82 research outputs found
Baseline monitoring and molecular characterization of the state endangered Enigmatic Cavesnail, Fontigens antrocetes (Hubrict 1940)
Ten different caves were evaluated in the present study (Table 1). In the six Illinois caves, F. antroecetes was detected only at Stemler Cave. In Missouri, four caves were sampled, with hydrobiid snails recovered from all of these caves. Species level identification of this material awaits molecular studies, as multiple Fontigens species are possible from these localities.Illinois Endangered Species Protection Board, Illinois Department of Natural Resources, Office of Resource Conservation/Operations, One Natural Resources Way, Springfield, Illinois 62702-127
Do biofilm communities respond to the chemical signatures of fracking? A test involving streams in North-central Arkansas
A complete set of elastic constants of crystalline anthracene by Brillouin scattering
All 13 elastic constants of a vapor grown, uncut, anthracene single crystal were determined from acoustic phonon velocities obtained by the Brillouin scattering method. The phonon velocities are plotted for three crystallographic planes containing the crystal axis. The relationships between phonon velocities and lattice dynamics are discussed. A minimizing procedure is introduced for converting phonon velocities of low symmetry systems into elasticity coefficients. This is shown to have several advantages over previous methods used. The results are compared with those obtained by previous studies of anthracene elastic constants
Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae)
Abstract Background Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson’s D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to explore potential effects of concatenation. Results We employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus. Conclusions Complex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages [Virgin River (UT) and Little Colorado River (AZ)] reflecting unique composition
Small Fish in a Large Landscape: Diversification of Rhinichthys osculus (Cyprinidae) in Western North America
gila_ub_introgress.tar.gz
Gzipped tar archive containing input files and R code for running genomic cline analyse
gila_ub.vcf.tar.gz
VCF file for running admixture. Analyses were completed using an open source pipeline by Steve Mussman, available at https://github.com/stevemussmann/admixturePipeline, which completes per-locus filtering (e.g. by coverage, minor allele freuency) internally using command-line options
gila_newhyb.tar.gz
Outputs and datafiles for running newhybrids and associated power analyses in the hybriddetective R packag
Deconstructing a Species-Complex: Geometric Morphometric and Molecular Analyses Define Species in the Western Rattlesnake (Crotalus viridis).
Morphological data are a conduit for the recognition and description of species, and their acquisition has recently been broadened by geometric morphometric (GM) approaches that co-join the collection of digital data with exploratory 'big data' analytics. We employed this approach to dissect the Western Rattlesnake (Crotalus viridis) species-complex in North America, currently partitioned by mitochondrial (mt)DNA analyses into eastern and western lineages (two and seven subspecies, respectively). The GM data (i.e., 33 dorsal and 50 lateral head landmarks) were gleaned from 2,824 individuals located in 10 museum collections. We also downloaded and concatenated sequences for six mtDNA genes from the NCBI GenBank database. GM analyses revealed significant head shape differences attributable to size and subspecies-designation (but not their interactions). Pairwise shape distances among subspecies were significantly greater than those derived from ancestral character states via squared-change parsimony, with the greatest differences separating those most closely related. This, in turn, suggests the potential for historic character displacement as a diversifying force in the complex. All subspecies, save one, were significantly differentiated in a Bayesian discriminant function analysis (DFA), regardless of whether our priors were uniform or informative (i.e., mtDNA data). Finally, shape differences among sister-clades were significantly greater than expected by chance alone under a Brownian model of evolution, promoting the hypothesis that selection rather than drift was the driving force in the evolution of the complex. Lastly, we combine head shape and mtDNA data so as to derived an integrative taxonomy that produced robust boundaries for six OTUs (operational taxonomic units) of the C. viridis complex. We suggest these boundaries are concomitant with species-status and subsequently provide a relevant nomenclature for its recognition and representation
gila_ub_snps.tar
Data files containing an all-SNP alignment (in pyRAD .snps format), unlinked SNPs (=1 sampled per locus) in phylip format, and a filtered unlinked SNP alignment in phylip format. A filtered dataset of unlinked SNPs were used to run STRUCTURE and DAPC. See Methods for more details
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