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Background Quaternary climate fluctuations are an engine of biotic diversification. Global cooling cycles, such as the Last Glacial Maximum (LGM), are known to have fragmented the ranges of higher-latitude fauna and flora into smaller refugia, dramatically reducing species ranges. However, relatively less is known about the effects of cooling cycles on tropical biota. Results We analyzed thousands of genome-wide DNA markers across an assemblage of three closely related understorey-inhabiting scrubwrens (Sericornis and Aethomyias; Aves) from montane forest along an elevational gradient on Mt. Wilhelm, the highest mountain of Papua New Guinea. Despite species-specific differences in elevational preference, we found limited differentiation within each scrubwren species, but detected a strong genomic signature of simultaneous population expansions at 27-29 ka, coinciding with the onset of the LGM. Conclusion The remarkable synchronous timing of population expansions of all three species demonstrates the importance of global cooling cycles in expanding highland habitat. Global cooling cycles have likely had strongly different impacts on tropical montane areas versus boreal and temperate latitudes, leading to population expansions in the former and serious fragmentation in the latter.

Quaternary climate oscillations are a well-known driver of animal diversification, but their effects are most well studied in areas where glaciations lead to habitat fragmentation. In large areas of the planet, however, glaciations have had the opposite effect, but here their impacts are much less well understood. This is especially true in Southeast Asia, where cyclical changes in land distribution have generated enormous land expansions during glacial periods. In this study, we selected a panel of five songbird species complexes covering a range of ecological specificities to investigate the effects Quaternary land bridges have had on the connectivity of Southeast Asian forest biota. Specifically, we combined morphological and bioacoustic analysis with an arsenal of population genomic and modelling approaches applied to thousands of genome-wide DNA markers across a total of more than 100 individuals. Our analyses show that species dependent on forest understorey exhibit deep differentiation between Borneo and western Sundaland, with no evidence of gene flow during the land bridges accompanying the last 1-2 ice ages. In contrast, dispersive canopy species and habitat generalists have experienced more recent gene flow. Our results argue that there remains much cryptic species-level diversity to be discovered in Southeast Asia even in well-known animal groups such as birds, especially in nondispersive forest understorey inhabitants. We also demonstrate that Quaternary land bridges have not been equally suitable conduits of gene flow for all species complexes and that life history is a major factor in predicting relative population divergence time across Quaternary climate fluctuations.

Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as compared with other bats (e.g., loss of echolocation, large size, and frugivory), fruit bats have undergone surprisingly limited change in their genic composition, perhaps apart from a potentially novel gene family expansion relating to telomere protection and longevity. In sharp contrast, within fruit bats, the new Cynopterus genome bears the signal of unusual gene loss and gene family contraction, despite its similar morphology and lifestyle to two other major fruit bat lineages. Most missing genes are regulatory, immune-related, and olfactory in nature, illustrating the diversity of genomic strategies employed by bats to contend with responses to viral infection and olfactory requirements. Our results underscore that significant fluctuations in gene family composition are not always associated with obvious examples of novel physiological and phenotypic adaptations but may often relate to less-obvious shifts in immune strategies.

Island biogeography is one of the most powerful subdisciplines of ecology: its mathematical predictions that island size and distance to mainland determine diversity have withstood the test of time. A key question is whether these predictions follow at a population-genomic level. Using rigorous ancient-DNA protocols, we retrieved approximately 1,000 genomic markers from approximately 100 historic specimens of two Southeast Asian songbird complexes from across the Sunda Shelf archipelago collected 1893–1957. We show that the genetic affinities of populations on small shelf islands defy the predictions of geographic distance and appear governed by Earth-historic factors including the position of terrestrial barriers (paleo-rivers) and persistence of corridors (Quaternary land bridges). Our analyses suggest that classic island-biogeographic predictors may not hold well for population-genomic dynamics on the thousands of shelf islands across the globe, which are exposed to dynamic changes in land distribution during Quaternary climate change.

