Claw asymmetry in crabs: approaching an old issue from a new point of view

Abstract Crabs are considered exceptional examples of antisymmetry resulting from the phenomenon of heterochely. Here we investigate morphometrically both the size and the shape of heterochely in 28 crab species, distributed unequally along a brachyuran phylogeny. We address the importance of investigating claw size and shape for interspecific comparisons by linking geometric morphometric outputs to phylogenetic data for 134 brachyuran species. New indices introduced as new sexual dimorphic characters of size and shape, namely heterometry (right chela size/left chela size) and heteromorphy (Procrustes distance between right and left chelae shape), revealed sexually dimorphic differences in diverse crab species. We demonstrate that both size and shape heterochely occur amongst the examined species, but there are no ecological correlations. Our study demonstrates that claw similarity between two or more species was due mainly to phylogenetic relatedness rather than ecological convergence, suggesting that claw morphological features could be useful morphological markers in phylogenetic studies. Although further investigation is needed, this study represents one of the first to thoroughly analyse the origin and evolution of heterochely within the Brachyura clade

An Annotated Checklist of the Crayfishes (Decapoda: Cambaridae) of Arkansas

Prior to the present study, 56 species with 3 additional subspecies for a total of 59 different taxa of crayfishes were recognized from Arkansas. We add a single species (Carmel Crayfish, Fallicambarus schusteri) to that list, subtract a documented synonym (Procambarus ferrugenius = Procambarus liberorum), update the classification to better reflect recent phylogenetic insights, and provide an updated annotated checklist of the 59 crayfish taxa of presently known from the state. There are 8 endemic species in Arkansas, including the Bayou Bodcau Crayfish (Bouchardina robisoni), Boston Mountains Crayfish (Cambarus causeyi), Hell Creek Cave Crayfish (C. zophonastes), Jefferson County Crayfish (Creaserinus gilpini), Ouachita Burrowing Crayfish (Fallicambarus harpi), Slenderwrist Burrowing Crayfish (F. petilicarpus), Saline Burrowing Crayfish (F. strawni), and Redspotted Stream Crayfish (Faxonius acares). There are also 2 federally endangered species, the Benton County Cave Crayfish (Cambarus aculabrum) and the Hell Creek Cave Crayfish (C. zophonastes) that inhabit Arkansas karst habitat. We expect that additional species will be included in the list with further DNA analyses

Divergence and diversification in North American Psoraleeae (Fabaceae) due to climate change

<p>Abstract</p> <p>Background</p> <p>Past studies in the legume family (Fabaceae) have uncovered several evolutionary trends including differential mutation and diversification rates across varying taxonomic levels. The legume tribe Psoraleeae is shown herein to exemplify these trends at the generic and species levels. This group includes a sizable diversification within North America dated at approximately 6.3 million years ago with skewed species distribution to the most recently derived genus, <it>Pediomelum</it>, suggesting a diversification rate shift. We estimate divergence dates of North American (NAm) Psoraleeae using Bayesian MCMC sampling in BEAST based on eight DNA regions (ITS, <it>waxy</it>, <it>matK</it>, <it>trnD-trnT</it>, <it>trnL-trnF</it>, <it>trnK</it>, <it>trnS-trnG</it>, and <it>rpoB-trnC</it>). We also test the hypothesis of a diversification rate shift within NAm Psoraleeae using topological and temporal methods. We investigate the impact of climate change on diversification in this group by (1) testing the hypothesis that a shift from mesic to xeric habitats acted as a key innovation and (2) investigating diversification rate shifts along geologic time, discussing the impact of Quaternary climate oscillations on diversification.</p> <p>Results</p> <p>NAm Psoraleeae represents a recent, rapid radiation with several genera originating during the Pleistocene, 1 to 2 million years ago. A shift in diversification rate is supported by both methods with a 2.67-fold increase suggested around 2 million years ago followed by a 8.73-fold decrease 440,000 years ago. The hypothesis that a climate regime shift from mesic to xeric habitats drove increased diversification in affected taxa was not supported. Timing of the diversification rate increase supports the hypothesis that glaciation-induced climate changes during the Quaternary influenced diversification of the group. Nonrandom spatial diversification also exists, with greater species richness in the American Southwest.</p> <p>Conclusion</p> <p>This study outlines NAm Psoraleeae as a model example of a recent, rapid radiation. Diversification rate shifts in NAm Psoraleeae are not due to current climate regimes as represented by habitat, but instead to past global climate change resulting from Quaternary glaciations. NAm Psoraleeae diversification is a good example of how earthly dynamics including global climate change and topography work together to shape biodiversity.</p

Calculating expected DNA remnants from ancient founding events in human population genetics

<p>Abstract</p> <p>Background</p> <p>Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations.</p> <p>Results</p> <p>We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current human population studies and what these studies infer about past population structure. Final mean allele frequencies varied from 0.0005 to over 0.50, depending on the parameters.</p> <p>Conclusion</p> <p>The results of the simulations illustrate that, while genetic data may be sensitive and powerful in large genetic studies, caution must be used when applying genetic information to small, recent admixture events. For some parameter sets, genetic data will not be adequate to detect historic admixture. In such cases, studies should consider anthropologic, archeological, and linguistic data where possible.</p

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.

