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Population sizes of endemic songbirds on Kaua‘i have decreased by an order of magnitude over the past 10–15 years to dangerously low numbers. The primary cause appears to be the ascent of invasive mosquitoes and Plasmodium relictum, the agent of avian malaria, into elevations formerly free of introduced malarial parasites and their vectors. Given that these declines in native bird populations appear to be continuing, last resort measures to save these species from extinction, such as conservation breeding, are being implemented. Using 200–1439 SNPs from across the genome, we assessed kinship among individuals, levels of genetic variation, and extent of population decline in wild birds of the two most critically endangered Kaua‘i endemic species, the ‘akikiki (Oreomystis bairdi) and ‘akeke‘e (Loxops caeruleirostris). We found relatively high genomic diversity within individuals and little evidence of spatial population genetic structure. Populations displayed genomic signatures of declining population size, but individual inbreeding coefficients were universally negative, likely indicating inbreeding avoidance. Diversity within the founding conservation breeding population largely mirrored that in the wild, indicating that genetic variation in the conservation breeding population is representative of the wild population and suggesting that the current breeding program captures existing variation. Thus, although existing genetic diversity is likely lower than in historical populations, contemporary variation has been retained through high gene flow and inbreeding avoidance. Nonetheless, current effective population size for both species was estimated at fewer than 20 individuals, highlighting the urgency of management actions to protect these species.

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., Phylogeography of taxa occupying Southeast Asia is poorly known despite its importance as a storehouse of tropical biological diversity. We use a combination of sequence capture, high‐throughput sequencing, and historical samples to conduct a region‐wide, multispecies comparative study that unveils phylogeographic patterns with unprecedented genetic resolution.

Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.

Hybrid zones offer a window into the processes and outcomes of evolution, from species formation or fusion to genomic underpinnings of specific traits and isolating mechanisms. Sexual selection is believed to be an important factor in speciation processes, and hybrid zones present special opportunities to probe its impact. The manakins (Aves, Pipridae) are a promising group in which to study the interplay of sexual selection and natural hybridization: they show substantial variation across the family in the strength of sexual selection they experience, they readily hybridize within and between genera, and they appear to have formed hybrid species, a rare event in birds. A hybrid zone between two manakins in the genus Manacus is unusual in that plumage and behavioral traits of one species have introgressed asymmetrically into populations of the second species through positive sexual selection, then apparently stalled at a river barrier. This is one of a handful of documented examples of asymmetric sexual trait introgression with a known selective mechanism. It offers opportunities to examine reproductive isolation, introgression, plumage color evolution, and natural factors enhancing or constraining the effects of sexual selection in real time. Here, we review previous work in this system, propose new hypotheses for observed patterns, and recommend approaches to test them.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

With the advent of high-resolution and cost-effective genomics and bioinformatics tools and methods contributing to a large database of both human (HAdV) and simian (SAdV) adenoviruses, a genomics-based re-evaluation of their taxonomy is warranted. Interest in these particular adenoviruses is growing in part due to the applications of both in gene transfer protocols, including gene therapy and vaccines, as well in oncolytic protocols. In particular, the re-evaluation of SAdVs as appropriate vectors in humans is important as zoonosis precludes the assumption that human immune system may be naive to these vectors. Additionally, as important pathogens, adenoviruses are a model organism system for understanding viral pathogen emergence through zoonosis and anthroponosis, particularly among the primate species, along with recombination, host adaptation, and selection, as evidenced by one long-standing human respiratory pathogen HAdV-4 and a recent re-evaluation of another, HAdV-76. The latter reflects the insights on amphizoonosis, defined as infections in both directions among host species including "other than human", that are possible with the growing database of nonhuman adenovirus genomes. HAdV-76 is a recombinant that has been isolated from human, chimpanzee, and bonobo hosts. On-going and potential impacts of adenoviruses on public health and translational medicine drive this evaluation of 174 whole genome sequences from HAdVs and SAdVs archived in GenBank. The conclusion is that rather than separate HAdV and SAdV phylogenetic lineages, a single, intertwined tree is observed with all HAdVs and SAdVs forming mixed clades. Therefore, a single designation of "primate adenovirus" (PrAdV) superseding either HAdV and SAdV is proposed, or alternatively, keeping HAdV for human adenovirus but expanding the SAdV nomenclature officially to include host species identification as in ChAdV for chimpanzee adenovirus, GoAdV for gorilla adenovirus, BoAdV for bonobo adenovirus, and ad libitum.

