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Ecological niche modeling has emerged as an useful tool in the investigation of the phylogeographic histories of species or communities in a region. The high biodiversity (oftentimes cryptic), and complex geography and geological history of Southeast Asia particularly call for multipronged approaches in phylogeographic investigations. Past studies have focused on taxa that are associated with lowland rainforests, which is the dominant natural vegetation type. Here, we combine published phylogenetic data, ecological niche modeling and paleo-climate models to reveal potential drivers of divergence in two open-forest bird species, the oriental magpie-robin Copsychus saularis and Coppersmith barbet Megalaima haemacephala. In spite of broad overlap in current distributions, there are subtle differences in their climatic niches, which result in different responses to past climatic changes. For C. saularis, both Last Glacial Maximum climate models indicated that the entire Sundaland was climatically suitable, while phylogenetic analyses found divergent eastern and western Sundaland lineages. We thus postulate that this genetic divergence was a result of past separations of coastal habitats into eastern and western portions due to the emergence of Sunda shelf as sea-level fell. The current separation of morphological subspecies in Borneo is maintained by low climatic suitability (high annual rainfall) in certain regions. The extirpation of M. haemacephala from Borneo and southern Malay Peninsula might have been driven by unsuitable conditions (high temperature seasonality) in central Sundaland and/or the lack of open woodlands. Our study shows that ecological niche modeling adds a powerful dimension to our attempt to understand lineage evolution in space.

The Rufous-tailed Tailorbird (Orthotomus sericeus)—a Sunda endemic—is divided into 3 morphologically based subspecies: one in western Sundaland (Malay Peninsula, Sumatra, and associated islands), one from the Natuna Islands in the South China Sea, and one on Borneo, Palawan, and smaller islands of the Sunda continental shelf east of Borneo. Previous study, however, suggested that these subspecies do not conform to molecular genetic subdivisions of the species. We reexamined the morphology and performed molecular phylogeographic and multi-locus coalescent analysis of two subspecies of Rufous-tailed Tailorbird comprising populations on the Malay Peninsula, Sumatra, Borneo, and Palawan. We found (1) little morphological difference among the two subspecies, (2) no substantial genetic differences between the Borneo and western Sunda populations, but (3) marked genetic divergence between the Palawan and other populations. We conclude that the Bornean and western Sunda populations interbred extensively ...

The Mountain Black-eye (Chlorocharis emiliae) is an endemic white-eye (Zosteropidae) of Borneo with a unique ‘‘sky island’’ distribution. We compared mitochondrial ND2, ND3, Cytb, and control region DNA sequences (2,194 nucleotides) to study the phylogeographic relationships of five populations of this species that span its range: Mounts Kinabalu, Trus Madi, Murud, Mulu, and Pueh. These comparisons showed that black-eyes are divided into two main clades that correspond generally to subspecific morphological groups: one in Sabah, Malaysia (Kinabalu and Trus Madi), and one in Sarawak, Malaysia (Murud, Mulu, and Pueh). The genetic and morphologic subdivision of black-eyes disputes the expected merging of populations during the Last Glacial Maximum (LGM), when montane forest presumably expanded and provided the opportunity for currently isolated populations to intermingle. Instead the genetic aging of black-eye populations indicates they diversified long before the LGM, and either did not expand sufficiently in range during the LGM to reach one another, or were reproductively isolated by the time of the LGM and thus prevented from interbreeding. Moreover, the subdivision between black-eyes in Sabah and Sarawak means that this species (and probably several other montane species) has a phylogeographic structure remarkably similar to Borneo’s lowland bird populations, which are presumed to have evolved under different paleo-geographic conditions. The similar phylogeographic pattern found in both montane and lowland species requires that we rethink the causes of bird population diversification on the island of Borneo.

The phylogeny of spiderhunters (Nectariniidae: Arachnothera) was reconstructed by comparing mitochondrial and nuclear DNA sequences of all currently recognized species and with broad geographic sampling of two particularly variable species complexes, the Little Spiderhunter (Arachnothera longirostra) and the streaky spiderhunters (A. modesta and A. affinis). It appears to be a relatively old group, whose diversification was not caused by recent sea-level changes. However, the modern, highly sympatric distribution of the large species in the Sunda lowlands was probably a result of dispersal via recent land bridges. Within the highly variable A. longirostra group, there are substantially diverged taxa in the Philippines that should be considered different species. Within the A. affinis—modesta complex, there are three distinct species and a closely related fourth, which describe a clear allopatric distribution: A. affinis in Java, A. modesta in the rest of the Sunda lowlands (except Sabah), A. mag...