Background The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known about spatial variation (biogeography) in nasal microenvironments and how sampling techniques may capture that microbial diversity. Findings We used targeted 16S rRNA MiSeq sequencing and two different sampling strategies [nasal washes (NW) and nasal brushes (NB)] to characterize the nasopharyngeal microbiota in 30 asthmatic children. Nasal brushing is more abrasive than nasal washing and targeted the inner portion of the inferior turbinate. This region is expected to be different from other nasal microenvironments. Nasal washing is not spatially specific. Our 30 × 2 nasal microbiomes generated 1,474,497 sequences, from which we identified an average of 157 and 186 OTUs per sample in the NW and NB groups, respectively. Microbiotas from NB showed significantly higher alpha-diversity than microbiotas from NW. Similarly, both nasal microbiotas were distinct from each other (PCoA) and significantly differed in their community composition and abundance in at least 9 genera (effective size ≥1 %). Conclusions Nasopharyngeal microenvironments in asthmatic children contain microbiotas with different diversity and structure. Nasal washes and brushes capture that diversity differently. Future microbial studies of the nasopharynx need to be aware of potential spatial variation (biogeography)

Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites

BACKGROUND: The molecular operational taxonomic unit(MOTU)has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of "reverse taxonomy" has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of "reverse taxonomy" has not been sufficiently evaluated. Therefore, the practical applicability of "reverse taxonomy" is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts. METHODOLOGY: Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types (= MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified. CONCLUSIONS: That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.Natsumi Kanzaki, Robin M. Giblin-Davis, Rudolf H. Scheffrahn, Hisatomo Taki, Alejandro Esquivel, Kerrie A. Davies and E. Allen Herr

Spatial diversity of the skin bacteriome

The bacterial communities of the human skin impact its physiology and homeostasis, hence elucidating the composition and structure of the healthy skin bacteriome is paramount to understand how bacterial imbalance (i.e., dysbiosis) may lead to disease. To obtain an integrated view of the spatial diversity of the skin bacteriome, we surveyed from 2019 to 2023 five skin regions (belly button, behind ears, between toes, calves and forearms) with different physiological characteristics (dry, moist and sebaceous) in 129 healthy adults (579 samples – after data cleaning). Estimating bacterial diversity through 16S rRNA metataxonomics, we identified significant (p &lt; 0.0001) differences in the bacterial relative abundance of the four most abundant phyla and 11 genera, alpha- and beta-diversity indices and predicted functional profiles (36 to 400 metabolic pathways) across skin regions and microenvironments. No significant differences, however, were observed across genders, ages, and ethnicities. As previously suggested, dry skin regions (forearms and calves) were more even, richer, and functionally distinct than sebaceous (behind ears) and moist (belly button and between toes) regions. Within skin regions, bacterial alpha- and beta-diversity also varied significantly for some of the years compared, suggesting that skin bacterial stability may be region and subject dependent. Our results, hence, confirm that the skin bacteriome varies systematically across skin regions and microenvironments and provides new insights into the internal and external factors driving bacterial diversity

Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleurenComment: 6 pages, 3 figures, accepted at BIBE 2017. Minor modifications to the text due to reviewer feedback and fixed typo

Molecular phylodynamics and protein modeling of infectious salmon anemia virus (ISAV)

<p>Abstract</p> <p>Background</p> <p>ISAV is a member of the <it>Orthomyxoviridae </it>family that affects salmonids with disastrous results. It was first detected in 1984 in Norway and from then on it has been reported in Canada, United States, Scotland and the Faroe Islands. Recently, an outbreak was recorded in Chile with negative consequences for the local fishing industry. However, few studies have examined available data to test hypotheses associated with the phylogeographic partitioning of the infecting viral population, the population dynamics, or the evolutionary rates and demographic history of ISAV. To explore these issues, we collected relevant sequences of genes coding for both surface proteins from Chile, Canada, and Norway. We addressed questions regarding their phylogenetic relationships, evolutionary rates, and demographic history using modern phylogenetic methods.</p> <p>Results</p> <p>A recombination breakpoint was consistently detected in the Hemagglutinin-Esterase (<it>he</it>) gene at either side of the Highly Polymorphic Region (HPR), whereas no recombination breakpoints were detected in Fusion protein (<it>f</it>) gene. Evolutionary relationships of ISAV revealed the 2007 Chilean outbreak group as a monophyletic clade for <it>f </it>that has a sister relationship to the Norwegian isolates. Their tMRCA is consistent with epidemiological data and demographic history was successfully recovered showing a profound bottleneck with further population expansion. Finally, selection analyses detected ongoing diversifying selection in <it>f </it>and <it>he </it>codons associated with protease processing and the HPR region, respectively.</p> <p>Conclusions</p> <p>Our results are consistent with the Norwegian origin hypothesis for the Chilean outbreak clade. In particular, ISAV HPR0 genotype is not the ancestor of all ISAV strains, although SK779/06 (HPR0) shares a common ancestor with the Chilean outbreak clade. Our analyses suggest that ISAV shows hallmarks typical of RNA viruses that can be exploited in epidemiological and surveillance settings. In addition, we hypothesized that genetic diversity of the HPR region is governed by recombination, probably due to template switching and that novel fusion gene proteolytic sites confer a selective advantage for the isolates that carry them. Additionally, protein modeling allowed us to relate the results of phylogenetic studies with the predicted structures. This study demonstrates that phylogenetic methods are important tools to predict future outbreaks of ISAV and other salmon pathogens.</p