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Outside of their functional relevance, UCE loci have demonstrated utility for recovering deeper-level phylogenetic relationships ( McCormack et al., 2013 Faircloth et al., 2015 Gilbert et al., 2015) and shallower-level genus and population relationships ( Smith et al., 2014 Harvey & Brumfield, 2015 Leaché et al., 2015 Harvey et al., 2016 Manthey et al., 2016 Oswald et al., 2016 Mason et al., 2018). We focus on the set of UCEs previously defined for tetrapods and now in widespread use ( McCormack et al., 2011 Faircloth et al., 2012). UCEs in vertebrates show little overlap with most types of paralogous genes, and, as a marker class, UCE loci are broadly distributed across the genome and are typically transposon-free ( Derti et al., 2006 Simons et al., 2006 McCormack et al., 2011 Harvey et al., 2016). Ultraconserved elements are conserved sequences shared among divergent animal genomes ( Bejerano et al., 2004 Siepel et al., 2005 Stephen et al., 2008 Janes et al., 2011), and many UCE loci are likely to be involved in controlling gene expression ( Marcovitz, Jia & Bejerano, 2016). Ultraconserved elements (UCEs) are one class of genome-wide marker that might provide a solution to these problems. This type of approach would provide a tractable number of loci for analyses while improving among-study comparisons and larger-scale comparative meta-analyses. The parallel difficulties of collecting a moderate sample of the genome from identical loci across diverse species argue for a sequence data collection approach that (a) subsamples the genome to (b) obtain orthologous markers across a broad taxonomic scope. However, the sheer quantity of data obtained from whole-genome sequencing can require excessively long computation times, and may be overkill for many questions. Improvements in sequencing platforms and genomic data collection approaches are changing this general pattern by enabling us to efficiently collect much larger samples of the genome, up to and including whole-genome sequences ( Ellegren, 2014). This lack of consistency in the loci used across different studies compromises our ability to make direct comparisons of population genetic parameters among taxa (e.g., in divergence statistics and in estimates of gene flow and effective population sizes). This approach usually provides answers to the specific questions asked by researchers, but the historic focus on markers with high substitution rates has produced studies that include relatively few loci and often have little to no overlap with loci used for other taxa.

Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.Īmong non-model organisms, population genetic studies have used a diverse set of markers, tending to concentrate on those with sufficiently high substitution rates to provide useful data at shallow levels of evolutionary divergence, for example, from the populations-to-species levels ( Avise, 1994 Hillis, Moritz & Mable, 1996 Pearse & Crandall, 2004).

Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). The demographic model best fitting the data was one of divergence with gene flow. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically ( F ST = 0.034 P = 0.03).

We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences.

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With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). We used UCEs to study population genomics in snow and McKay’s buntings ( Plectrophenax nivalis and P. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes.