Search

Background Nuclear Receptor Subfamily 2 Group F (Nr2f) orphan nuclear hormone transcription factors (TFs) are fundamental regulators of many developmental processes in invertebrates and vertebrates. Despite the importance of these TFs throughout metazoan development, previous work has not clearly outlined their evolutionary history. Results We integrated molecular phylogeny with comparisons of intron/exon structure, domain architecture, and syntenic conservation to define critical evolutionary events that distinguish the Nr2f gene family in Metazoa. Our data indicate that a single ancestral eumetazoan Nr2f gene predated six main Bilateria subfamilies, which include single Nr2f homologs, here referred to as Nr2f1/2/5/6, that are present in invertebrate protostomes and deuterostomes, Nr2f1/2 homologs in agnathans, and Nr2f1, Nr2f2, Nr2f5, and Nr2f6 orthologs that are found in gnathostomes. Four cnidarian Nr2f1/2/5/6 and three agnathan Nr2f1/2 members are each due to independent expansions, while the vertebrate Nr2f1/Nr2f2 and Nr2f5/Nr2f6 members each form paralogous groups that arose from the established series of whole-genome duplications (WGDs). Nr2f6 members are the most divergent Nr2f subfamily in gnathostomes. Interestingly, in contrast to the other gnathostome Nr2f subfamilies, Nr2f5 has been independently lost in numerous vertebrate lineages. Furthermore, our analysis shows there are differential expansions and losses of Nr2f genes in teleosts following their additional rounds of WGDs. Conclusion Overall, our analysis of Nr2f gene evolution helps to reveal the origins and previously unrecognized relationships of this ancient TF family, which may allow for greater insights into the conservation of Nr2f functions that shape Metazoan body plans.

Despite a long-documented history of severe harmful algal blooms (HABs) in New England coastal waters, corresponding HAB-associated marine mammal mortality events in this region are far less frequent or severe relative to other regions where HABs are common. This long-term survey of the HAB toxins saxitoxin (STX) and domoic acid (DA) demonstrates significant and widespread exposure of these toxins in New England marine mammals, across multiple geographic, temporal and taxonomic groups. Overall, 19% of the 458 animals tested positive for one or more toxins, with 15% and 7% testing positive for STX and DA, respectively. 74% of the 23 different species analyzed demonstrated evidence of toxin exposure. STX was most prevalent in Maine coastal waters, most frequently detected in common dolphins (Delphinus delphis), and most often detected during July and October. DA was most prevalent in animals sampled in offshore locations and in bycaught animals, and most frequently detected in mysticetes, with humpback whales (Megaptera novaeangliae) testing positive at the highest rates. Feces and urine appeared to be the sample matrices most useful for determining the presence of toxins in an exposed animal, with feces samples having the highest concentrations of STX or DA. No relationship was found between the bloom season of toxin-producing phytoplankton and toxin detection rates, however STX was more likely to be present in July and October. No relationship between marine mammal dietary preference and frequency of toxin detection was observed. These findings are an important part of a framework for assessing future marine mammal morbidity and mortality events, as well as monitoring ecosystem health using marine mammals as sentinel organisms for predicting coastal ocean changes.

The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12–11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint.

Globally, millions of animals are rescued and rehabilitated by wildlife carers each year. Information gathered in this process is useful for uncovering threats to native wildlife, particularly those from anthropogenic causes. However, few studies using rehabilitation data include a diverse range of fauna, cover large geographical areas, and consider long-term trends. Furthermore, few studies have statistically modelled causes of why animals come into care, and what are their chances of survival. This study draws on 469,553 rescues reported over six years by wildlife rehabilitators for 688 species of bird, reptile, and mammal from New South Wales, Australia. For birds and mammals, ‘abandoned/orphaned’ and ‘collisions with vehicles’ were the dominant causes for rescue, however for reptiles this was ‘unsuitable environment’. Overall rescue numbers were lowest in winter, and highest in spring, with six-times more ‘abandoned/orphaned’ individuals in spring than winter. Of the 364,461 rescues for which the fate of an animal was known, 92% fell within two categories: ‘dead’, ‘died or euthanased’ (54.8% of rescues with known fate) and animals that recovered and were subsequently released (37.1% of rescues with known fate). Modelling of the fate of animals indicated that the likelihood of animal survival (i.e. chance of: being released, left and observed, or permanent care), was related to the cause for rescue. In general, causes for rescue involving physical trauma (collisions, attacks, etc.) had a much lower likelihood of animals surviving than other causes such as ‘unsuitable environment’, ‘abandoned/orphaned’, and this also showed some dependence upon whether the animal was a bird, reptile, or mammal. This suggests rehabilitation efforts could be focused on particular threats or taxa to maximise success, depending on the desired outcomes. The results illustrate the sheer volume of work undertaken by rehabilitation volunteers and professionals toward both animal welfare and to the improvement of wildlife rehabilitation in the future.

International audience; The cephalochordates amphioxus or lancelets are benthic marine animals representing the earliest divergent evolutionary lineage within chordates. Although amphioxus are present in most of the world's tropical and temperate oceans, only about thirty different species grouped into three different genera, Branchiostoma, Epigonichthys and Asymmetron have been described. In the genus Asymmetron, only two species have been characterized, although for one of them, A. lucayanum, several cryptic lineages exist. In this work we have sequenced and analyzed the mitogenome of an A. lucayanum population previously described in the Red Sea. The phylogenetic study using this complete mitogenome as well as the analysis of COI gene sequences of several individuals of this Red Sea population show that the Red Sea population is a new cryptic species. We propose to call this new species Asymmetron rubrum.

Rice paddy irrigation ponds can sustain surprisingly high taxonomic richness and make significant contributions to regional biodiversity. We evaluated the impacts of pesticides and other environmental stressors (including eutrophication, decreased macrophyte coverage, physical habitat destruction, and invasive alien species) on the taxonomic richness of freshwater animals in 21 irrigation ponds in Japan. We sampled a wide range of freshwater animals (reptiles, amphibians, fishes, mollusks, crustaceans, insects, annelids, bryozoans, and sponges) and surveyed environmental variables related to pesticide contamination and other stressors listed above. Statistical analyses comprised contraction of highly correlated environmental variables, best-subset model selection, stepwise model selection, and permutation tests. Results showed that: (i) probenazole (fungicide) was a significant stressor on fish (i.e., contamination with this compound had a significantly negative correlation with fish taxonomic richness), (ii) the interaction of BPMC (insecticide; also known as fenobucarb) and bluegill (invasive alien fish) was a significant stressor on a "large insect" category (Coleoptera, Ephemeroptera, Hemiptera, Lepidoptera, Odonata, and Trichoptera), (iii) the interaction of BPMC and concrete bank protection was a significant stressor on an "invertebrate" category, (iv) the combined impacts of BPMC and the other stressors on the invertebrate and large insect categories resulted in an estimated mean loss of taxonomic richness by 15% and 77%, respectively, in comparison with a hypothetical pond with preferable conditions.

Mammalian and bird ribosomes are nearly twice the mass of prokaryotic ribosomes in part because of their extraordinarily long rRNA tentacles. Human rRNA tentacles are not fully observable in current three-dimensional structures and their conformations remain to be fully resolved. In previous work we identified sequences that favor G-quadruplexes in silico and in vitro in rRNA tentacles of the human large ribosomal subunit. We demonstrated by experiment that these sequences form G-quadruplexes in vitro. Here, using a more recent motif definition, we report additional G-quadruplex sequences on surfaces of both subunits of the human ribosome. The revised sequence definition reveals expansive arrays of potential G-quadruplex sequences on LSU tentacles. In addition, we demonstrate by a variety of experimental methods that fragments of the small subunit rRNA form G-quadruplexes in vitro. Prior to this report rRNA sequences that form G-quadruplexes were confined to the large ribosomal subunit. Our combined results indicate that the surface of the assembled human ribosome contains numerous sequences capable of forming G-quadruplexes on both ribosomal subunits. The data suggest conversion between duplexes and G-quadruplexes in response to association with proteins, ions, or other RNAs. In some systems it seems likely that the integrated population of RNA G-quadruplexes may be dominated by rRNA, which is the most abundant cellular RNA.

