Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA

Abstract

Indochina and Sundaland are biologically diverse, interconnected regions of Southeast Asia with complex geographic histories. Few studies have examined phylogeography of bird species that span the two regions because of inadequate population sampling. To determine how geographic barriers/events and disparate dispersal potential have influenced the population structure, gene flow, and demographics of species that occupy the entire area, we studied five largely codistributed rainforest bird species: Arachnothera longirostra, Irena puella, Brachypodius atriceps, Niltava grandis, and Stachyris nigriceps. We accomplished relatively thorough sampling and data collection by sequencing ultraconserved elements (UCEs) using DNA extracted from modern and older (historical) specimens. We obtained a genome‐wide set of 753–4,501 variable loci and 3,919–18,472 single nucleotide polymorphisms. The formation of major within‐species lineages occurred within a similar span of time (0.5–1.5 mya). Major patterns in population genetic structure are largely consistent with the dispersal potential and habitat requirements of the study species. A population break across the Isthmus of Kra was shared only by the two hill/submontane insectivores (N. grandis and S. nigriceps). Across Sundaland, there is little structure in B. atriceps, which is a eurytopic and partially frugivorous species that often utilizes forest edges. Two other eurytopic species, A. longirostra and I. puella, possess highly divergent populations in peripheral Sunda Islands (Java and/or Palawan) and India. These species probably possess intermediate dispersal abilities that allowed them to colonize new areas, and then remained largely isolated subsequently. We also observed an east–west break in Indochina that was shared by B. atriceps and S. nigriceps, species with very different habitat requirements and dispersal potential. By analyzing high‐throughput DNA data, our study provides an unprecedented comparative perspective on the process of avian population divergence across Southeast Asia, a process that is determined by geography, species characteristics, and the stochastic nature of dispersal and vicariance events.

Genomic investigation of colour polymorphism and phylogeographic variation among populations of black‐headed bulbul (Brachypodius atriceps) in insular southeast Asia

“…Earlier studies found that B. atriceps exhibits little to no population structure across most of its range, except between eastern and western Indochina, and between Maratua Island the rest of Sundaland (Chua et al, 2015; Dejtaradol et al, 2015; Lim et al, 2020). In their UCE study, Lim et al (2020) included only a single grey specimen of B. atriceps (from Bawean Island) and found that it barely differed from other populations (they did not compare individuals from Maratua). However, the UCE data of that grey specimen were derived from a toe‐pad sample >100 years old and comprised few complete loci.…”

Phylogeography of mangrove pit vipers (Viperidae, Trimeresurus erythrurus‐purpureomaculatus complex)

“…cf. purpureomaculatus occurs at the Isthmus of Kra (De Bruyn et al, 2005; Hughes et al, 2003; Parnell, 2013), which serves as a biogeographic divide for numerous vertebrate species including reptiles (Grismer et al, 2022; Mulcahy et al, 2017; Olivier S.G. Pauwels et al, 2016; Trivalairat et al, 2022; van Rooijen & Vogel, 2010; Vogel et al, 2012; Zug et al, 2017), amphibians (Buddhachat & Suwannapoom, 2018; Poyarkov et al, 2020; Yodthong et al, 2014), birds (Hughes et al, 2003; Lim et al, 2020), and mammals (Tougard, 2001). Our results also show that phylogeographic structure is latitudinally stratified and consistent with IBD and IBE, with colour polymorphisms appearing to be latitudinally structured as well.…”

Little genetic structure in a Bornean endemic small mammal across a steep ecological gradient

“…Additionally, the average heterozygosity of our UCE-derived SNPs is 0.23, similar to that reported in RAD-seq studies of other small mammal populations, including mice of the genera Apodemus In summary, although more research is needed into the substitution rate of UCE loci and its effect on demographic inferences, our results show that UCE capture methods can be used for finescale population genomics, providing an additional tool for studying nongenome-enabled species. UCE capture produces data with similar information content and has several benefits over RAD-seq, including: (i) enabling the 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); (ii) offering repeatability such that studies can compare inferences for the same species across time and geographical regions (Harvey et al, 2016); and (iii) enabling the use of low-quality DNA, including DNA derived from historical museum specimens (Hawkins et al, 2016;Lim & Braun, 2016;Lim et al, 2020;Tsai et al, 2019).…”