Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

Abstract

Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species, we recovered 776-1516 UCE loci across the five species. Across species, 53-77% of the loci were polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic locus, on average. We performed species tree construction, coalescent modeling, and species delimitation, and we found that the five co-distributed species exhibited discordant phylogeographic histories. We also found that species trees and divergence times estimated from UCEs were similar to the parameters obtained from mtDNA. The species that inhabit the understory had older divergence times across barriers, contained a higher number of cryptic species, and exhibited larger effective population sizes relative to the species inhabiting the canopy. Because orthologous UCEs can be obtained from a wide array of taxa, are polymorphic at shallow evolutionary timescales, and can be generated rapidly at low cost, they are an effective genetic marker for studies investigating evolutionary patterns and processes at shallow timescales.

In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

“…3). This mirrors the pattern found in several studies that had evaluated posterior variances as a function of the number of subsampled loci (Jennings and Edwards 2005;Lee and Edwards 2008;Smith et al 2013). To our knowledge, this is the first time two independent data sets of drastically different numbers of loci (fivefold difference) have been compared to show the benefits of larger numbers of independent loci in phylogenomic studies.…”

“…In studies of recently diverged populations or species, the researcher should use more variable markers such as ALs (Chen and Li 2001;Yang 2002;Rannala and Yang 2003;Jennings and Edwards 2005;Lee and Edwards 2008;Thomson et al 2010;Bertozzi et al 2012; or introns (Li et al 2010; Thomson et al 2010). Because the flanking sequences of AE and UCE loci tend to exhibit much variation, these loci may also perform well in studies involving recent divergences Smith et al 2013). However, for studies involving deep divergences spanning tens or hundreds of millions of years, the researcher must resort to highly conserved loci such as conserved exons (Li et al 2007; Thomson et al 2010), AE loci , or UCE loci .…”

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…A phylogenomic approach targeting thousands of independently evolved nuclear loci may be the only way to assess the current taxonomy of this group, and dissect the roles of hybridization and introgression in the origin and rapid diversification of this insular lineage. Phylogenomic methods based on markers identified from, e.g., restriction site associated DNA sequencing (RADseq) (Cruaud et al, 2014;Eaton and Ree, 2013;Smith et al, 2014), targeted enrichment of ultraconserved elements (UCEs) or conserved ortholog sequences (COS) (Mandel et al, 2014;Smith et al, 2014), and RNA-Seq (Wen et al, 2013;Wickett et al, 2014) could be suitable methods to resolve Hawaiian mint relationships. However, these approaches are also associated with challenges, including accurately inferring orthology in high polyploid plants, slow mutation rates in exonic regions, which may be too low to resolve recent radiations (Giarla and Esselstyn, 2015), and the need to obtaining high quality RNA and DNA.…”

Geographic variation, null hypotheses, and subspecies limits in the California Gnatcatcher: A response to McCormack and Maley

“…We mapped alleles onto the species tree based on the sampled populations in Zink et al (2013) and included 1 Black-tailed Gnatcatcher (P. melanura) as an outgroup. In taxa in which discrete units exist despite a shallow evolutionary scale, populations can be used as terminals for species tree estimation (Smith et al 2014). We included all data used by Zink et al (2013) with the same settings as for their extended Bayesian skyline plot, but excluded the locus beta-Fibrinogen Intron 7 (see McCormack and Maley [2015]).…”