MHC molecules are essential for the adaptive immune response, and they are the most polymorphic genetic loci in vertebrates. Extreme genetic variation at these loci is paradoxical given their central importance to host health. Classic models of MHC gene evolution center on antagonistic host-pathogen interactions to promote gene diversification and allelic diversity in host populations. However, all multicellular organisms are persistently colonized by their microbiota that perform essential metabolic functions for their host and protect from infection. Here, we provide data to support the hypothesis that MHC heterozygote advantage (a main force of selection thought to drive MHC gene evolution), may operate by enhancing fitness advantages conferred by the host’s microbiome. We utilized fecal 16S rRNA gene sequences and their predicted metagenome datasets collected from multiple MHC congenic homozygote and heterozygote mouse strains to describe the influence of MHC heterozygosity on microbiome form and function. We find that in contrast to homozygosity at MHC loci, MHC heterozygosity promotes functional diversification of the microbiome, enhances microbial network connectivity, and results in enrichment for a variety of microbial functions that are positively associated with host fitness. We demonstrate that taxonomic and functional diversity of the microbiome is positively correlated in MHC heterozygote but not homozygote animals, suggesting that heterozygote microbiomes are more functionally adaptive under similar environmental conditions than homozygote microbiomes. Our data complement previous observations on the role of MHC polymorphism in sculpting microbiota composition, but also provide functional insights into how MHC heterozygosity may enhance host health by modulating microbiome form and function. We also provide evidence to support that MHC heterozygosity limits functional redundancy among commensal microbes and may enhance the metabolic versatility of their microbiome. Results from our analyses yield multiple testable predictions regarding the role of MHC heterozygosity on the microbiome that will help guide future research in the area of MHC-microbiome interactions.

Larval swimming with cilia, unaided by muscles, is the presumed ancestral condition for echinoderms, but use of muscles in swimming has evolved several times. Ciliation and musculature of the arms of brachiolaria-stage larvae in the family Asteriidae provide unusual versatility in the use of muscles in swimming. The muscles affect swimming in two different ways. (1) Contraction of muscles moves the arms, propelling the larva. (2) Contraction of muscles changes orientation of the arms, thereby changing direction of ciliary currents and direction of swimming. New observations of the brachiolaria of the asteriid seastar Pisaster ochraceus demonstrate more versatility in both of these uses of muscles than had been previously described: the posterolateral arms stroke in more ways to propel the larva forward and to change the direction of swimming, and more pairs of the arms point ciliary currents in more directions for changes in direction of swimming. Morphology of brachiolariae suggests that these uses of muscles in swimming evolved before divergence of the families Stichasteridae and Asteriidae within forcipulate asteroids. This versatile use of muscles for swimming, both alone and in combination with ciliary currents, further distinguishes the swimming of these brachiolariae from swimming by larvae of other echinoderms and larvae of acorn worms in the sister phylum Hemichordata.

The yellowtail rockfish, Sebastes flavidus, is a widespread and abundant mesopredator in the California Current Large Marine Ecosystem. We utilized stomach content and stable isotope analyses to investigate the trophic ecology of this species at three sites off central California just before (August–October 2013) and during (August and October 2014) a marine heat wave. Sebastes flavidus largely consumed pelagic prey (zooplankton and micronekton). Diets were dominated by tunicates (salps and pyrosomes), pelagic crustaceans (euphausiids, hyperid amphipods, larval decapods), and fishes, with the relative contribution of these prey taxa varying spatially (sample location, longitude, depth) and temporally (year, month), based on complementary multivariate analyses. Prey-specific indices demonstrated that individual S. flavidus diet composition typically was dominated by one of these prey groups, and that prey switching occurred based on the relative availability of prey and their energetic importance. Stable isotope analysis of δ15N indicated that the S. flavidus populations sampled in 2014 had been feeding at an elevated trophic position and more variable prey spectrum relative to 2013, probably as a consequence of greater piscivory and the incorporation of temporal changes in diet composition. Because its opportunistic feeding behavior reflects the dynamism and heterogeneity of the pelagic forage preyscape, S. flavidus may be an important ecosystem indicator species. For example, the novel incorporation of pyrosomes as a large portion of the diet of S. flavidus during 2013–2014 directly related to the massive increase in pyrosome abundance in the California Current during the 2014 marine heat wave.

The composition and abundance of the major zooplankton taxon tunicates were analyzed in a multi-year study and correlated with environmental parameters in the area around the hydrothermal vent field of Kueishantao (Turtle Island) in Taiwan. This provided the first study about tunicates above hydrothermal vents worldwide. We chose seven different stations for sample collection. Sampling was carried out in September of 2009, 2014, and 2015 (autumn) and June 2015 (summer). A total of ten tunicate species were identified belonging to the classes Appendicularia and Thaliacea during the above periods throughout the area. Considering the limited diversity of these organisms worldwide (40 species are identified in each class), we affirm that Kueishantao, a shallow water hydrothermal vent field, with 10 species provided an unexpected biodiversity hot spot for pelagic tunicates. The sampling of the organisms in the surface waters provided higher abundances compared to oblique tows. Comparing results from three autumn seasons we found that temperature values correlated with changes in tunicate abundances. We discovered strong seasonal changes in pelagic tunicate abundances over the entire survey period, with the highest abundances observed during autumn.

Lipids are key compounds in marine ecosystems being involved in organism growth, reproduction, and survival. Despite their biological significance and ease of measurement, the use of lipids in deep-sea studies is limited, as is our understanding of energy and nutrient flows in the deep ocean. Here, a comprehensive analysis of total lipid content, and lipid class and fatty acid composition, was used to explore functional diversity and nutritional content within a deep-sea faunal assemblage comprising 139 species from 8 phyla, including the Chordata, Arthropoda, and Cnidaria. A wide range of total lipid content and lipid class composition suggested a diversified set of energy allocation strategies across taxa. Overall, phospholipid was the dominant lipid class. While triacylglycerol was present in most taxa as the main form of energy storage, a few crustaceans, fish, jellyfishes, and corals had higher levels of wax esters/steryl esters instead. Type and amount of energy reserves may reflect dietary sources and environmental conditions for certain deep-sea taxa. Conversely, the composition of fatty acids was less diverse than that of lipid class composition, and large proportions of unsaturated fatty acids were detected, consistent with the growing literature on cold-water species. In addition, levels of unsaturation increased with depth, likely suggesting an adaptive strategy to maintain normal membrane structure and function in species found in deeper waters. Although proportions of n-3 fatty acids were high across all phyla, representatives of the Chordata and Arthropoda were the main reservoirs of these essential nutrients, thus suggesting health benefits to their consumers.

Phylogeographical studies can reveal hidden patterns in the evolutionary history of species. Comparative analyses of closely related species can further help disentangle the relative contributions of processes responsible for such patterns. In this work, the phylogeography of two aristeid species, Aristeus antennatus and Aristaeomorpha foliacea, was compared through multiple genetic markers. These marine shrimp species are of high commercial importance, and are exploited in the Mediterranean Sea (MED) and in Mozambique Channel (MOZ) where they occur in partial sympatry. Aristeus antennatus (N = 50) from Western and Eastern Mediterranean (WM and EM, respectively), Atlantic Ocean (AO) and MOZ, and Aristaeomorpha foliacea (N = 40) from WM, EM, MOZ North-Western Australia (AUS) were analyzed with two nuclear genes (PEPCK and NaK) and one mitochondrial (COI) gene. Within the study area differences were found between the two species in their phylogeographical patterns, suggesting distinct responses to environmental changes. Monophyly of Aristeus antennatus was found across its distributional range. This pattern contrasted by a deep evolutionary split within Aristaeomorpha foliacea where genetic diversity followed geography distinguishing MED-MOZ and AUS. We propose that the AUS lineage of A. foliacea warrants consideration as a distinct species, with consequent implications in systematics and resource management.

Over the last 25 years, research on biodiversity has expanded dramatically, fuelled by increasing threats to the natural world. However, the number of published studies is heavily weighted towards certain taxa, perhaps influencing conservation awareness of and funding for less-popular groups. Few studies have systematically quantified these biases, although information on this topic is important for informing future research and conservation priorities. We investigated: i) which animal taxa are being studied; ii) if any taxonomic biases are the same in temperate and tropical regions; iii) whether the taxon studied is named in the title of papers on biodiversity, perhaps reflecting a perception of what biodiversity is; iv) the geographical distribution of biodiversity research, compared with the distribution of biodiversity and threatened species; and v) the geographical distribution of authors' countries of origin. To do this, we used the search engine Web of Science to systematically sample a subset of the published literature with 'biodiversity' in the title. In total 526 research papers were screened-5% of all papers in Web of Science with biodiversity in the title. For each paper, details on taxonomic group, title phrasing, number of citations, study location, and author locations were recorded. Compared to the proportions of described species, we identified a considerable taxonomic weighting towards vertebrates and an under-representation of invertebrates (particularly arachnids and insects) in the published literature. This discrepancy is more pronounced in highly cited papers, and in tropical regions, with only 43% of biodiversity research in the tropics including invertebrates. Furthermore, while papers on vertebrate taxa typically did not specify the taxonomic group in the title, the converse was true for invertebrate papers. Biodiversity research is also biased geographically: studies are more frequently carried out in developed countries with larger economies, and for a given level of species or threatened species, tropical countries were understudied relative to temperate countries. Finally, biodiversity research is disproportionately authored by researchers from wealthier countries, with studies less likely to be carried out by scientists in lower-GDP nations. Our results highlight the need for a more systematic and directed evaluation of biodiversity studies, perhaps informing more targeted research towards those areas and taxa most depauperate in research. Only by doing so can we ensure that biodiversity research yields results that are relevant and applicable to all regions and that the information necessary for the conservation of threatened species is available to conservation practitioners.

DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two–week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.

International audience; Background to the work: For centuries taxonomy has relied on dead animal specimens, a practice that persists today despite the emergence of innovative biodiversity assessment methods. Taxonomists and conservationists are engaged in vigorous discussions over the necessity of killing animals for specimen sampling, but quantitative data on taxonomic trends and specimen sampling over time, which could inform these debates, are lacking.Methods: We interrogated a long-term research database documenting 2,723 land vertebrate and 419 invertebrate taxa from Madagascar, and their associated specimens conserved in the major natural history museums. We further compared specimen collection and species description rates for the birds, mammals and scorpions over the last two centuries, to identify trends and links to taxon descriptions.Results: We located 15,364 specimens documenting endemic mammals and 11,666 specimens documenting endemic birds collected between 1820 and 2010. Most specimens were collected at the time of the Mission Zoologique Franco-Anglo-Américaine (MZFAA) in the 1930s and during the last two decades, with major differences according to the groups considered. The small mammal and bat collections date primarily from recent years, and are paralleled by the description of new species. Lemur specimens were collected during the MZFAA but the descriptions of new taxa are recent, with the type series limited to non-killed specimens. Bird specimens, particularly of non-passerines, are mainly from the time of the MZFAA. The passerines have also been intensely collected during the last two decades; the new material has been used to solve the phylogeny of the groups and only two new endemic taxa of passerine birds have been described over the last two decades.Conclusions: Our data show that specimen collection has been critical for advancing our understanding of the taxonomy of Madagascar’s biodiversity at the onset of zoological work in Madagascar, but less so in recent decades. It is crucial to look for alternatives to avoid killing animals in the name of documenting life, and encourage all efforts to share the information attached to historical and recent collections held in natural history museums. In times of conservation crisis and the advancement in digital technologies and open source sharing, it seems obsolete to kill animals in well-known taxonomic groups for the sake of enriching natural history collections around the world.

Copyright: © 2017 Choo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited., Our understanding of early gnathostome evolution has been hampered by a generally scant fossil record beyond the Devonian. Recent discoveries from the late Silurian Xiaoxiang Fauna of Yunnan, China, have yielded significant new information, including the earliest articulated osteichthyan fossils from the Ludlow-aged Kuanti Formation. Here we describe the partial postcranium of a new primitive bony fish from the Kuanti Formation that represents the second known taxon of pre-Devonian osteichthyan revealing articulated remains. The new form, Sparalepis tingi gen. et sp. nov., displays similarities with Guiyu and Psarolepis, including a spine-bearing pectoral girdle and a placoderm-like dermal pelvic girdle, a structure only recently identified in early osteichthyans. The squamation with particularly thick rhombic scales shares an overall morphological similarity to that of Psarolepis. However, the anterior flank scales of Sparalepis possess an unusual interlocking system of ventral bulges embraced by dorsal concavities on the outer surfaces. A phylogenetic analysis resolves Sparalepis within a previously recovered cluster of stem-sarcopterygians including Guiyu, Psarolepis and Achoania. The high diversity of osteichthyans from the Ludlow of Yunnan strongly contrasts with other Silurian vertebrate assemblages, suggesting that the South China block may have been an early center of diversification for early gnathostomes, well before the advent of the Devonian “Age of Fishes”.

International audience; Growth series of Palaeozoic fishes are rare because of the fragility of larval and juvenile specimens owing to their weak mineralisation and the scarcity of articulated specimens. This rarity makes it difficult to describe early vertebrate growth patterns and processes in extinct taxa. Indeed, only a few growth series of complete Palaeozoic fishes are available; however, they allow the growth of isolated elements to be described and individual growth from these isolated elements to be inferred. In addition, isolated and in situ scales are generally abundant and well-preserved, and bring information on (1) their morphology and structure relevant to phylogenetic relationships and (2) individual growth patterns and processes relative to species ontogeny. The Late Devonian acanthodian Triazeugacanthus affinis from the Miguasha Fossil-Lagerstä tte preserves one of the best known fossilised ontogenies of early vertebrates because of the exceptional preservation, the large size range, and the abundance of complete specimens. Here, we present morphological, histological, and chemical data on scales from juvenile and adult specimens (scales not being formed in lar-vae). Histologically, Triazeugacanthus scales are composed of a basal layer of acellular bone housing Sharpey's fibers, a mid-layer of mesodentine, and a superficial layer of ganoine. Developmentally, scales grow first through concentric addition of mesodentine and bone around a central primordium and then through superposition of ganoine layers. Onto-genetically, scales form first in the region below the dorsal fin spine, then squamation spreads anteriorly and posteriorly, and on fin webs. Phylogenetically, Triazeugacanthus scales show similarities with acanthodians (e.g. " box-in-box " growth), chondrichthyans (e.g. squamation pattern), and actinopterygians (e.g. ganoine). Scale histology and growth are interpreted in the light of a new phylogenetic analysis of gnathostomes supporting acantho-dians as stem chondrichthyans.

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited., A series of recent studies recovered consistent phylogenetic scenarios of jawed vertebrates, such as the paraphyly of placoderms with respect to crown gnathostomes, and antiarchs as the sister group of all other jawed vertebrates. However, some of the hylogenetic relationships within the group have remained controversial, such as the positions of Entelognathus, ptyctodontids, and the Guiyu-lineage that comprises Guiyu, Psarolepis and Achoania. The revision of the dataset in a recent study reveals a modified phylogenetic hypothesis, which shows that some of these phylogenetic conflicts were sourced from a few inadvertent miscodings. The interrelationships of early gnathostomes are addressed based on a combined new dataset with 103 taxa and 335 characters, which is the most comprehensive morphological dataset constructed to date. This dataset is investigated in a phylogenetic context using maximum parsimony (MP), Bayesian inference (BI) and maximum likelihood (ML) approaches in an attempt to explore the consensus and incongruence between the hypotheses of early gnathostome interrelationships recovered from different methods. Our findings consistently corroborate the paraphyly of placoderms, all `acanthodians' as a paraphyletic stem group of chondrichthyans, Entelognathus as a stem gnathostome, and the Guiyu-lineage as stem sarcopterygians. The incongruence using different methods is less significant than the consensus, and mainly relates to the positions of the placoderm Wuttagoonaspis, the stem chondrichthyan Ramirosuarezia, and the stem osteichthyan LophosteusÐthe taxa that are either poorly known or highly specialized in character complement. Given that the different performances of each phylogenetic approach, our study provides an empirical case that the multiple phylogenetic analyses of morphological data are mutually complementary rather than redundant.

Although genotype-by-environment interaction has long been used to unveil the genetic variation that affects Darwinian fitness, the mechanisms underlying the interaction usually remain unknown. Genetic variation at the dimeric glycolytic enzyme phosphoglucoisomerase (Pgi) has been observed to interact with temperature to explain the variation in the individual performance of the butterfly Melitaea cinxia. At relatively high temperature, individuals with Pgi-non-f genotypes generally surpass those with Pgi-f genotypes, while the opposite applies at relatively low temperature. In this study, we did protein structure predictions and BlastP homology searches with the aim to understand the structural basis for this temperature-dependent difference in the performance of M. cinxia. Our results show that, at amino acid (AA) site 372, one of the two sites that distinguish Pgi-f (the translated polypeptide of the Pgi-f allele) from Pgi-non-f (the translated polypeptide of the Pgi-non-f allele), the Pgi-non-f-related residue strengthens an electrostatic attraction between a pair of residues (Glu373-Lys472) that are from different monomers, compared to the Pgi-f-related residue. Further, BlastP searches of animal protein sequences reveal a dramatic excess of electrostatically attractive combinations of the residues at the Pgi AA sites equivalent to sites 373 and 472 in M. cinxia. This suggests that factors enhancing the inter-monomer interaction between these two sites, and therefore helping the tight association of two Pgi monomers, are favourable. Our homology-modelling results also show that, at the second AA site that distinguishes Pgi-f from Pgi-non-f in M. cinxia, the Pgi-non-f-related residue is more entropy-favourable (leading to higher structural stability) than the Pgi-f-related residue. To sum up, this study suggests a higher structural stability of the protein products of the Pgi-non-f genotypes than those of the Pgi-f genotypes, which may explain why individuals carrying Pgi-non-f genotypes outperform those carrying Pgi-f genotypes at stressful high temerature.

Phylum Hemichordata, composed of worm-like Enteropneusta and colonial Pterobranchia, has been reported to only contain about 100 species. However, recent studies of hemichordate phylogeny and taxonomy suggest the species number has been largely underestimated. One issue is that species must be described by experts, and historically few taxonomists have studied this group of marine invertebrates. Despite this previous lack of coverage, interest in hemichordates has piqued in the past couple of decades, as they are critical to understanding the evolution of chordates–as acorn worms likely resemble the deuterostome ancestor more closely than any other extant animal. This review provides an overview of our current knowledge of hemichordates, focusing specifically on their global biodiversity, geographic distribution, and taxonomy. Using information available in the World Register of Marine Species and published literature, we assembled a list of 130 described, extant species. The majority (83%) of these species are enteropneusts, and more taxonomic descriptions are forthcoming. Ptychoderidae contained the greatest number of species (41 species), closely followed by Harrimaniidae (40 species), of the recognized hemichordate families. Hemichordates are found throughout the world’s oceans, with the highest reported numbers by regions with marine labs and diligent taxonomic efforts (e.g. North Pacific and North Atlantic). Pterobranchs are abundant in Antarctica, but have also been found at lower latitudes. We consider this a baseline report and expect new species of Hemichordata will continue to be discovered and described as new marine habitats are characterized and explored.

The S100 proteins are a large family of signaling proteins that play critical roles in biology and disease. Many S100 proteins bind Zn2+, Cu2+, and/or Mn2+ as part of their biological functions; however, the evolutionary origins of binding remain obscure. One key question is whether divalent transition metal binding is ancestral, or instead arose independently on multiple lineages. To tackle this question, we combined phylogenetics with biophysical characterization of modern S100 proteins. We demonstrate an earlier origin for established S100 subfamilies than previously believed, and reveal that transition metal binding is widely distributed across the tree. Using isothermal titration calorimetry, we found that Cu2+ and Zn2+ binding are common features of the family: the full breadth of human S100 paralogs-as well as two early-branching S100 proteins found in the tunicate Oikopleura dioica-bind these metals with μM affinity and stoichiometries ranging from 1:1 to 3:1 (metal:protein). While binding is consistent across the tree, structural responses to binding are quite variable. Further, mutational analysis and structural modeling revealed that transition metal binding occurs at different sites in different S100 proteins. This is consistent with multiple origins of transition metal binding over the evolution of this protein family. Our work reveals an evolutionary pattern in which the overall phenotype of binding is a constant feature of S100 proteins, even while the site and mechanism of binding is evolutionarily labile.

While studies of taxonomy usually focus on species description, there is also a taxonomic correction process that retests and updates existing species circumscriptions on the basis of new evidence. These corrections may themselves be subsequently retested and recorrected. We studied this correction process by using the Check-List of North and Middle American Birds, a well-known taxonomic checklist that spans 130 years. We identified 142 lumps and 95 splits across sixty-three versions of the Check-List and found that while lumping rates have markedly decreased since the 1970s, splitting rates are accelerating. We found that 74% of North American bird species recognized today have never been corrected (i.e., lumped or split) over the period of the checklist, while 16% have been corrected exactly once and 10% have been corrected twice or more. Since North American bird species are known to have been extensively lumped in the first half of the 20th century with the advent of the biological species concept, we determined whether most splits seen today were the result of those lumps being recorrected. We found that 5% of lumps and 23% of splits fully reverted previous corrections, while a further 3% of lumps and 13% of splits are partial reversions. These results show a taxonomic correction process with moderate levels of recorrection, particularly of previous lumps. However, 81% of corrections do not revert any previous corrections, suggesting that the majority result in novel circumscriptions not previously recognized by the Check-List. We could find no order or family with a significantly higher rate of correction than any other, but twenty-two genera as currently recognized by the AOU do have significantly higher rates than others. Given the currently accelerating rate of splitting, prediction of the end-point of the taxonomic recorrection process is difficult, and many entirely new taxonomic concepts are still being, and likely will continue to be, proposed and further tested.

The taxonomy of Early Devonian placoderm material from the Lochkovian and Pragian of the Prague basin, previously attributed to the genera Radotina and Holopetalichthys, is revised. The Pragian species Radotina tesselata Gross 1958 shares detailed similarities with the holotype of the Lochkovian Radotina kosorensis Gross 1950, which is also the holotype of the genus; the assignation of both species to Radotina is supported. However, the Lochkovian material previously attributed to Radotina kosorensis also contains two unrecognised taxa, distinguishable from Radotina at the generic level: these are here named Tlamaspis and Sudaspis. The disputed genus Holopetalichthys, synonymised with Radotina by some previous authors, is shown to be valid. Furthermore, whereas Radotina, Tlamaspis and Sudaspis can all be assigned to the group Acanthothoracii, on the basis of several features including possession of a projecting prenasal region of the endocranium, Holopetalichthys lacks such a region and is probably not an acanthothoracid. Skull roof patterns and other aspects of morphology vary greatly between these taxa. Radotina has a substantially tesselated skull roof, whereas the skull roofs of Tlamaspis and Holopetalichthys appear to lack tesserae altogether. Tlamaspis has an extremely elongated facial region and appears to lack a premedian plate. Sudaspis has a long prenasal region, but unlike Tlamaspis the postnasal face is not elongated. Past descriptions of the braincase of ' Radotina' and the skull roofs of ' Radotina' and ' Holopetalichthys' incorporate data from more than one taxon, giving rise to spurious characterisations including an apparently extreme degree of skull roof variability. These descriptions should all be disregarded.

A new horseshoe crab species, Limulus darwini, is described from the uppermost Jurassic (ca. 148 Ma) near-shore sediments of the Kcynia Formation, central Poland. The only extant species Limulus polyphemus (Linnaeus) inhabits brackish-marine, shallow water environments of the east coast of the United States. Here it is shown that there are no important morphological differences between the Kcynia Formation specimens and extant juvenile representatives of the genus Limulus. The palaeoecological setting inhabited by the new species and the trophic relationships of extant horseshoe crabs are discussed in an attempt to determine the potential range of food items ingested by these Mesozoic xiphosurans. In this paper we propose the adoption of a new term stabilomorphism, this being: an effect of a specific formula of adaptative strategy among organisms whose taxonomic status does not exceed genus-level. A high effectiveness of adaptation significantly reduces the need for differentiated phenotypic variants in response to environmental changes and provides for long-term evolutionary success.

The neurohypophysial hormone arginine vasopressin (AVP) plays important roles in fluid regulation and vascular resistance. Differences in AVP receptor expression, particularly mediated through variation in the noncoding promoter region of the primary receptor for AVP (AVPR1a), may play a role in social phenotypes, particularly social monogamy, in rodents and humans. Among primates, social monogamy is rare, but is common among New World monkeys (NWM). AVP is a nonapeptide and generally conserved among eutherian mammals, although a recent paper demonstrated that some NWM species possess a novel form of the related neuropeptide hormone, oxytocin. We therefore characterized variation in the AVP and AVPR1a genes in 22 species representing every genus in the three major platyrrhine families (Cebidae, Atelidae and Pitheciidae). For AVP, a total of 16 synonymous substitutions were detected in 15 NWM species. No non-synonymous substitutions were noted, hence, AVP is conserved in NWM. By contrast, relative to the human AVPR1a, 66 predicted amino acids (AA) substitutions were identified in NWM. The AVPR1a N-terminus (ligand binding domain), third intracellular (G-protein binding domain), and C-terminus were variable among species. Complex evolution of AVPR1a is also apparent in NWM. A molecular phylogenetic tree inferred from AVPR1a coding sequences revealed some consensus taxonomic separation by families, but also a mixed group composed of genera from all three families. The overall dN/dS ratio of AVPR1a was 0.11, but signals of positive selection in distinct AVPR1a regions were observed, including the N-terminus, in which we identified six potential positive selection sites. AA substitutions at positions 241, 319, 399 and 409 occurred uniquely in marmosets and tamarins. Our results enhance the appreciation of genetic diversity in the mammalian AVP/AVPR1a system, and set the stage for molecular modeling of the neurohypophyseal hormones and social behavior in primates.

This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.

Oysters, with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. Our study is intended to generate new EST-SNP markers and to evaluate their potential for cross-species utilization in phylogenetic study of the genus Crassostrea. In the study, 57 novel SNPs were developed from an EST database of C. gigas by the HRM (high-resolution melting) method. Transferability of 377 SNPs developed for C. gigas was examined on four other Crassostrea species: C. sikamea, C. angulata, C. hongkongensis and C. ariakensis. Among the 377 primer pairs tested, 311 (82.5%) primers showed amplification in C. sikamea, 353 (93.6%) in C. angulata, 254 (67.4%) in C. hongkongensis and 253 (67.1%) in C. ariakensis. A total of 214 SNPs were found to be transferable to all four species. Phylogenetic analyses showed that C. hongkongensis was a sister species of C. ariakensis and that this clade was sister to the clade containing C. sikamea, C. angulata and C. gigas. Within this clade, C. gigas and C. angulata had the closest relationship, with C. sikamea being the sister group. In addition, we detected eight SNPs as potentially being under selection by two outlier tests (fdist and hierarchical methods). The SNPs studied here should be useful for genetic diversity, comparative mapping and phylogenetic studies across species in Crassostrea and the candidate outlier SNPs are worth exploring in more detail regarding association genetics and functional studies.

Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical.

Background The overabundance of synonyms is an unavoidable by-product of taxonomic practice in insects. How to reduce or even eliminate synonymy has long been a great challenge for insect taxonomists. The scorpionflies Panorpa obtusa Cheng, 1949 and Panorpa leei Cheng, 1949 (Insecta: Mecoptera: Panorpidae) were originally described from Taibaishan in the Qinling Mountains with identical collection data and both are based on a single gender, the former on a male and the latter on two females. However, whether P. leei is conspecific with P. obtusa or a good species remains an unsolved problem. Results On the basis of intensive morphological comparison of 93 males and 53 females of scorpionflies collected from the type locality using light and scanning electron microscopy, we found P. obtusa has considerable morphological variation (especially the wing markings and genitalia in both male and female), and Panorpa leei is totally comprised of one of the morphs of P. obtusa. Conclusions In combination with identical type localities and overlapping morphological variation, P. leei Cheng is proposed as a junior subjective synonym of P. obtusa Cheng. To avoid synonyms, taxonomists should pay more attention to individual variation and base decisions on a series of specimens to describe new species.

Coalescent theory provides powerful models for population genetic inference and is now increasingly important in estimates of divergence times and speciation research. We use molecular data and methods based on coalescent theory to investigate whether genetic evidence supports the hypothesis of A. pretrei and A. tucumana as separate species and whether genetic data allow us to assess which allopatric model seems to better explain the diversification process in these taxa. We sampled 13 A. tucumana from two provinces in northern Argentina and 28 A. pretrei from nine localities of Rio Grande do Sul, Brazil. A 491 bp segment of the mitochondrial gene cytochrome c oxidase I was evaluated using the haplotype network and phylogenetic methods. The divergence time and other demographic quantities were estimated using the isolation and migration model based on coalescent theory. The network and phylogenetic reconstructions showed similar results, supporting reciprocal monophyly for these two taxa. The divergence time of lineage separation was estimated to be approximately 1.3 million years ago, which corresponds to the lower Pleistocene. Our results enforce the current taxonomic status for these two Amazon species. They also support that A. pretrei and A. tucumana diverged with little or no gene flow approximately 1.3 million years ago, most likely after the establishment of a small population in the Southern Yungas forest by dispersion of a few founders from the A. pretrei ancestral population. This process may have been favored by habitat corridors formed in hot and humid periods of the Quaternary. Considering that these two species are considered threatened, the results were evaluated for their implications for the conservation of these two species. Fil: Rocha, Amanda V.. Universidade do Brasília; Brasil Fil: Rivera, Luis Osvaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia de Jujuy. Universidad Nacional de Jujuy. Centro de Investigaciones y Transferencia de Jujuy; Argentina Fil: Martinez, Jaime. Associação Amigos do Meio Ambiente.Projeto Charão; Brasil Fil: Prestes, Nêmora P.. Associação Amigos do Meio Ambiente.Projeto Charão; Brasil Fil: Caparroz, Renato. Universidade do Brasília; Brasil