Janzen's influential "mountain passes are higher in the tropics" hypothesis predicts restricted gene flow and genetic isolation among populations spanning elevational gradients in the tropics. Few studies have tested this prediction, and studies that focus on population genetic structure in Southeast Asia are particularly underrepresented in the literature. Here, we test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited dispersal across their broad elevational range which spans ~2,300 m on two peaks in Kinabalu National Park (KNP) in Borneo: Mt Tambuyukon (MT) and Mt Kinabalu (MK). We sampled 83 individuals across elevations on both peaks and performed population genomics analyses on mitogenomes and single nucleotide polymorphisms from 4,106 ultraconserved element loci. We detected weak genetic structure and infer gene flow both across elevations and between peaks. We found higher genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of historical processes and limited upslope gene flow on MT. Importantly, our results serve as a foundational estimate of genetic diversity and population structure from which to track potential future effects of climate change on mountain treeshrews in KNP, an important conservation stronghold for the mountain treeshrew and other montane species.

Aim: A current model of rain forest population diversification in Sundaland specifieseast–west vicariance into refugia during the early Pleistocene. In some taxa, thisdivision was followed by dispersal and apparent secondary contact on Borneo in thelate Pleistocene. To investigate genetic, morphological, spatial and temporal charac-teristics of the model, we compared genomic population and plumage variationamong 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 andTrichastoma malaccense), and compared them with population genetic patternsdetermined from (1) SNPs produced by RAD-Seq and (2) previously sequencedmtDNA. Results: All four species exhibit east–west variation in morphological and somegenetic characters, but patterns are idiosyncratic. Copsychus saularis’ mtDNA andplumage change gradually across Borneo, but RAD-Seq comparisons indicate nopopulation structure. In K. malabarica, all three characteristics change abruptly andconcurrently on Borneo. In M. gularis, the main east–west break occurs betweenBorneo and western Sundaland, with marginal mtDNA, plumage and RAD-Seq struc-ture on Borneo. T. malaccense exhibits two distinct mtDNA and genomic transitions,an early Pleistocene break between western Sundaland and Borneo, and a Pliocenebreak between the north-east and the rest of Borneo. Despite this deep geneticdivision, its plumage changes clinally across Borneo.Main conclusions: MtDNA, plumage and RAD-Seq patterns may vary depending onsuch factors as pre-Pleistocene distribution, habitat requirements and dispersalpropensity, differential introgression among the three character types, selection onplumage and phylogenetic relationships.

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Emergent fungal diseases are critical factors in global biodiversity declines. The fungal pathogenNosema bombiwas recently found to be widespread in declining species of North American bumble bees (Bombus), with circumstantial evidence suggesting an exotic introduction from Europe. This interpretation has been hampered by a lack of knowledge of global genetic variation, geographic origin, and changing prevalence patterns ofN. bombiin declining North American populations. Thus, the temporal and spatial emergence ofN. bombiand its potential role in bumble bee decline remain speculative. We analyzeNosemaprevalence and genetic variation in the United States and Europe from 1980, before an alleged introduction in the early 1990s, to 2011, extractingNosemaDNA fromBombusnatural history collection specimens from across this time period.Nosema bombiprevalence increased significantly from low detectable frequency in the 1980s to significantly higher frequency in the mid- to late-1990s, corresponding to a period of reported massive infectious outbreak ofN. bombiin commercial bumble bee rearing stocks in North America. Despite the increased frequency, we find no conclusive evidence of an exoticN. bombiorigin based on genetic analysis of globalNosemapopulations; the widespreadNosemastrain found currently in declining United States bumble bees was present in the United States before commercial colony trade. Notably, the USN. bombiis not detectably different from that found predominantly throughout Western Europe, with both regions characterized by low genetic diversity compared with high levels of diversity found in Asia, where commercial bee breeding activities are low or nonexistent.

Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (Branta canadensis). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes, Proteobacteria, and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages.

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.

