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

Smith, BT, Harvey, MG, Faircloth, BC, Glenn, TC, and RT Brumfield. 2013. Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Timescales. Systematic Biology. In press.

This is the first paper out using ultraconserved elements (UCE’s) to look at intraspecific genetic variation at shallow evolutionary timescales. UCE’s are short (usually 50-200bp) stretches of DNA that have been conserved across disparate groups. About 5,000 have been identified so far in amniotes, and they’ve been a productive target for resolving phylogenies at deep evolutionary timescales. Within each locus genetic variability increases with distance from the center of the locus, which suggests that they might also be useful for resolving genetic variation at shallow evolutionary timescales. Here the authors sequenced UCE’s from 5 species of neotropical bird in order to assess how intraspecific divergence times across barriers to dispersal differ between canopy and understory species. The empirical results are limited by relatively light sampling across geographic ranges (2 individuals per species from each of 4 areas) and the limited number of species assessed, but the real point of the paper, as the title suggests, is as a proof-of-concept for using UCE’s in population genetic analysis. The authors report that inferred divergence times were consistent with and had narrower credibility intervals than analysis using cytB data from the sample individuals, which is great. Species tree topology and estimated effective population sizes were also consistent with cytB. To compensate for missing data across species/locations the authors cut down the dataset to varying levels of consistency, but where analysis of both full and reduced datasets was possible there was no significant difference in the result. In some cases, as with *BEAST, analysis of the full dataset would have taken months or years of computing time, which is a little worrying for anyone hoping to analyze a UCE dataset with larger sample sizes and/or greater geographic scope.

We thought generally that the paper was a nice illustration of the utility of UCE’s in population genetic analysis, but as always the group came up with some critiques. In general it would have been nice to see a more relevant empirical hypothesis tested with this data – the goal of assessing patterns of relative divergence time across geographic barriers between canopy and understory birds seems unfeasible with just five species, and sampling was light by pop-gen standards even within those species. In terms of figure design, the use of cloudograms to illustrate the species tree estimation was cool, but didn’t seem to get any particular point across. Some participants also objected to the use of “highly multilocus”, instead of just “multilocus”. Overall, this paper showed that UCE’s are a good target for multilocus population genetic studies and did a good job exploring the ability of some current computational approaches (*BEAST, GPho-CS) to deal with these huge datasets.
[UW Phylogenetics Seminar, 10/31/13; CJ Battey]

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