Peninsular India is an important region for mammalian diversification and harbors major biogeographic barriers. However, little is known about the role of this region in the diversification of bats though it harbors high chiropteran diversity. In this study, we used phenotypic, acoustic, and genetic markers to assess the diversification of Rhinolophus lepidus bats in South Asia. We first investigated if peninsular India is associated with speciation of R. lepidus. Further, we tested if the Palghat Gap acts as a biogeographic barrier to gene flow in this species. Our results revealed cryptic genetic diversity in peninsular India suggesting that this region holds at least one endemic species level lineage of the R. lepidus species complex. Analyses of populations of R. lepidus across the Palghat Gap in the Western Ghats revealed clinal variation in phenotype, with bats south of this barrier being bigger and emitting echolocation calls of higher frequency. We also observed that populations on either side of the Palghat Gap have remained genetically isolated since the mid-Holocene.

Urgent conservation action for terminally endangered species is sometimes hampered by taxonomic uncertainty, especially in illegally traded animals that are often cross‐bred in captivity. To overcome these problems, we used a genomic approach to analyze historical DNA from museum samples across the Asian Pied Starling (Gracupica contra) complex in tropical Asia, a popular victim of the ongoing songbird crisis whose distinct Javan population (“Javan Pied Starling”) is extinct in the wild and subject to admixture in captivity. Comparing genomic profiles across the entire distribution, we detected three deeply diverged lineages at the species level characterized by a lack of genomic intermediacy near areas of contact. Our study demonstrates that the use of historical DNA can be instrumental in delimiting species in situations of taxonomic uncertainty, especially when modern admixture may obfuscate species boundaries. Results of our research will enable conservationists to commence a dedicated ex situ breeding program for the Javan Pied Starling, and serve as a blueprint for similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.

Cyclical periods of global cooling have been important drivers of biotic differentiation throughout the Quaternary. Ice age-induced sea level fluctuations can lead to changing patterns of land connections, both facilitating and disrupting gene flow. In this study, we test if species with differing life histories are differentially affected by Quaternary land connections. We used genome-wide SNPs in combination with mitochondrial gene sequences to analyse levels of divergence and gene flow between two songbird complexes across two Wallacean islands that have been repeatedly connected during glaciations. Although the two bird complexes are similar in ecological attributes, the forest and edge-inhabiting golden whistler Pachycephala pectoralis is comparatively flexible in its diet and niche requirements as compared to the henna-tailed jungle-flycatcher Cyornis colonus, which is largely restricted to the forest interior. Using population-genomic and coalescent approaches, we estimated levels of gene flow, population differentiation and divergence time between the two island populations. We observed higher levels of differentiation, an approximately two to four times deeper divergence time and near-zero levels of gene flow between the two island populations of the more forest-dependent henna-tailed jungle-flycatcher as compared to the more generalist golden whistler. Our results suggest that Quaternary land bridges act as semipermeable agents of gene flow in Wallacea, allowing only certain taxa to connect between islands while others remain isolated. Quaternary land bridges do not accommodate all terrestrial species equally, differing in suitability according to life history and species biology. More generalist species are likely to use Quaternary land connections as a conduit for gene flow between islands whereas island populations of more specialist species may continue to be reproductively isolated even during periods of Quaternary land bridges.

In the last two decades, unsustainable levels of wildlife trade have led to an unprecedented biological crisis. Southeast Asia has become an epicentre for wildlife trade in general and specifically for the cage-bird trade, resulting in numerous regional extinctions. To assess the impact of regional extinction on the loss of genetic diversity in affected cage-birds, we obtained > 18,000 genome-wide markers across 60 Southeast Asian samples of the white-rumped shama (Copsychus malabaricus), a prized songbird that has gone extinct across wide swathes of its Southeast Asian range following heavy poaching. High levels of genomic uniformity across its mainland Southeast Asian range indicate that future reintroductions of birds from regions with less poaching could help bolster populations in regions with intense poaching pressure. Genomic assignment tests demonstrate that birds in the only Sundaic country with strict enforcement of poaching bans, Singapore, are a mosaic of both native populations and escaped cage-birds of mostly peninsular Malaysian origin, indicating that inadvertent reintroductions of caged shamas have led to the recovery of a local population that was nearly extinct and now constitutes a safe haven for the subspecies tricolor. Our study underscores the potential of genome-wide SNPs in identifying implications of trade on wildlife populations.

