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

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

gila_ub_introgress.tar.gz

Gzipped tar archive containing input files and R code for running genomic cline analyse

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

bondi

Raw fastq files split by individual

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