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Morphology has been a leading taxonomic guiding light to systematists for the last couple of hundred years. However, the genetic and – more recently – genomic revolution have produced numerous demonstrations of erroneous classifications that were based on labile morphological traits. We used thousands of genome-wide markers to shed light on evolutionary dynamics in a confusing and taxonomically obscure group of Asian Cyornis flycatchers. Using genomic data, we corroborated recent findings based on three mitochrondrial and five nuclear genes that the two taxa hainanus and klossi which were previously treated as separate species (Cyornis hainanus and Cyornis rubeculoides klossi, respectively) are genomically homogeneous and form a single species, C. hainanus. We also uncovered a novel case of interbreeding between C. hainanus and a non-sister species, C. glaucicomans, illustrating these flycatchers' ability to hybridise in marginal situations even after substantial times of divergence. Our study illustrates how genome-wide loci can shed light on complicated taxonomic problems, resulting in a better integration of phenotypic and genotypic data.

The common paradise-kingfisher, Tanysiptera galatea, species complex comprises 19 taxa distributed across New Guinea and Wallacea. Owing to its highly conserved morphological features, the lineage has been taxonomically confused, with 15 similar-plumaged taxa currently treated as conspecific. To shed light on species limits, we analysed eight bioacoustic parameters across 107 sound recordings using principal component analysis and the Isler criterion, among other methods. Our results show that multiple geographical entities of Tanysiptera paradise-kingfishers form discrete bioacoustic clusters across several vocal parameters, suggesting that species diversity of the common paradise-kingfisher complex has been greatly underestimated. Based on our results, we propose splitting T. galatea into six species: (1) Obi paradise-kingfisher, Tanysiptera obiensis; (2) Rossel paradise-kingfisher, Tanysiptera rosseliana; (3) Papuan paradise-kingfisher, T. galatea; (4) Halmahera paradise-kingfisher, Tanysiptera margarethae; (5) Morotai paradise-kingfisher, Tanysiptera doris; and (6) Amboyna paradise-kingfisher, Tanysiptera nais. Our work highlights that the non-invasive collection of avian vocal data is a crucial taxonomic tool and adds to increasing evidence that bioacoustic analyses are effective in elucidating cryptic diversity.

Blood parasites comprise some of the most prevalent pathogens in nature, and their detection and identification are major objectives in varied fields such as ecology and biomedicine. Two approaches were compared, one based on Sanger sequencing and the other next-generation sequencing (NGS) based, in terms of their performance in detecting avian blood parasites across tropical Southeast Asian birds. Across a panel of 528 bird individuals, 43 birds were ascertained to be infected with avian haemosporidians using a polymerase chain reaction-based detection method. Among these samples, NGS-based barcoding confirmed co-infections by multiple blood parasites in all eight cases where Sanger sequencing produced double peaks. Importantly however, the NGS-based method produced another five diagnoses of co-infections (62.5%) in which Sanger-based barcoding remained equivocal. In contrast to Sanger sequencing, the NGS-based method was able to identify co-infecting haemosporidian lineages via their barcodes. The accuracy of avian haemosporidian lineage identification was not compromised by the shorter length of NGS sequences, with ~94% of NGS barcodes producing matches identical to those of the Sanger barcodes. The application of NGS-based barcoding methods promises to enhance parasite identification and reduce erroneous inferences based on artefacts.

Research on island species–area relationships (ISAR) has expanded to incorporate functional (IFDAR) and phylogenetic (IPDAR) diversity. However, relative to the ISAR, we know little about IFDARs and IPDARs, and lack synthetic global analyses of variation in form of these three categories of island diversity–area relationship (IDAR). Here, we undertake the first comparative evaluation of IDARs at the global scale using 51 avian archipelagic data sets representing true and habitat islands. Using null models, we explore how richness-corrected functional and phylogenetic diversity scale with island area. We also provide the largest global assessment of the impacts of species introductions and extinctions on the IDAR. Results show that increasing richness with area is the primary driver of the (non-richness corrected) IPDAR and IFDAR for many data sets. However, for several archipelagos, richness-corrected functional and phylogenetic diversity changes linearly with island area, suggesting that the dominant community assembly processes shift along the island area gradient. We also find that archipelagos with the steepest ISARs exhibit the biggest differences in slope between IDARs, indicating increased functional and phylogenetic redundancy on larger islands in these archipelagos. In several cases introduced species seem to have ‘re-calibrated’ the IDARs such that they resemble the historic period prior to recent extinctions. info:eu-repo/semantics/publishedVersion