Müllerian mimicry rings are remarkable symbiotic species assemblages in which multiple members share a similar phenotype. However, their evolutionary origin remains poorly understood. Although gene flow among species has been shown to generate mimetic patterns in some Heliconius butterflies, mimicry is believed to be due to true convergence without gene flow in many other cases. We investigated the evolutionary history of multiple members of a passerine mimicry ring in the poisonous Papuan pitohuis. Previous phylogenetic evidence indicates that the aposematic coloration shared by many, but not all, members of this genus is ancestral and has only been retained by members of the mimicry ring. Using a newly assembled genome and thousands of genomic DNA markers, we demonstrate gene flow from the hooded pitohui (Pitohui dichrous) into the southern variable pitohui (Pitohui uropygialis), consistent with shared patterns of aposematic coloration. The vicinity of putatively introgressed loci is significantly enriched for genes that are important in melanin pigment expression and toxin resistance, suggesting that gene flow may have been instrumental in the sharing of plumage patterns and toxicity. These results indicate that interspecies gene flow may be a more general mechanism in generating mimicry rings than hitherto appreciated.

Species identification has traditionally relied on morphology. However, morphological conservatism can lead to a high incidence of cryptic species, as characters other than morphological ones can be biologically important. In birds, the combined application of bioacoustic and molecular criteria has led to an avalanche of cryptic species discoveries over the last two decades in which findings of deep vocal differentiation have usually been corroborated by molecular data or vice versa. In this study, we use genome-wide DNA data to uncover an unusual case of cryptic speciation in two species within the South-east Asian Streak-eared Bulbul Pycnonotus blanfordi complex, in which both morphology and vocalizations have remained extremely similar. Despite a considerable pre-Pleistocene divergence of these two bulbul species, bioacoustic analysis failed to uncover differences in their main vocalization, but examination of live birds revealed important differences in eye color that had been overlooked in museum material. Our study demonstrates that genome-wide DNA data can be helpful in the detection of cryptic speciation, especially in species that have evolved limited morphological and behavioral differences.

Endangered species are often characterized by low genetic diversity and it is imperative for conservation efforts to incorporate the knowledge obtained from genetic studies for effective management. However, despite the promise of technological advances in sequencing, application of genome-wide data to endangered populations remains uncommon. In the present study we pursued a holistic conservation-genomic approach to inform a field-based management programme of a Critically Endangered species, the Siamese crocodile Crocodylus siamensis. Using thousands of single nucleotide polymorphisms from throughout the genome, we revealed signals of introgression from two other crocodile species within our sample of both wild and captive-bred Siamese crocodiles from Cambodia. Our genetic screening of the Siamese crocodiles resulted in the subsequent re-introduction of 12 individuals into the wild as well as the selection of four individuals for captive breeding programmes. Comparison of intraspecific genetic diversity revealed an alarmingly low contemporary effective population size in the wild (

Background Pleistocene climatic fluctuations are known to be an engine of biotic diversification at higher latitudes, but their impact on highly diverse tropical areas such as the Andes remains less well-documented. Specifically, while periods of global cooling may have led to fragmentation and differentiation at colder latitudes, they may – at the same time – have led to connectivity among insular patches of montane tropical habitat with unknown consequences on diversification. In the present study we utilized ~5.5 kb of DNA sequence data from eight nuclear loci and one mitochondrial gene alongside diagnostic morphological and bioacoustic markers to test the effects of Pleistocene climatic fluctuations on diversification in a complex of Andean tyrant-flycatchers of the genus Elaenia. Results Population genetic and phylogenetic approaches coupled with coalescent simulations demonstrated disparate levels of gene flow between the taxon chilensis and two parapatric Elaenia taxa predominantly during the last glacial period but not thereafter, possibly on account of downward shifts of montane forest habitat linking the populations of adjacent ridges. Additionally, morphological and bioacoustic analyses revealed a distinct pattern of character displacement in coloration and vocal traits between the two sympatric taxa albiceps and pallatangae, which were characterized by a lack of gene flow. Conclusion Our study demonstrates that global periods of cooling are likely to have facilitated gene flow among Andean montane Elaenia flycatchers that are more isolated from one another during warm interglacial periods such as the present era. We also identify a hitherto overlooked case of plumage and vocal character displacement, underpinning the complexities of gene flow patterns caused by Pleistocene climate change across the Andes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1047-3) contains supplementary material, which is available to authorized users.

