Aim: A current model of rain forest population diversification in Sundaland specifies east-west vicariance into refugia during the early Pleistocene. In some taxa, this division was followed by dispersal and apparent secondary contact on Borneo in the late Pleistocene. To investigate genetic, morphological, spatial and temporal characteristics of the model, we compared genomic population and plumage variation among four bird species with east-west mtDNA and plumage structure. Location: Borneo and western Sundaland (Sumatra and the Malay Peninsula). Methods: We quantified plumage patterns among populations of two muscicapids (Copsychus saularis and Kittacincla malabarica) and two timaliids (Mixornis gularis and Trichastoma malaccense), and compared them with population genetic patterns determined from (1) SNPs produced by RAD-Seq and (2) previously sequenced mtDNA. Results: All four species exhibit east-west variation in morphological and some genetic characters, but patterns are idiosyncratic. Copsychus saularis' mtDNA and plumage change gradually across Borneo, but RAD-Seq comparisons indicate no population structure. In K. malabarica, all three characteristics change abruptly and concurrently on Borneo. In M. gularis, the main east-west break occurs between Borneo and western Sundaland, with marginal mtDNA, plumage and RAD-Seq structure on Borneo. T. malaccense exhibits two distinct mtDNA and genomic transitions, an early Pleistocene break between western Sundaland and Borneo, and a Pliocene break between the north-east and the rest of Borneo. Despite this deep genetic division, its plumage changes clinally across Borneo.Main conclusions: MtDNA, plumage and RAD-Seq patterns may vary depending on such factors as pre-Pleistocene distribution, habitat requirements and dispersal propensity, differential introgression among the three character types, selection on plumage and phylogenetic relationships.

Aim Our understanding of population diversification in the lowlands of Sundaland has improved substantially over the last 20 years through phylogeographical study, but we know almost nothing about population diversification in the mountains of the region. Here, we apply genomic analysis and habitat modelling to the phylogeography of Chlorocharis emiliae, the Mountain Blackeye, an endemic montane bird of Borneo with a sky-island distribution, to investigate the structure and interconnectivity of its populations. In the process, we consider factors driving population diversification in the mountains versus lowlands on the island, and how population structure of C. emiliae compares with structure of previously studied lowland species.Location Borneo.Methods Using RAD-seq, we produced thousands of SNPs in 25 individuals from five sky-island populations of C. emiliae. These populations represent the species entire range across Borneo. Genetic structure and species tree analyses were applied to measure population relationships and connectivity. Ecological niche modelling was used to estimate habitat distributions during current and LGM time periods. ResultsWe identified slight to moderate genetic distinctiveness among all populations. Based on demographic models, isolation with migration was the main pattern of divergence, and the most admixture occurred among three populations in north-eastern Borneo: Kinabalu, Trus Madi and Murud. The most divergent population, Pueh, in north-western Borneo, has low genetic diversity and a small effective population size, is geographically isolated and has diverged in isolation without notable gene flow. These results, based on a large genomic dataset, contradict the evolutionary relationships identified in an earlier mitochondrial DNA study.Main conclusions Genomic phylogeographical comparisons indicate that diversification among sky-island populations of C. emiliae was driven largely by distance and historical habitat distribution, resulting in isolation but also some inter-population gene flow. During Pleistocene glacial events, cooler temperatures would have caused montane forest to descend and spread, thereby increasing connectivity among sky-island populations. However, despite increased montane habitat, the north-western population of Pueh remained isolated. This montane pattern contrasts with phylogeographical patterns in the Bornean lowlands, where populations often display evidence of vicariance followed by secondary contact.

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. Keywords: Greater Sunda Islands, last glacial maximum, montane avifauna, phylogeography, refugia, sky islands, ZosteropidaePatrons de diversification aviaireà Bornéo: Le cas d'une espèce endémique, Chlorocharis emiliae RÉSUMÉ Chlorocharis emiliae est une espèce endémique de Zosteropidae de Bornéo ayant une répartition unique de type ''sky island.'' Nous avons comparé les séquences d'ADN mitochondrial ND2, ND3, Cytb, et de la région de contrôle (2,194 nucléotides) afin d'étudier les relations phylogéographiques de cinq populations de cette espèce qui couvrent toute son aire de répartition: Les Monts Kinabalu, Trus Madi, Murud, Mulu, et Pueh. Ces comparaisons ont montré que C. emiliae se divise en deux principaux clades qui correspondent généralement aux groupes morphologiques sousspécifiques: unà Sabah, en Malaisie (Kinabalu et Trus Madi) et unà Sarawak, en Malaisie (Murud, Mulu, et Pueh). La subdivision génétique et morphologique de C. emiliae conteste l'hypothèse de fusion des populations au cours du dernier maximum glaciaire (DMG), lorsque la forêt montagnarde s'est vraisemblablement développée et a fourni aux populations actuellement isolées l'occasion de se mélanger. Au lieu de cela, le vieillissement génétique des populations de C. emiliae indique qu'elles se sont diversifiées bien avant le DMG, et que leur aire de répartition ne s'est pas suffisammentélargie au cours du DMG pour se rejoindr...