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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.

Captive management of many wildlife species can be challenging, with individuals displaying health disorders that are not generally described in the wild population. Retrospective studies have identified gastrointestinal (GI) diseases, in particular inflammatory bowel disease (IBD), as the second leading cause of captive adult red wolf (Canis rufus) mortality. Recent molecular studies show that imbalanced gut microbial composition is tightly linked to IBD in the domestic dog. The goal of the present study was to address two main questions: (1) how do red wolf gut microbiomes differ between animals with loose stool consistency, indicative of GI issues, and those with normal stool consistency and (2) how does dietary type relate to stool consistency and red wolf gut microbiomes? Fresh fecal samples were collected from 48 captive wolves housed in eight facilities in the United States and from two wild wolves living in Alligator River National Wildlife Refuge, NC, United States. For each individual, the stool consistency was categorized as loose or normal using a standardized protocol and their diet was categorized as either wild, whole meat, a mix of whole meat and kibble or kibble. We characterized gut microbiome structure using 16S rRNA gene amplicon sequencing. We found that red wolves with a loose stool consistency differed in composition than wolves with normal stool consistency, suggesting a link between GI health and microbiome composition. Diet was not related to stool consistency but did significantly impact gut microbiome composition; gut microbiome composition of wolves fed a kibble diet were significantly different than the gut microbiome composition of wolves fed a mixed, whole meat and wild diet. Findings from this study increase the understanding of the interplay between diet and GI health in the red wolf, a critical piece of information needed to maintain a healthy red wolf population ex situ.

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.

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.

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.

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.

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.

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.

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 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