hernández; C. Sáenz-Romero

2017-01-01

Over the last 200 years, humans have impacted the genetic diversity of forest trees. Because of widespread deforestation and over-exploitation, about 9,000 tree species are listed worldwide as threatened with extinction, including more than half of the ~600 known conifer taxa. A comprehensive review of the floristic-taxonomic literature compiled a list of 4,331...

Discovery of trypanosomatid parasites in globally distributed Drosophila species.

PubMed

Chandler, James Angus; James, Pamela M

2013-01-01

Microbial parasites of animals include bacteria, viruses, and various unicellular eukaryotes. Because of the difficulty in studying these microorganisms in both humans and disease vectors, laboratory models are commonly used for experimental analysis of host-parasite interactions. Drosophila is one such model that has made significant contributions to our knowledge of bacterial, fungal, and viral infections. Despite this, less is known about other potential parasites associated with natural Drosophila populations. Here, we surveyed sixteen Drosophila populations comprising thirteen species from four continents and Hawaii and found that they are associated with an extensive diversity of trypanosomatids (Euglenozoa, Kinetoplastea). Phylogenetic analysis finds that Drosophila-associated trypanosomatids are closely related to taxa that are responsible for various types of leishmaniases and more distantly related to the taxa responsible for human African trypanosomiasis and Chagas disease. We suggest that Drosophila may provide a powerful system for studying the interactions between trypanosomatids and their hosts.

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

PubMed Central

Hsu, Tiffany; Joice, Regina; Vallarino, Jose; Abu-Ali, Galeb; Hartmann, Erica M.; Shafquat, Afrah; DuLong, Casey; Baranowski, Catherine; Gevers, Dirk; Green, Jessica L.; Spengler, John D.

2016-01-01

ABSTRACT Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics. All surfaces were dominated by human skin and oral commensals such as Propionibacterium, Corynebacterium, Staphylococcus, and Streptococcus. The detected taxa not associated with humans included generalists from alphaproteobacteria, which were especially abundant on outdoor touchscreens. Shotgun metagenomics further identified viral and eukaryotic microbes, including Propionibacterium phage and Malassezia globosa. Functional profiling showed that Propionibacterium acnes pathways such as propionate production and porphyrin synthesis were enriched on train holding surfaces (holds), while electron transport chain components for aerobic respiration were enriched on touchscreens and seats. Lastly, the transit environment was not found to be a reservoir of antimicrobial resistance and virulence genes. Our results suggest that microbial communities on transit surfaces are maintained from a metapopulation of human skin commensals and environmental generalists, with enrichments corresponding to local interactions with the human body and environmental exposures. IMPORTANCE Mass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we

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

Revisiting the Phylogeny of the Animal Formins: Two New Subtypes, Relationships with Multiple Wing Hairs Proteins, and a Lost Human Formin.

PubMed

Pruyne, David

2016-01-01

Formins are a widespread family of eukaryotic cytoskeleton-organizing proteins. Many species encode multiple formin isoforms, and for animals, much of this reflects the presence of multiple conserved subtypes. Earlier phylogenetic analyses identified seven major formin subtypes in animals (DAAM, DIAPH, FHOD, FMN, FMNL, INF, and GRID2IP/delphilin), but left a handful of formins, particularly from nematodes, unassigned. In this new analysis drawing from genomic data from a wider range of taxa, nine formin subtypes are identified that encompass all the animal formins analyzed here. Included in this analysis are Multiple Wing Hairs proteins (MWH), which bear homology to formin N-terminal domains. Originally identified in Drosophila melanogaster and other arthropods, MWH-related proteins are also identified here in some nematodes (including Caenorhabditis elegans), and are shown to be related to a novel MWH-related formin (MWHF) subtype. One surprising result of this work is the discovery that a family of pleckstrin homology domain-containing formins (PHCFs) is represented in many vertebrates, but is strikingly absent from placental mammals. Consistent with a relatively recent loss of this formin, the human genome retains fragments of a defunct homologous formin gene.

Adult sex ratios and reproductive strategies: a critical re-examination of sex differences in human and animal societies

PubMed Central

2017-01-01

It is increasingly recognized that the relative proportion of potential mates to competitors in a population impacts a range of sex-specific behaviours and in particular mating and reproduction. However, while the adult sex ratio (ASR) has long been recognized as an important link between demography and behaviour, this relationship remains understudied. Here, we introduce the first inter-disciplinary collection of research on the causes and consequences of variation in the ASR in human and animal societies. This important topic is relevant to a wide audience of both social and biological scientists due to the central role that the relative number of males to females in a population plays for the evolution of, and contemporary variation in, sex roles across groups, species and higher taxa. The articles in this theme issue cover research on ASR across a variety of taxa and topics. They offer critical re-evaluations of theoretical foundations within both evolutionary and non-evolutionary fields, and propose innovative methodological approaches, present new empirical examples of behavioural consequences of ASR variation and reveal that the ASR plays a major role in determining population viability, especially in small populations and species with labile sex determination. This introductory paper puts the contributions of the theme issue into a broader context, identifies general trends across the literature and formulates directions for future research. This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies'. PMID:28760753

How ecology shapes exploitation: a framework to predict the behavioural response of human and animal foragers along exploration-exploitation trade-offs.