During the last 15–20 years, phylogenetic, phylogeographic, paleontological, geological, and habitat modeling studies have improved our knowledge of Sundaic biogeography dramatically. In light of these advances, we review (or postulate) where Sundaic rainforest birds came from, the causes of their endemism, and the influence of Pleistocene climatic perturbations on their diversification. We suggest that four scenarios make up a coherent, plausible explanation of patterns of extant diversity. First, relictual lineages, which represent hangovers from the warm, wet Eocene, survived the hard climatic times of the colder, drier Oligocene and Pliocene in the mountains and adjacent lowlands of eastern Borneo, where rainforest has existed continuously for the last 20–30 million years. Second, most modern SE Asian genera developed during the Miocene. Third, the rainforest of Sundaland and its avifauna were largely isolated from the rest of SE Asia during the late Miocene and Pliocene by seasonal habitats in southern Indochina and ocean boundaries elsewhere, increasing regional endemism. Finally, the advent of global glaciation in the Pleistocene introduced a different diversification dynamic to Sundaland. Early glacial events caused sufficient drying in central Sundaland to fragment rainforest and its avifauna into refugia in eastern and western Sundaland and to allow dry-habitat taxa to reach Java from Indochina. More recent glacial events resulted in sufficient perhumid habitat in central Sundaland to reconnect previously vicariated rainforest populations, creating the lowland and elevational parapatry we see today. This Pleistocene dynamic was probably not simply one period of separation and one period of connection, but rather a complex interplay of isolation and colonization, influenced by highly variable population sizes, changing levels of gene flow, and behavioral idiosyncrasies of the species involved. Throughout all of these events, Borneo played a seminal role in rainforest bird evolution by providing the habitat necessary for diversification and the long-term survival of taxa.

Journal of Tropical Ecology, 27, ISSN:0266-4674, ISSN:1469-7831

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 ...

Cream-vented Bulbul Pycnonotus simplex of Borneo was previously considered to be polymorphic in iris colour, having either red or white (creamy-yellow) irides. Mitochondrial DNA sequence comparisons, however, indicate that white- and red-eyed Bornean individuals are not closely related to one another. Instead, white-eyed birds are sister to Ashy-fronted Bulbul P. cinereifrons of Palawan Island, in the south-west Philippines, and red-eyed birds are sister to white-eyed P. simplex of the Thai-Malay Peninsula. Consequently, we elect to treat the white-eyed Bornean population as a distinct, previously overlooked species. In respect to plumage, white- and red-eyed individuals are almost identical, varying only slightly in the amount of yellow coloration in their feathers. The two taxa are sympatric at some localities, but white-eyed individuals are rarer and more consistently associated with mature forest than red-eyed birds.

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...

Sundaland has a dynamic geographic history because its landmasses were periodically interconnected when sea levels fell during glacial periods. Superimposed on this geographic dynamism were environmental changes related to climatic oscillations. To investigate how tropical taxa responded to such changes, we studied the divergence and demographic history of two co-distributed rainforest passerine species, Arachnothera longirostra and Malacocincla malaccensis. We sampled birds primarily from Borneo and the Malay Peninsula, which straddle the now-submerged Sunda shelf, and analysed multilocus DNA data with a variety of coalescent and gene genealogy methods. Cross-shelf divergence in both species occurred well before the last glacial maximum, i.e., before the most recent land connection. However, post-divergence gene flow occurred, and it was more pronounced in A. longirostra (a highly vagile nectarivore/insectivore) than in M. malaccensis (an understory insectivore). Despite current habitat continuity on Borneo, the population of M. malaccensis in northeastern Borneo is substantially divergent from that on the rest of the island. The NE population experienced dramatic demographic fluctuations, probably because of competition with the other population, which expanded from western Borneo after the mid-Pleistocene. In contrast, the Borneo population of A. longirostra has little structure and appears to have experienced demographic expansion 16 kya, long after it had diverged from the Malay Peninsula population (630-690 kya). Malay Peninsula populations of both species have remained relatively stable. Overall, the most recent glacial period was not the chief determinant of the evolutionary dynamics of our study species, and in this respect, they are different from temperate species.

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.

