Unlinked Mendelian inheritance of red and black pigmentation in snakes: Implications for Batesian mimicry

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135324/1/evo12902_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135324/2/evo12902.pd

Speciation dynamics during the global radiation of extant bats

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/1/evo12681-sup-0008-FIGURE7.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/2/evo12681-sup-0003-FIGURE2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/3/evo12681.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/4/evo12681-sup-0002-FIGURE1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/5/evo12681-sup-0009-FIGURE8.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/6/evo12681-sup-0007-FIGURE6.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/7/evo12681-sup-0006-FIGURE5.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/8/evo12681-sup-0004-FIGURE3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/9/evo12681-sup-0005-FIGURE4.pd

FiSSE: A simple nonparametric test for the effects of a binary character on lineage diversification rates

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137596/1/evo13227.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137596/2/evo13227_am.pd

World Heritage lizard: population genetics and species status of the range-restricted Hamelin skink, Ctenotus zastictus

The Shark Bay World Heritage region in western Australia is home to a number of species of substantial conservation concern. Among these is a small scincid lizard, Ctenotus zastictus, which represents one of the most geographically-restricted vertebrates on the Australian mainland. The long-term persistence of Ctenotus zastictus is threatened due to the small size of its range, isolation from suitable habitat patches elsewhere, and potential impacts from climate change and mining. Accordingly, conservation efforts in Australia have targeted C. zastictus as the focus of protection. But this attention might be unwarranted – the species might not be evolutionarily unique. Previous genetic assessments have suggested limited differentiation between C. zastictus and its putative sister taxon, and the taxonomic status of C. zastictus has never been formally evaluated. Here, we use population genomic, phylogenetic, and ecoclimatic analyses to characterize the species status of C. zastictus in context of its closely-related congeners. In doing so, we explore the practical and conceptual challenges of revising species boundaries in threatened species, many of which are also rare and range-restricted. We demonstrate that C. zastictus is a coherent evolutionary unit that has been isolated from its putative sister species for at least two million years. Based on these results, we recommend that C. zastictus should retain its taxonomic status

Squamate Conserved Loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles

The identification of conserved loci across genomes, along with advances in target capture methods and high‐throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches—anchored hybrid enrichment (AHE) and ultraconserved elements (UCE)—and both approaches have proven useful for addressing questions in phylogenomics, phylogeography and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci set, a single integrated probe set that can generate high‐quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness and suggest areas for future improvement.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139986/1/men12681_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139986/2/men12681-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139986/3/men12681.pd