Predicting speciation probability from replicated population histories

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/162730/2/mec15577.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162730/1/mec15577_am.pd

History cleans up messes: The impact of time in driving divergence and introgression in a tropical suture zone

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137755/1/evo13278-sup-0001-SuppMat.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137755/2/evo13278.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137755/3/evo13278_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

Is genomic diversity a useful proxy for census population size? Evidence from a species‐rich community of desert lizards

Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long‐term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome‐wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long‐term estimates of abundance, occupancy and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to investigate whether ecological preference exerts a measurable effect on genetic diversity. We find that heterozygosity is significantly correlated with species abundance and occupancy, but not habitat specialization. Demonstrating the power of genomic sampling, the correlation between heterozygosity and abundance/occupancy emerged from considering just one or two individuals per species. However, genetic diversity does no better at predicting abundance than a single day of traditional sampling in this community. We conclude that genetic diversity is a useful proxy for regional‐scale species abundance and occupancy, but a large amount of unexplained variation in heterozygosity suggests additional constraints or a failure of ecological sampling to adequately capture variation in true population size.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149326/1/mec15042_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149326/2/mec15042.pd

Transcriptome-Based Exon Capture Enables Highly Cost-Effective Comparative Genomic Data Collection At Moderate Evolutionary Scales

Background: To date, exon capture has largely been restricted to species with fully sequenced genomes, which has precluded its application to lineages that lack high quality genomic resources. We developed a novel strategy for designing array-based exon capture in chipmunks (Tamias) based on de novo transcriptome assemblies. We evaluated the performance of our approach across specimens from four chipmunk species. Results: We selectively targeted 11,975 exons (similar to 4 Mb) on custom capture arrays, and enriched over 99% of the targets in all libraries. The percentage of aligned reads was highly consistent (24.4-29.1%) across all specimens, including in multiplexing up to 20 barcoded individuals on a single array. Base coverage among specimens and within targets in each species library was uniform, and the performance of targets among independent exon captures was highly reproducible. There was no decrease in coverage among chipmunk species, which showed up to 1.5% sequence divergence in coding regions. We did observe a decline in capture performance of a subset of targets designed from a much more divergent ground squirrel genome (30 My), however, over 90% of the targets were also recovered. Final assemblies yielded over ten thousand orthologous loci (similar to 3.6 Mb) with thousands of fixed and polymorphic SNPs among species identified. Conclusions: Our study demonstrates the potential of a transcriptome-enabled, multiplexed, exon capture method to create thousands of informative markers for population genomic and phylogenetic studies in non-model species across the tree of life

Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change

Many species have experienced dramatic changes in their abundance and distribution during recent climate change, but it is often unclear whether such ecological responses are accompanied by evolutionary change. We used targeted exon sequencing of 294 museum specimens (160 historic, 134 modern) to generate independent temporal genomic contrasts spanning a century of climate change (1911–2012) for two co-distributed chipmunk species: an endemic alpine specialist (Tamias alpinus) undergoing severe range contraction and a stable mid-elevation species (T. speciosus). Using a novel analytical approach, we reconstructed the demographic histories of these populations and tested for evidence of recent positive directional selection. Only the retracting species showed substantial population genetic fragmentation through time and this was coupled with positive selection and substantial shifts in allele frequencies at a gene, Alox15, involved in regulation of inflammation and response to hypoxia. However, these rapid population and gene-level responses were not detected in an analogous temporal contrast from another area where T. alpinus has also undergone severe range contraction. Collectively, these results highlight that evolutionary responses may be variable and context dependent across populations, even when they show seemingly synchronous ecological shifts. Our results demonstrate that temporal genomic contrasts can be used to detect very recent evolutionary responses within and among contemporary populations, even in the face of complex demographic changes. Given the wealth of specimens archived in natural history museums, comparative analyses of temporal population genomic data have the potential to improve our understanding of recent and ongoing evolutionary responses to rapidly changing environments