PubMed

Monk, Christopher T; Barbier, Matthieu; Romanczuk, Pawel; Watson, James R; Alós, Josep; Nakayama, Shinnosuke; Rubenstein, Daniel I; Levin, Simon A; Arlinghaus, Robert

2018-06-01

Understanding how humans and other animals behave in response to changes in their environments is vital for predicting population dynamics and the trajectory of coupled social-ecological systems. Here, we present a novel framework for identifying emergent social behaviours in foragers (including humans engaged in fishing or hunting) in predator-prey contexts based on the exploration difficulty and exploitation potential of a renewable natural resource. A qualitative framework is introduced that predicts when foragers should behave territorially, search collectively, act independently or switch among these states. To validate it, we derived quantitative predictions from two models of different structure: a generic mathematical model, and a lattice-based evolutionary model emphasising exploitation and exclusion costs. These models independently identified that the exploration difficulty and exploitation potential of the natural resource controls the social behaviour of resource exploiters. Our theoretical predictions were finally compared to a diverse set of empirical cases focusing on fisheries and aquatic organisms across a range of taxa, substantiating the framework's predictions. Understanding social behaviour for given social-ecological characteristics has important implications, particularly for the design of governance structures and regulations to move exploited systems, such as fisheries, towards sustainability. Our framework provides concrete steps in this direction. © 2018 John Wiley & Sons Ltd/CNRS.

Analysis of Reptile Biodiversity and Ecosystem Services within ...

EPA Pesticide Factsheets

A focus for resource management, conservation planning, and environmental decision analysis has been mapping and quantifying biodiversity and ecosystem services. The challenge has been to integrate ecology with economics to better understand the effects of human policies and actions and their subsequent impacts on human well-being and ecosystem function. Biodiversity is valued by humans in varied ways, and thus is an important input to include in assessing the benefits of ecosystems to humans. Some biodiversity metrics more clearly reflect ecosystem services (e.g., game species, threatened and endangered species), whereas others may indicate indirect and difficult to quantify relationships to services (e.g., taxa richness and cultural value). In the present study, we identify and map reptile biodiversity and ecosystem services metrics. The importance of reptiles to biodiversity and ecosystems services is not often described. We used species distribution models for reptiles in the conterminous United States from the U.S. Geological Survey’s Gap Analysis Program. We focus on species richness metrics including all reptile species richness, taxa groupings of lizards, snakes and turtles, NatureServe conservation status (G1, G2, G3) species, IUCN listed reptiles, threatened and endangered species, Partners in Amphibian and Reptile Conservation listed reptiles, and rare species. These metrics were analyzed with the Protected Areas Database of the United States to

Humanized mouse models: Application to human diseases.

PubMed

Ito, Ryoji; Takahashi, Takeshi; Ito, Mamoru

2018-05-01

Humanized mice are superior to rodents for preclinical evaluation of the efficacy and safety of drug candidates using human cells or tissues. During the past decade, humanized mouse technology has been greatly advanced by the establishment of novel platforms of genetically modified immunodeficient mice. Several human diseases can be recapitulated using humanized mice due to the improved engraftment and differentiation capacity of human cells or tissues. In this review, we discuss current advanced humanized mouse models that recapitulate human diseases including cancer, allergy, and graft-versus-host disease. © 2017 Wiley Periodicals, Inc.

Postmortem microbial communities in burial soil layers of skeletonized humans.

PubMed

Thomas, Torri B; Finley, Sheree J; Wilkinson, Jeremy E; Wescott, Daniel J; Gorski, Azriel; Javan, Gulnaz T