Islands provide exciting opportunities for exploring ecological and evolutionary mechanisms. The oceanic island of Sao Tome in the Gulf of Guinea exhibits high diversity of fauna including the endemic caecilian amphibian, Schistometopum thomense. Variation in pigmentation, morphology and size of this taxon over its c. 45 km island range is extreme, motivating a number of taxonomic, ecological, and evolutionary hypotheses to explain the observed diversity. We conducted a population genetic study of S. thomense using partial sequences of two mitochondrial DNA genes (ND4 and 16S), together with morphological examination, to address competing hypotheses of taxonomic or clinal variation. Using Bayesian phylogenetic analysis and Spatial Analysis of Molecular Variance, we found evidence of four geographic clades, whose range and approximated age (c. 253 Kya – 27 Kya) are consistent with the spread and age of recent volcanic flows. These clades explained 90% of variation in ND4 (φCT = 0.892), and diverged by 4.3% minimum pairwise distance at the deepest node. Most notably, using Mismatch Distributions and Mantel Tests, we identified a zone of population admixture that dissected the island. In the northern clade, we found evidence of recent population expansion (Fu's Fs = −13.08 and Tajima's D = −1.80) and limited dispersal (Mantel correlation coefficient = 0.36, p = 0.01). Color assignment to clades was not absolute. Paired with multinomial regression of chromatic data, our analyses suggested that the genetic groups and a latitudinal gradient together describe variation in color of S. thomense. We propose that volcanism and limited dispersal ability are the likely proximal causes of the observed genetic structure. This is the first population genetic study of any caecilian and demonstrates that these animals have deep genetic divisions over very small areas in accordance with previous speculations of low dispersal abilities.

Made available in DSpace on 2015-03-18T15:56:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-06-10Bitstream added on 2015-03-18T16:28:30Z : No. of bitstreams: 1 WOS000340947700009.pdf: 18707739 bytes, checksum: 543c697fb1e779c87a9d2fd452f2af88 (MD5) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The Drosophila saltans group consists of five subgroups and 21 species, most of which have been identified only by morphological aspects of the male terminalia revealed by drawings using a camera lucida and a bright-field microscope. However, several species in the group, mainly those included in the saltans subgroup, are difficult to differentiate using only these characteristics. In this study, we used scanning electron microscopy (SEM) to analyze 19 structures of the male terminalia in 10 species from the five saltans subgroups. Among these structures, nine could be identified only through SEM analysis. We aimed to find other characteristics useful for morphological recognition of these species and to use these characteristics for phylogenetic reconstruction. These morphological differences enabled us to effectively distinguish among sibling species. These findings confirmed the monophyly of this group as previously determined in evolutionary studies based on other markers. The single most parsimonious tree (CI = 87 and RI = 90) indicated that the cordata subgroup is the most basal lineage and the saltans subgroup is the most apical lineage, as shown in earlier studies based on morphological data. However, our findings differed somewhat from these studies with respect to the phylogenetic relationships of species in the saltans group indicating that this group is still a puzzle that remains to be deciphered. Univ Sao Paulo, Dept Genet, BR-14049 Ribeirao Preto, Brazil Sao Paulo State Univ, UNESP IBILCE, Dept Bot & Zool, Sao Jose Do Rio Preto, SP, Brazil Sao Paulo State Univ, UNESP IBILCE, Dept Biol, Sao Jose Do Rio Preto, SP, Brazil Sao Paulo State Univ, UNESP IBILCE, Dept Bot & Zool, Sao Jose Do Rio Preto, SP, Brazil Sao Paulo State Univ, UNESP IBILCE, Dept Biol, Sao Jose Do Rio Preto, SP, Brazil FAPESP: 07/07180-3

Two species of fossil polydesmidan millipedes (Diplopoda: Polydesmida) embedded in amber are described from Miocene strata near Simojovel, in the Chiapas Highlands, Mexico. Maatidesmus paachtun gen. et sp. nov., placed into Chelodesmidae Cook, 1895, and Anbarrhacus adamantis gen. et sp. nov., assigned in the family Platyrhacidae Pocock, 1895. Morphological data from fossil specimens have been recovered using 3D X-ray micro-computed tomography and regular to infrared-reflected microscopy. Both fossil species are recognizable as new primarily but not exclusively, by collum margin modification and remarkable paranotal and metatergite dorsal sculpture.

Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, occupying benthic marine habitats across all depths and latitudes. Actiniaria comprises approximately 1,200 species of solitary and skeleton-less polyps and lacks any anatomical synapomorphy. Although monophyly is anticipated based on higher-level molecular phylogenies of Cnidaria, to date, monophyly has not been explicitly tested and at least some hypotheses on the diversification of Hexacorallia have suggested that actiniarians are para- or poly-phyletic. Published phylogenies have demonstrated the inadequacy of existing morphological-based classifications within Actiniaria. Superfamilial groups and most families and genera that have been rigorously studied are not monophyletic, indicating conflict with the current hierarchical classification. We test the monophyly of Actiniaria using two nuclear and three mitochondrial genes with multiple analytical methods. These analyses are the first to include representatives of all three currently-recognized suborders within Actiniaria. We do not recover Actiniaria as a monophyletic clade: the deep-sea anemone Boloceroides daphneae, previously included within the infraorder Boloceroidaria, is resolved outside of Actiniaria in several of the analyses. We erect a new genus and family for B. daphneae, and rank this taxon incerti ordinis. Based on our comprehensive phylogeny, we propose a new formal higher-level classification for Actiniaria composed of only two suborders, Anenthemonae and Enthemonae. Suborder Anenthemonae includes actiniarians with a unique arrangement of mesenteries (members of Edwardsiidae and former suborder Endocoelantheae). Suborder Enthemonae includes actiniarians with the typical arrangement of mesenteries for actiniarians (members of former suborders Protantheae, Ptychodacteae, and Nynantheae and subgroups therein). We also erect subgroups within these two newly-erected suborders. Although some relationships among these newly-defined groups are still ambiguous, morphological and molecular results are consistent enough to proceed with a new higher-level classification and to discuss the putative functional and evolutionary significance of several morphological attributes within Actiniaria.

Although stream-dwelling gudgeons (Cyprinidae, genus: Gobio) are widespread in Central Europe, the taxonomy of this group and the distribution of its species are still unexplored in detail. The aims of our study are to ascertain taxonomic composition and distribution of the former Gobio gobio superspecies in the inner area of the Carpathian Basin. Since the presence of cryptic species is suspected in this area, we examined the taxonomic and phylogenetic relationships of Central European Gobio taxa by sequencing the mitochondrial DNA control region (mtCR). Additionally, we characterized the genetic structure of 27 stream-dwelling gudgeon populations of this area by Amplified Fragment Length Polymorphism (AFLP). Results of mtCR analysis proved the presence of three species already known as G. obtusirostris (dominant in NW-Hungary), G. gobio (sporadic) and G. carpathicus (sporadic). Additionally, the analysis revealed the existence of one doubtful taxon, G. sp1 (dominant in NE-Hungary), and a new isolated haplogroup (dominant in SW-Hungary). Although Network analysis showed significant detachment among haplogroups, their genetic distances were quite small. Therefore Bayesian phylogenetic analysis showed weak nodal support for the branching pattern both for newly described haplotypes, and for the already accepted species. AFLP data showed distinct population structure and a clear pattern of isolation was revealed by distance of stocks. At the same time, level of separation was not affected by the altitudinal position of sites. Moreover we found three major clusters of populations which were separated according to hydrographic regions, and corresponded to the findings of mtCR analysis. Our results suggest the on-going speciation of gudgeons in the Carpathian Basin, however the separation of haplogroups seems to only be an intermediate phase. The discovered natural pattern seems to be only slightly influenced by anthropogenic impacts. Additionally our results put into question the suitability of the recently accepted within Gobio genus taxonomy.