H. C. Lim (hlim1@tigers.lsu.edu) and F. H. Sheldon, Mus. of Nat. Sci. and Dept. of Biol. Sci., Louisiana State Univ., Baton Rouge,LA 70803, USA. R. G. Moyle, Dept. of Ecol. and Evol. Biol. and Biodiv. Res. Centre, Univ. of Kansas, Lawrence, KS 66045, USA.Extensive plumage color polymorphism in the oriental dwarf kingfisher Ceyx erithaca has long intrigued ornithologists ofthe Indo Malayan region. A large proportion of birds in Sumatra, Peninsular Malaysia and Borneo have plumagesintermediate between the northerly black form and the southerly rufous form. We used molecular genetic techniques toinvestigate whether the pattern is likely caused by selection, contemporary hybridization or past introgression of genes.These data consist of DNA sequences of a mitochondrial gene (ND2) and five nuclear intronic loci. Phylogenetic analysesindicated that birds from continental southeast Asia (excluding the Thai Malay Peninsula) are well differentiated fromthose from insular southeast Asia. This genetic distinction correlates well with a fixed difference in mantle coloration.Northern birds have black mantles and are consistently dark; southern birds, though highly variable in parts of theplumage, consistently possess a rusty brown mantle. Multivariate analyses of morphometric data also support clusteringbirds in the two groups defined by mantle coloration. Coalescent analyses suggest that gene flow occurred after initialpopulation splitting. We hypothesized that the dynamic geography of the Indo Malayan Archipelago, as driven byeustatic sea-level changes related to glacial cycles, is responsible for extensive secondary contact, and gene flow, betweenthe two color forms. Such periodic contacts, after initial separation of the populations, may be equally common in othergeographically dynamic regions of the world.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Aim The oriental magpie-robin (Copsychus saularis) of South and Southeast Asia is a phenotypically variable species that appears to be closely related to two endemic species of the western Indian Ocean: the Madagascar magpie-robin (Copsychus albospecularis) and the Seychelles magpie-robin (Copsychus sechellarum). This unusual distribution led us to examine evolutionary relationships in magpie-robins, and also the taxonomic significance of their plumage variation, via a molecular phylogenetic and population genetic analysis of C. saularis and C. albospecularis. Location Southern Asia from Nepal across Indochina to southern China, and the Indian Ocean from Madagascar to the Greater Sunda and Philippine islands. Methods We sequenced 1695 nucleotides of mitochondrial DNA comprising the complete second subunit of the nicotinamide adenine dinucleotide dehydrogenase (ND2) gene and 654 bases of the cytochrome c oxidase subunit I (COI) region in 51 individuals of eight C. saularis subspecies, 10 individuals of C. albospecularis (one subspecies) and single individuals of two other Copsychus species as outgroups. The data were analysed phylogenetically, with maximum likelihood, Bayesian, relaxed clock and parsimony methods, and geographically for patterns of genetic diversity. Results Phylogenetic analysis indicated that C. albospecularis lies within the nominal C. saularis, making C. saularis polyphyletic. Malagasy and non-Philippine Asian populations form a monophyletic group that is sister to a clade of Philippine populations. Within non-Philippine Asian populations, two groups are evident: black-bellied birds in the eastern Greater Sunda islands and white-bellied birds in the western Sundas and on mainland Asia. Main conclusions The phylogeny of magpie-robins suggests a novel pattern of dispersal and differentiation in the Old World. Ancestral magpie-robins appear to have spread widely among islands of the Indian Ocean in the Pliocene, probably aided by their affinity for coastal habitats. Populations subsequently became isolated in island groups, notably the Philippines, Madagascar and the Greater Sundas, leading to speciation in all three areas. Isolation in the Philippines may have been aided by competitive exclusion of C. saularis from Palawan by a congener, the white-vented shama (Copsychus niger). In the Greater Sundas, white-bellied populations appear to have invaded Borneo and Java recently, where they hybridize with resident black-bellied birds.

The Grey-cheeked Fulvetta, Alcippe morrisonia, is a polytypic species of Quaker babbler (Timaliidae) occurring mainly in highlands from Burma across southern China to Taiwan. To examine gene flow among populations, we sequenced the mitochondrial ND2 gene of 39 individuals of six of the seven subspecies, plus multiple individuals of three outgroup Alcippe species. A lack of shared haplotypes and high FST values suggested no gene flow among populations. The nucleotide divergence between geographically juxtaposed subspecies ranged from 0.8% between Guangdong and Hainan to 9.4% between Yunnan and Vietnam. Phylogenetic analysis of the populations yielded a well resolved tree with two major clades. One clade consisted of the geographically central subspecies schaefferi and davidi, which are located largely in the "Mid-central" zoogeographic region of China's "Oriental" realm. The other clade, the geographically peripheral group, consisted of all other A. morrisonia subspecies, as well as an erstwhile outgroup, the Mountain Fulvetta (Alcippe peracensis annamensis) from central Vietnam. This peripheral group was further divided into two clades, one consisting of taxa occurring in China's "Southwest" zoogeographic region (fratercula and A. p. annamensis), and one occurring in China's "Southern" region (morrisonia, rufescentior, and hueti). These three geographic and phylogenetic groups represent at least four different species based on plumage differences and genetic differentiation. The phylogeny provides the first avian molecular evidence of area relationships among China's zoogeographic zones. It also highlights a remarkable and unexpected amount of genetic divergence and structure in a Sino-Indian "species". If such diversity occurs in other groups of birds with similar distribution, the ramifications are important for conservation planning.

Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27-43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 10(6) bp (Arachnothera, modern samples) to 1.98 × 10(6) bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering.

Avian ecology in tropical urban area is poorly understood. We determined, through surveys in 29 sites, how birds with different dietary and nesting requirements responded in terms of guild richness and abundance to various facets of urbanisation in Singapore. The sites selected were representative of the full range of urbanisation outside of the undisturbed native forests. Among the dietary guilds, we found that insectivores and carnivores were adversely affected by increased urbanisation. Frugivores were favoured by low-density housing, probably because more fruit-bearing ornamental plants were planted in such estates. Richness and abundance of shrub and shrub/tree nesters, and primary cavity excavators declined with increased urbanisation. We believe that the availability of nesting sites was an important factor in their decline. Exotic species accounted for only 13% of the total species richness detected in our surveys but they were numerically dominant (accounting for 61% of overall bird abundance). Abundance of native resident birds declined monotonically with increasing amount of built-up environment while birds of exotic species appeared to be more abundant in sites with intermediate amount of built-up environment. While urban greenery serves architectural and other functions, it has little effect on overall bird community assembly. The preponderance of exotic species in Singapore city suggests that birds of tropical rainforests are poor colonisers of this relatively novel environment. Many of the native urban species originated from mangrove and coastal scrub forests, so the maintenance of rainforests is necessary for the preservation of many native bird species.

Biological invasions are a major environmental concern due to their negative impacts on biodiversity and economics. We determined the population sizes and habitat-abundance relationships of the three most successful invasive bird species in Singapore: the house crow Corvus splendens, white-vented myna Acridotheres javanicus and common myna A. tristis. Estimated population sizes of the three species between February 2000 and February 2001 were between 106 000-176 000, 122 000-155 000 and 20 000-29 000, respectively. Population size of the house crow grew dramatically (>30-fold) in the last 15-16 y while that of the white-vented and common myna declined. Habitat-abundance relationships suggest that house crows are highly dependent on anthropogenic food. Their abundance was also positively related to proximity to coast. The common myna associated closely with agricultural areas while the white-vented myna probably preferred urban greenery among residential buildings. Our study shows that the three invasive bird species associated with different aspects of human-modified environment.

The lowland tailorbirds of Southeast Asia (Orthotomus) offer an excellent opportunity for comparative biogeography because of their diversity in the Greater Sunda and Philippine islands. We reconstructed the phylogeny of all species in the genus using maximum likelihood, Bayesian, and coalescent methods on DNA sequences of three gene segments: an autosomal intron (TGF), a Z-linked intron (MUSK), and a mitochondrial coding gene (ND2). Although resolution is low in parts of the phylogeny, several well defined clades emerge. When considered in light of distribution, these clades indicate that the Greater Sunda and Philippine islands were occupied early in Orthotomus history by the ancestors of O. sericeus in the Greater Sundas and O. frontalis in the Philippines. Subsequently, tailorbirds diversified further in each island group: O. atrogularis, O. ruficeps, and O. sepium arose in the Greater Sundas, and O. castaneiceps castaneiceps, O. c. chloronotus, O. derbianus, O. samarensis, O. nigriceps, and O. cinereiceps in the Philippines. Among the continental taxa (including Sundaic birds), the older lineages (O. sutorius and O. sericeus) are habitat generalists and the recently evolved taxa are more specialized. In the Philippines, several taxa once considered conspecific with O. atrogularis turn out to be highly divergent species (>9% in ND2). Indeed, all Philippine allospecies are well diverged from one another. This finding supports the recent assertion of higher-than-appreciated bird endemicity in the Philippines.

