Sundaland, a biogeographic region of Southeast Asia, is a major biodiversity hotspot. However, little is known about the relative importance of Pleistocene habitat barriers and rivers in structuring populations and promoting diversification here. We sampled 16 lowland rainforest bird species primarily from peninsular Malaysia and Borneo to test the long-standing hypothesis that animals on different Sundaic landmasses intermixed extensively when lower sea-levels during the Last Glacial Maximum (LGM) exposed land-bridges. This hypothesis was rejected in all but five species through coalescent simulations. Furthermore, we detected a range of phylogeographic patterns; Bornean populations are often genetically distinct from each other, despite their current habitat connectivity. Environmental niche modeling showed that the presence of unsuitable habitats between western and eastern Sundaland during the LGM coincided with deeper interpopulation genetic divergences. The location of this habitat barrier had been hypothesized previously based on other evidence. Paleo-riverine barriers are unlikely to have produced such a pattern, but we cannot rule out that they acted with habitat changes to impede population exchanges across the Sunda shelf. The distinctiveness of northeastern Borneo populations may be underlied by a combination of factors such as rivers, LGM expansion of montane forests and other aspects of regional physiography.
Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric "species-pump" model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by "ecological speciation" along an elevational gradient.
The mountains of Borneo are well known for their high endemicity and historical role in preserving Southeast Asian rainforest biodiversity, but the diversification of populations inhabiting these mountains is poorly studied. Here we examine the genetic structure of 12 Bornean montane passerines by comparing complete mtDNA ND2 gene sequences of populations spanning the island. Maximum likelihood and Bayesian phylogenetic trees and haplotype networks are examined for common patterns that might signal important historical events or boundaries to dispersal. Morphological and ecological characteristics of each species are also examined using phylogenetic generalized least-squares (PGLS) for correlation with population structure. Populations in only four of the 12 species are subdivided into distinct clades or haplotype groups. Although this subdivision occurred at about the same time in each species (ca. 0.6-0.7Ma), the spatial positioning of the genetic break differs among the species. In two species, northeastern populations are genetically divergent from populations elsewhere on the island. In the other two species, populations in the main Bornean mountain chain, including the northeast, are distinct from those on two isolated peaks in northwestern Borneo. We suggest different historical forces played a role in shaping these two distributions, despite commonality in timing. PGLS analysis showed that only a single characteristic-hand-wing index-is correlated with population structure. Birds with longer wings, and hence potentially more dispersal power, have less population structure. To understand historical forces influencing montane population structure on Borneo, future studies must compare populations across the entirety of Sundaland.