Aim: To comprehend the phylogeographic patterns of genetic variation in anurans at Taiwan Island, this study attempted to examine (1) the existence of various geological barriers (Central Mountain Ranges, CMRs); and (2) the genetic variation of Bufo bankorensis using mtDNA sequences among populations located in different regions of Taiwan, characterized by different climates and existing under extreme conditions when compared available sequences of related species B. gargarizans of mainland China. Methodology/Principal Findings: Phylogenetic analyses of the dataset with mitochondrial DNA (mtDNA) D-loop gene (348 bp) recovered a close relationship between B. bankorensis and B. gargarizans, identified three distinct lineages. Furthermore, the network of mtDNA D-loop gene (564 bp) amplified (279 individuals, 27 localities) from Taiwan Island indicated three divergent clades within B. bankorensis (Clade W, E and S), corresponding to the geography, thereby verifying the importance of the CMRs and Kaoping River drainage as major biogeographic barriers. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the total population and Clade W, with horizons dated to approximately 0.08 and 0.07 Mya, respectively. These results suggest that the population expansion of Taiwan Island species B. bankorensis might have resulted from the release of available habitat in post-glacial periods, the genetic variation on mtDNA showing habitat selection, subsequent population dispersal, and codistribution among clades. Conclusions: The multiple origins (different clades) of B. bankorensis mtDNA sequences were first evident in this study. The divergent genetic clades found within B. bankorensis could be independent colonization by previously diverged lineages; inferring B. bankorensis originated from B. gargarizans of mainland China, then dispersal followed by isolation within Taiwan Island. Highly divergent clades between W and E of B. bankorensis, implies that the CMRs serve as a genetic barrier and separated the whole island into the western and eastern phylogroups.

If potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species. However, mitochondrial DNA introgression hampers the correct estimation of ecological divergence. We test the hypothesis that estimated niche divergence differs when considering nuclear DNA composition or mitochondrial DNA type as representing the true species range. We use empirical data of two crested newt species (Amphibia: Triturus) which possess introgressed mitochondrial DNA from a third species in part of their ranges. We analyze the data in environmental space by determining Fisher distances in a principal component analysis and in geographical space by determining geographical overlap of species distribution models. We find that under mtDNA guidance in one of the two study cases niche divergence is overestimated, whereas in the other it is underestimated. In the light of our results we discuss the role of estimated niche divergence in species delineation.

Citizen science is a research practice that relies on public contributions of data. The strong recognition of its educational value combined with the need for novel methods to handle subsequent large and complex data sets raises the question: Is citizen science effective at science? A quantitative assessment of the contributions of citizen science for its core purpose – scientific research – is lacking. We examined the contribution of citizen science to a review paper by ornithologists in which they formulated ten central claims about the impact of climate change on avian migration. Citizen science was never explicitly mentioned in the review article. For each of the claims, these ornithologists scored their opinions about the amount of research effort invested in each claim and how strongly the claim was supported by evidence. This allowed us to also determine whether their trust in claims was, unwittingly or not, related to the degree to which the claims relied primarily on data generated by citizen scientists. We found that papers based on citizen science constituted between 24 and 77% of the references backing each claim, with no evidence of a mistrust of claims that relied heavily on citizen-science data. We reveal that many of these papers may not easily be recognized as drawing upon volunteer contributions, as the search terms “citizen science” and “volunteer” would have overlooked the majority of the studies that back the ten claims about birds and climate change. Our results suggest that the significance of citizen science to global research, an endeavor that is reliant on long-term information at large spatial scales, might be far greater than is readily perceived. To better understand and track the contributions of citizen science in the future, we urge researchers to use the keyword “citizen science” in papers that draw on efforts of non-professionals.

The bryozoan genus Scrupocellaria comprises about 80 species in the family Candidae. We propose a hypothesis for the phylogenetic relationships among species assigned to Scrupocellaria to serve as framework for a phylogenetic classification using 35 morphological characters. Our results suggest that the genus Scrupocellaria is polyphyletic. Scrupocellaria s. str. is redefined according to four morphological features: vibracular chamber with a curved setal groove, ooecium with a single ectooecial fenestra, two axillary vibracula, and a membranous operculum with a distinct distal rim. Thus, the genus includes only 11 species: Scrupocellaria aegeensis, Scrupocellaria delilii, Scrupocellaria harmeri, Scrupocellaria incurvata, Scrupocellaria inermis, Scrupocellaria intermedia, Scrupocellaria jullieni, Scrupocellaria minuta, Scrupocellaria puelcha, Scrupocellaria scrupea, and Scrupocellaria scruposa. The monophyly of Cradoscrupocellaria is supported and five new genera are erected: Aquiloniella n. gen., Aspiscellaria n. gen., Paralicornia n. gen., Pomocellaria n. gen. and Scrupocaberea n. gen. Two other new genera, Bathycellaria n. gen. and Sinocellaria n. gen., are erected to accommodate two poorly known species, Scrupocellaria profundis Osburn and Scrupocellaria uniseriata Liu, respectively. Scrupocellaria congesta is tentatively assigned to Tricellaria. Fifteen species are reassigned to Licornia: Licornia cookie n. comb., Licornia micheli n. comb., Licornia milneri n. comb., Licornia curvata n. comb., Licornia diegensis n. comb., Licornia drachi n. comb., Licornia mexicana n. comb., Licornia pugnax n. comb., Licornia raigadensis n. comb., Licornia regularis n. comb., Licornia resseri n. comb., Licornia securifera n. comb., Licornia spinigera n. comb., Licornia tridentata n. comb., and Licornia wasinensis n. comb. Notoplites americanus n. name is proposed as a replacement name for Scrupocellaria clausa Canu & Bassler. Three fossil species are reassigned to Canda: Canda rathbuni n. comb., Canda triangulata n. comb. and Canda williardi n. comb. A species is reassigned to Notoplites, Notoplites elegantissima n. comb. The generic assignment of eleven species of Scrupocellaria, including Scrupocellaria macandrei, remains uncertain.

Background: Fossil species that can be conclusively identified as stem-relatives of stick- and leaf-insects (Phasmatodea) are extremely rare, especially for the Mesozoic era. This dearth in the paleontological record makes assessments on the origin and age of the group problematic and impedes investigations of evolutionary key aspects, such as wing development, sexual size dimorphism and plant mimicry. Methodology/Principal Findings: A new fossil insect species, Cretophasmomima melanogramma Wang, Bethoux and Ren sp. nov., is described on the basis of one female and two male specimens recovered from the Yixian Formation (Early Cretaceous, ca. 126 +/- 4 mya; Inner Mongolia, NE China; known as 'Jehol biota'). The occurrence of a female abdominal operculum and of a characteristic 'shoulder pad' in the forewing allows for the interpretation of a true stem-Phasmatodea. In contrast to the situation in extant forms, sexual size dimorphism is only weakly female-biased in this species. The peculiar wing coloration, viz. dark longitudinal veins, suggests that the leaf-shaped plant organ from the contemporaneous 'gymnosperm' Membranifolia admirabilis was used as model for crypsis. Conclusions/Significance: As early as in the Early Cretaceous, some stem-Phasmatodea achieved effective leaf mimicry, although additional refinements characteristic of recent forms, such as curved fore femora, were still lacking. The diversification of small-sized arboreal insectivore birds and mammals might have triggered the acquisition of such primary defenses.

The skeleton of a natural whale fall discovered in the Southern Ocean at 1,445 m was densely covered by one small, janirid isopod. Jaera tyleri sp. nov. is the first of its genus found in the southern hemisphere and in the deep sea and is described herein. Morphological and molecular investigations revealed the systematic position of this species new to science. Phylogenetic analysis of the 18S locus confirms that this species falls in a strongly supported monophyletic clade of Jaera species. The whale bone habitat of J. tyleri sp. nov. is quite different from those of other species of the genus Jaera. The analysis of bathymetric and distribution patterns of the Janiridae in general and Jaera specifically confirm the unusualness of the habitat for this isopod species. The abundance of J. tyleri sp. nov. on the whale bones and its absence from other nearby habitats suggests it to be a whale-fall specialist. The analysis of the size-frequency distributions of J. tyleri sp. nov. suggests multimodal population structure with continuous breeding activity throughout the year. The fecundity of the species is low but in line with reduced fecundity observed in polar and small-sized isopods.