Observations on mating behaviours and strategies guide our understanding of mating systems and variance in reproductive success. However, the presence of cryptic strategies often results in situations where social mating system is not reflective of genetic mating system. We present such a study of the genetic mating system of a harem-forming bat Cynopterus sphinx where harems may not be true indicators of male reproductive success. This temporal study using data from six seasons on paternity reveals that social harem assemblages do not play a role in the mating system, and variance in male reproductive success is lower than expected assuming polygynous mating. Further, simulations reveal that the genetic mating system is statistically indistinguishable from promiscuity. Our results are in contrast to an earlier study that demonstrated high variance in male reproductive success. Although an outcome of behavioural mating patterns, standardized variance in male reproductive success (I(m)) affects the opportunity for sexual selection. To gain a better understanding of the evolutionary implications of promiscuity for mammals in general, we compared our estimates of I(m) and total opportunity for sexual selection (I(m) /I(f), where I(f) is standardized variance in female reproductive success) with those of other known promiscuous species. We observed a broad range of I(m) /I(f) values across known promiscuous species, indicating our poor understanding of the evolutionary implications of promiscuous mating.

Cryptic species are difficult to identify using morphological identification tools. They represent hitherto unknown biodiversity and their discovery helps formulate more efficient conservation management policies. In this study we assess intraspecific diversity of Rhinolophus rouxii and investigate the presence of cryptic lineages. We characterize acoustic, morphological and genetic differences between allopatric populations of this species in Southern India. Our results reveal the presence of two distinct acoustic lineages (80 and 90 kHz phonic types). Forearm length also differs significantly between the two phonic types. They share a sister taxa relationship and the average genetic distance between them is over 8 %. Phylogenetic reconstruction and the associated divergence time suggest an evolutionary history that correlates with a middle Miocene separation. We propose that these two phonic types be called sibling species and evolutionarily significant units (ESU) within the subgenus Indorhinolophus. We recommend a new name, R. indorouxii for the species representing the 90 kHz phonic type. This study reiterates our lack of accurate taxonomic knowledge of bats, and highlights the value in combining genetics with behavioral (phonic characterization) and morphological measurements in the discovery of cryptic species.

In this study, we investigated the genetic social structure of a polygynous fruit bat, Cynopterus sphinx. We tested whether colonies of C. sphinx are substructured and if genetic relatedness among group members is non-random. Although we did not find statistical evidence of genetic structuring of harems within a colony, significant levels of inbreeding within colonies and social associations between related individuals were observed. The average pairwise relatedness was higher for females within a harem (average: 0.02) than within the colony (average: −0.03) (p < 0.005). In most harems, the harem male was highly related to one harem female (with an average relatedness of 0.2). Further, statistical resampling suggested that this association is non-random, potentially suggesting mate selection. Although the average relatedness among males in colonies was zero, the range of relatedness (−0.43 to 0.49) was high. We conclude that colonies, to some extent are inbred units, comprising of both related and unrelated individuals, and that social associations might be kin based.

Background The Oriental fruit bat genus Cynopterus, with several geographically overlapping species, presents an interesting case study to evaluate the evolutionary significance of coexistence versus isolation. We examined the morphological and genetic variability of congeneric fruit bats Cynopterus sphinx and C. brachyotis using 405 samples from two natural contact zones and 17 allopatric locations in the Indian subcontinent; and investigated the population differentiation patterns, evolutionary history, and the possibility of cryptic diversity in this species pair. Results Analysis of microsatellites, cytochrome b gene sequences, and restriction digestion based genome-wide data revealed that C. sphinx and C. brachyotis do not hybridize in contact zones. However, cytochrome b gene sequences and genome-wide SNP data helped uncover a cryptic, hitherto unrecognized cynopterine lineage in northeastern India coexisting with C. sphinx. Further analyses of shared variation of SNPs using Patterson’s D statistics suggest introgression between this lineage and C. sphinx. Multivariate analyses of morphology using genetically classified grouping confirmed substantial morphological overlap between C. sphinx and C. brachyotis, specifically in the high elevation contact zones in southern India. Conclusion Our results uncover novel diversity and detect a pattern of genetic introgression in a cryptic radiation of bats, demonstrating the complicated nature of lineage diversification in this poorly understood taxonomic group. Our results highlight the importance of genome-wide data to study evolutionary processes of morphologically similar species pairs. Our approach represents a significant step forward in evolutionary research on young radiations of non-model species that may retain the ability of interspecific gene flow. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0599-y) contains supplementary material, which is available to authorized users.