Utility of UCEs for fine-scale population genomics
Since the original design of DNA hybridization probes to capture and sequence UCEs for tetrapods (Faircloth et al., 2012), UCEs have proven capable of resolving phylogenies at multiple timescales and across taxa (e.g. Hawkins et al., 2016; McCormack et al., 2012; Smith et al., 2014; Sun et al., 2014). UCEs can resolve phylogeographic patterns, population structure, and demographic history of recently diverged species (e.g. Harvey et al., 2016; Winker et al., 2018; Zarza et al., 2016). Here, we show that sequence capture of ca. 5,000 UCEs yielded two highly informative datasets suitable for landscape-scale population genomics. These datasets were able to resolve patterns of population structure in mountain treeshrews within KNP, an area of approximately 754 km2. The SNP dataset provided sufficient statistical power to identify individuals with high probability (PIDsib = 1.54 × 10-199 ) and to identify putative family groups using pairwise kinship estimates. This suggests the potential for UCEs to be used for population genomic studies.
UCEs are valuable for studying species like the mountain treeshrew for which few genomic resources are available. Although RAD-seq methods also do not require reference genomes, UCE capture produces data with similar information content and has several benefits over RAD-seq: 1) UCEs enable direct comparison of inferences drawn from the same set of loci across species, allowing conclusions to be drawn about the effects of historical processes on diverse taxa (Lim et al., 2020), 2) UCE capture offers repeatability such that studies can compare inferences for the same species across time and geographic regions (Harvey et al., 2016), and 3) UCE capture can be performed on low-quality DNA, including DNA derived from historical museum specimens (Hawkins et al., 2016; Lim et al., 2020; Lim & Braun, 2016, Tsai et al., 2019).