2017-07-01

Microorganisms are major ecological participants in the successional decomposition of vertebrates. The relative abundance, or the scarcity, of certain microbial taxa in gravesoil has the potential to determine the ecological status of skeletons. However, there are substantial knowledge gaps that warrant consideration in the context of the surrounding terrestrial ecosystem. In the current study, we hypothesized that i.) soil microbial diversity is disparate in the latter stage of decomposition (skeletonization) compared to the earlier stages (fresh, bloat, active and advanced decay), and ii.) the three layers of gravesoil (top, middle, and bottom) encompass similar microbial taxa and are analogous with control soil. To test these hypotheses, microbial communities in layers of burial soil of skeletonized bodies (treated) and from control soil, obtained from burial plots with no bodies (untreated), were compared using sequencing data of the 16S rRNA gene. The results demonstrated that Acidobacteria was confirmed as the most abundant microbial genus in all treated and untreated soil layers. Furthermore, Proteobacteria demonstrated a relatively low abundance in skeletonized gravesoil which is dissimilar from previous findings that assessed soil from earlier stages of human decomposition. Also, these results determined that soil microbial signatures were analogous in all three soil layers under the effects of similar abiotic and biotic factors, and they were similar to the communities in untreated soil. Therefore, the current study produced empirical data that give conclusive evidence of soil microbial successional changes, particularly for Proteobacteria, for potential use in forensic microbiology research. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

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

Ticks collected from humans, domestic animals, and wildlife in Yucatan, Mexico.

PubMed

Rodríguez-Vivas, R I; Apanaskevich, D A; Ojeda-Chi, M M; Trinidad-Martínez, I; Reyes-Novelo, E; Esteve-Gassent, M D; Pérez de León, A A

2016-01-15

Domestic animals and wildlife play important roles as reservoirs of zoonotic pathogens that are transmitted to humans by ticks. Besides their role as vectors of several classes of microorganisms of veterinary and public health relevance, ticks also burden human and animal populations through their obligate blood-feeding habit. It is estimated that in Mexico there are around 100 tick species belonging to the Ixodidae and Argasidae families. Information is lacking on tick species that affect humans, domestic animals, and wildlife through their life cycle. This study was conducted to bridge that knowledge gap by inventorying tick species that infest humans, domestic animals and wildlife in the State of Yucatan, Mexico. Amblyomma ticks were observed as euryxenous vertebrate parasites because they were found parasitizing 17 animal species and human. Amblyomma mixtum was the most eryxenous species found in 11 different animal species and humans. Both A. mixtum and A. parvum were found parasitizing humans. Ixodes near affinis was the second most abundant species parasitizing six animal species (dogs, cats, horses, white-nosed coati, white-tail deer and black vulture) and was found widely across the State of Yucatan. Ixodid tick populations may increase in the State of Yucatan with time due to animal production intensification, an increasing wildlife population near rural communities because of natural habitat reduction and fragmentation. The diversity of ticks across host taxa documented here highlights the relevance of ecological information to understand tick-host dynamics. This knowledge is critical to inform public health and veterinary programs for the sustainable control of ticks and tick-borne diseases. Copyright © 2015. Published by Elsevier B.V.

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.

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.

CO2 and O2 Gas Exchange in an Experimental Model of the Btlss with Plant Wastes and Human Wastes Included in the Mass Exchange

NASA Astrophysics Data System (ADS)

Ushakova, Sofya; Tikhomirov, Alexander A.; Velichko, Vladimir; Tikhomirova, Natalia; Trifonov, Sergey V.

2016-07-01

Mass exchange processes in the new experimental model of the biotechnical life support system (BTLSS) constructed at the Institute of Biophysics SB RAS have a higher degree of closure than in the previous BTLSS, and, thus, the technologies employed in the new system are more complex. Therefore, before closing the loops of mass exchange processes for several months, the new model of the BTLSS was run to match the technologies employed to cultivate plants and the methods used to involve inedible plant parts and human wastes into the mass exchange with the CO2 absorption rate and the amount of the resulting O2. The plant compartment included vegetables grown on the soil-like substrate (SLS) (chufa, beet, carrot, radish, and lettuce), plants hydroponically grown on expanded clay aggregate (wheat, soybean, watercress), and plants grown in aquaculture (common glasswort and watercress). Nutrient solutions for hydroponically grown plants were prepared by using products of physicochemical mineralization of human wastes. Growing the plants in aquaculture enabled maintaining NaCl concentration in the irrigation solution for hydroponically grown plants at a level safe for the plants. Inedible plant biomass was added to the SLS. Three cycles of closing the system were run, which lasted 7, 7, and 10 days. The comparison of the amount of CO2 fed into the system over 24 h (simulating human respiration) and the amount of CO2 daily exhaled by a 70-kg middle-aged human showed that between 1% and 4% of the daily emissions of CO2 were assimilated in the system, and about 3% of the average human daily O2 requirement accumulated in the system. Plant productivity was between 4 and 4.7% of the human daily vegetable requirement, or between 3 and 3.5% of the total human daily food requirement. Thus, testing of the BTLSS showed a match between the technologies employed to arrange mass exchange processes. This study was supported by the grant of the Russian Science Foundation (Project No. 14-14-00599).

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