Aim Magpie-robins and shamas are forest and woodland birds of south Asia. There are two genera: Trichixos for the monotypic T. pyrrhopygus, and Copsychus for other species. Two species are widespread, whereas the others are restricted to specific islands. Endemicity is highest in the Philippines. Using phylogenetic methods, we examined how this group came to its unusual distribution. Location Mainland Asia from India to southern China, and islands from Madagascar to the Philippines. Particular emphasis is placed on the Greater Sundas and Philippines. Methods The phylogeny was estimated from DNA sequences of 14 ingroup taxa representing all nine currently recognized Copsychus and Trichixos species. The entire mitochondrial ND2 gene and portions of nuclear myoglobin intron 2 (Myo2) and transforming growth factor beta 2 intron 5 (TGFb2-5) were sequenced for all but two species. The phylogeny was reconstructed using maximum likelihood and Bayesian methods. The timing of divergence events was estimated using a relaxed molecular clock approach, and ancestral areas were examined using stochastic modelling. Results The group comprises three main clades corresponding to ecological types: Trichixos, a primary-forest specialist; Copsychus magpie-robins, openwoodland and coastal species; and Copsychus shamas, thick-forest species. Trichixos appears to be sister to the magpie-robins, rendering Copsychus polyphyletic. The dating of phylogenetic nodes was too ambiguous to provide substantial insight into specific geographical events responsible for divergence within the group. Some patterns are nevertheless clear. Copsychus shamas reached the Philippines, probably in two separate invasions, and split into endemic species. Copsychus malabaricus and C. saularis expanded widely in the Greater Sundas and mainland Southeast Asia without species-level diversification. Main conclusions Magpie-robins are excellent dispersers and have diversified into distinct species only on isolated oceanic islands. Trichixos, a poor disperser, is restricted to mature forests of the Malay Peninsula, Sumatra and Borneo. Copsychus shamas are intermediate in habitat preference and dispersal capabilities. Their endemism in the Philippines may be attributed to early colonization and specialization to interior forests. In the Greater Sundas, C. malabaricus and C. saularis populations split and came together on Borneo to form two separate subspecies (of each species), which now hybridize.

We present the first species-level molecular phylogenetic hypothesis for the Asian trogons, using DNA sequences of multiple mitochondrial and nuclear loci, and Bayesian and maximum likelihood tree reconstruction methods. The two genera of Asian trogons, Harpactes and Apalharpactes, are distantly related to each other. Within the widespread Southeast Asian genus Harpactes, we recovered three species groups: (1) H. oreskios; (2) H. orrhophaeus and H. duvaucelii; and (3) a clade of the seven large-bodied species. Short internal branch lengths link species in the large-bodied group, suggesting rapid diversification. Apalharpactes, which is currently restricted to the montane forests of Sumatra and Java, appears to be a relictual lineage distantly related to all other trogons. Bayesian and maximum likelihood analyses indicate Apalharpactes is sister to the African genus Apaloderma, although this result was not strongly supported. Overall, the extant Asian trogon species appear to have diversified prior to the Pleistocene, based on large pair-wise mitochondrial divergences between taxa.

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Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA) to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs) belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5%) bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.

Corrigendum to ‘‘Molecular phylogenetic analysis of the Grey-cheeked Fulvetta (Alcippe morrisonia) of China and Indochina: A case of remarkable genetic divergence in a ‘species’ ” [Mol. Phylogenet. Evol. 44 (2007) 165–174] Fasheng Zou , Haw Chuan Lim , Ben D. Marks , Robert G. Moyle , Frederick H. Sheldon b,* a South China Institute of Endangered Animals, Guangzhou 510260, China Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA

The Indian house crow (Corvus splendens) has successfully invaded tropical and subtropical regions well beyond its native range, reaching pest proportions in many areas. The invasive population of house crows in Singapore (Southeast Asia) has increased at least 30-fold since 1985 and now numbers in excess of 130,000 birds. To understand the population ecology and behavior of the house crow in Singapore, we undertook regular population size and roost surveys, dissections of birds shot (to provide age structure and breeding status), detailed nestsite observations, and monitoring of coastal dispersal. Using a discrete-time, density-dependent population model to synthesize this information, we demonstrated that at least 41,000 crows will need to be culled in the first year of a control program, and equivalent effort committed each year thereafter, to be confident of suppressing the Singapore population from its 2001 density of 190 birds/km(2) to the management target of