We evaluate the intra- and interspecific diversity in the four South African rodent species of the genus Dendromus. The molecular phylogenetic analysis on twenty-three individuals have been conducted on a combined dataset of nuclear and mitochondrial markers. Moreover, the extent and processes underlying chromosomal variation, have been investigated on three species by mean of G-, C-bands, NORs and Zoo-FISH analysis. The molecular analysis shows the presence of six monophyletic lineages corresponding to D. mesomelas, D. mystacalis and four lineages within D. cfr. melanotis with high divergence values (ranges: 10.6% – 18.3%) that raises the question of the possible presence of cryptic species. The first description of the karyotype for D. mesomelas and D. mystacalis and C- and G- banding for one lineage of D. cfr. melanotis are reported highlighting an extended karyotype reorganization in the genus. Furthermore, the G-banding and Zoo-FISH evidenced an autosome-sex chromosome translocation characterizing all the species and our timing estimates this mutation date back 7.4 mya (Late Miocene). Finally, the molecular clock suggests that cladogenesis took place since the end of Miocene to Plio-Pleistocene, probably due to ecological factors, isolation in refugia followed by differential adaptation to the mesic or dry habitat.

Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

The theraphosid spider genera Heterophrictus Pocock, 1900 and Neoheterophrictus Siliwal & Raven, 2012 are rediagnosed in this paper and a new genus, Sahydroaraneus gen. nov. is described from Southern Western Ghats. Four new species (two each of Heterophrictus and Neoheterophrictus) and one of Sahydroaraneus gen. nov. are described from the Western Ghats. Plesiophrictus mahabaleshwari Tikader, 1977 is removed from the synonymy of Heterophrictus milleti Pocock, 1900 and is treated as a junior synonym of Heterophrictus blatteri (Gravely, 1935). Plesiophrictus bhori Gravely, 1915 is transferred to the genus Neoheterophrictus, Neoheterophrictus bhori (Gravely, 1915) new combination. The genus, Sahydroaraneus gen. nov., resembles tarantula belonging to the genus, Neoheterophrictus but differs with respect to structure of tibial apophysis and spermathecae. Detailed ultra-structure of setae type of the Indian Eumenophorinae is presented for the first time along with notes on their biogeography. Common elements among Africa, Madagascar and India like the Eumenophorinae and several other mygalomorph spiders advocate mygalomorphae as an important group for evolutionary investigation due to their inability for long distance dispersal rendering the members restrictive in distribution.

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity—past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens “from all angles” and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. (“Natural-colour” is used to contrast with “false-colour”, i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control.

Background The freshwater calanoid Mastigodiaptomus is a genus with high richness in the Americas and is composed of nine species, seven recorded in Mexico and four that are apparently endemic to small areas. Mastigodiaptomus albuquerquensis is a common, widely distributed species ranging from the southern USA to Central America. This species can be easily identified by a notable butterfly-like sclerotization on the basis of the right fifth leg of males. Nevertheless, morphological differences observed among populations throughout this species distributional range have led to the description of several related species or subspecies, such as M. albuquerquensis patzcuarensis from Lake Patzcuaro in the Central Plateau of Mexico. Methods Genetic results based on barcodes, morphology based on scanning electron and light microscopy images, and morphometric analyses were used to describe cryptic species within the M. albuquerquensis complex. Results The morphological analyses coincided partially with the genetic markers, suggesting the existence of at least two sibling species: M. albuquerquensis s. str. and M. patzcuarensis. A third species was genetically separated but was morphologically indistinguishable from the M. patzcuarensis group. Conclusions Hidden diversity has been a major problem in establishing real patterns of species distribution and genetic acquisition from megadiverse hotspots such as Mexico, where the Nearctic and the Neotropical regions of the Americas meet. Barcodes can help taxonomists to reveal and formally name these new species. Here, we describe two of three potential species highlighted by the use of barcodes: M. albuquerquensis s. str. in the northern semi-desert and M. patzcuarensis on the Central Plateau at more than 2000 m above sea level.

Insect phylogeny has recently been the focus of renewed interest as advances in sequencing techniques make it possible to rapidly generate large amounts of genomic or transcriptomic data for a species of interest. However, large numbers of markers are not sufficient to guarantee accurate phylogenetic reconstruction, and the choice of the model of sequence evolution as well as adequate taxonomic sampling are as important for phylogenomic studies as they are for single-gene phylogenies. Recently, the sequence of the genome of a strepsipteran has been published and used to place Strepsiptera as sister group to Coleoptera. However, this conclusion relied on a data set that did not include representatives of Neuropterida or of coleopteran lineages formerly proposed to be related to Strepsiptera. Furthermore, it did not use models that are robust against the long branch attraction artifact. Here we have sequenced the transcriptomes of seven key species to complete a data set comprising 36 species to study the higher level phylogeny of insects, with a particular focus on Neuropteroidea (Coleoptera, Strepsiptera, Neuropterida), especially on coleopteran taxa considered as potential close relatives of Strepsiptera. Using models robust against the long branch attraction artifact we find a highly resolved phylogeny that confirms the position of Strepsiptera as a sister group to Coleoptera, rather than as an internal clade of Coleoptera, and sheds new light onto the phylogeny of Neuropteroidea.

The Lourinha Formation (Kimmeridgian-Tithonian) of Central West Portugal is well known for its diversified dinosaur fauna similar to that of the Morrison Formation of North America; both areas share dinosaur taxa including the top predator Torvosaurus, reported in Portugal. The material assigned to the Portuguese T. tanneri, consisting of a right maxilla and an incomplete caudal centrum, was briefly described in the literature and a thorough description of these bones is here given for the first time. A comparison with material referred to Torvosaurus tanneri allows us to highlight some important differences justifying the creation of a distinct Eastern species. Torvosaurus gurneyi n. sp. displays two autapomorphies among Megalosauroidea, a maxilla possessing fewer than eleven teeth and an interdental wall nearly coincidental with the lateral wall of the maxillary body. In addition, it differs from T. tanneri by a reduced number of maxillary teeth, the absence of interdental plates terminating ventrally by broad V-shaped points and falling short relative to the lateral maxillary wall, and the absence of a protuberant ridge on the anterior part of the medial shelf, posterior to the anteromedial process. T. gurneyi is the largest theropod from the Lourinha Formation of Portugal and the largest land predator discovered in Europe hitherto. This taxon supports the mechanism of vicariance that occurred in the Iberian Meseta during the Late Jurassic when the proto-Atlantic was already well formed. A fragment of maxilla from the Lourinha Formation referred to Torvosaurus sp. is ascribed to this new species, and several other bones, including a femur, a tibia and embryonic material all from the Kimmeridgian-Tithonian of Portugal, are tentatively assigned to T. gurneyi. A standard terminology and notation of the theropod maxilla is also proposed and a record of the Torvosaurus material from Portugal is given.

Cryptic species continue to be uncovered in many fish taxa, posing challenges for fisheries conservation and management. In Sardinella gibbosa, previous investigations revealed subtle intra-species variations, resulting in numerous synonyms and a controversial taxonomy for this sardine. Here, we tested for cryptic diversity within S. gibbosa using genetic data from two mitochondrial and one nuclear gene regions of 248 individuals of S. gibbosa, collected from eight locations across the Philippine archipelago. Deep genetic divergence and subsequent clustering was consistent across both mitochondrial and nuclear markers. Clade distribution is geographically limited: Clade 1 is widely distributed in the central Philippines, while Clade 2 is limited to the northernmost sampling site. In addition, morphometric analyses revealed a unique head shape that characterized each genetic clade. Hence, both genetic and morphological evidence strongly suggests a hidden diversity within this common and commercially-important sardine.