The seasonal migration of birds is a fascinating natural wonder. Avian migratory behaviour changes are common and are probably a polygenic process as avian migration is governed by multiple correlated components with a variable genetic basis. However, the genetic and phenotypic changes involving migration changes are poorly studied. Using one annotated near-chromosomal level de novo genome assembly, 50 resequenced genomes, hundreds of morphometric data and species distribution information, we investigated population structure and genomic and phenotypic differences associated with differences in migratory behaviour in a songbird species, Yellow-throated Bunting Emberiza elegans (Aves: Emberizidae). Population genomic analyses reveal extensive gene flow between the southern resident and the northern migratory populations of this species. The hand-wing index is significantly lower in the resident populations than in the migratory populations, indicating reduced flight efficiency of the resident populations. Here, we discuss the possibility that nonmigratory populations may have originated from migratory populations though migration loss. We further infer that the alterations of genes related to energy metabolism, nervous system and circadian rhythm may have played major roles in regulating migration change. Our study sheds light on phenotypic and polygenic changes involving migration change.

Impending anthropogenic climate change will severely impact coastal organisms at unprecedented speed. Knowledge on organisms’ evolutionary responses to past sea‐level fluctuations and estimation of their evolutionary potential is therefore indispensable in efforts to mitigate the effects of future climate change. We sampled tens of thousands of genomic markers of ~300 individuals in two of the four extant horseshoe crab species across the complex archipelagic Singapore Straits. Carcinoscorpius rotundicauda Latreille, a less mobile mangrove species, has finer population structure and lower genetic diversity compared with the dispersive deep‐sea Tachypleus gigas Müller. Even though the source populations of both species during the last glacial maximum exhibited comparable effective population sizes, the less dispersive C. rotundicauda seems to lose genetic diversity much more quickly because of population fragmentation. Contra previous studies’ results, we predict that the more commonly sighted C. rotundicauda faces a more uncertain conservation plight, with a continuing loss in evolutionary potential and higher vulnerability to future climate change. Our study provides important genomic baseline data for the redirection of conservation measures in the face of climate change and can be used as a blueprint for assessment and mitigation of the adverse effects of impending sea‐level rise in other systems.

Quantifying the magnitude of the global extinction crisis is important but remains challenging, as many extinction events pass unnoticed owing to our limited taxonomic knowledge of the world’s organisms. The increasing rarity of many taxa renders comprehensive sampling difficult, further compounding the problem. Vertebrate lineages such as birds, which are thought to be taxonomically well understood, are therefore used as indicator groups for mapping and quantifying global extinction. To test whether extinction patterns are adequately gauged in well-studied groups, we implemented ancient-DNA protocols and retrieved whole genomes from the historic DNA of museum specimens in a widely known songbird radiation of shamas (genus Copsychus) that is assumed to be of least conservation concern. We uncovered cryptic diversity and an unexpected degree of hidden extinction and terminal endangerment. Our analyses reveal that >40% of the phylogenetic diversity of this radiation is already either extinct in the wild or nearly so, including the two genomically most distinct members of this group (omissus and nigricauda), which have so far flown under the conservation radar as they have previously been considered subspecies. Comparing the genomes of modern samples with those from roughly a century ago, we also found a significant decrease in genetic diversity and a concomitant increase in homozygosity affecting various taxa, including small-island endemics that are extinct in the wild as well as subspecies that remain widespread across the continental scale. Our application of modern genomic approaches demonstrates elevated levels of allelic and taxonomic diversity loss in a songbird clade that has not been listed as globally threatened, highlighting the importance of ongoing reassessments of extinction incidence even across well-studied animal groups.Key words: extinction, introgression, white-rumped shama, conservation.

Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships within a clade comprising eight species of passerine birds (Phylloscopidae, Phylloscopus, leaf warblers) using one de novo genome assembly and 78 resequenced genomes. On the basis of hypothesis-exclusion trials based on D-statistics, phylogenetic network analysis, and demographic inference analysis, we identified ancient gene flow affecting large parts of the genome between one species and the ancestral lineage of a sister species pair. This ancient gene flow consistently caused erroneous reconstruction of the phylogeny when using large amounts of genome-wide sequence data. In contrast, the true relationships were captured when smaller parts of the genome were analyzed, showing that the “winner-takes-all democratic majority tree” is not necessarily the true species tree. Under this condition, smaller amounts of data may sometimes avoid the effects of gene flow due to stochastic sampling, as hidden reticulation histories are more likely to emerge from the use of larger data sets, especially whole-genome data sets. In addition, we also found that genomic regions affected by ancient gene flow generally exhibited higher genomic differentiation but a lower recombination rate and nucleotide diversity. Our study highlights the importance of considering reticulation in phylogenetic reconstructions in the genomic era.[Bifurcation; introgression; recombination; reticulation; Phylloscopus.]

Estimating the total number of species on Earth has been a longstanding pursuit. Models project anywhere between 2 and 10 million species, and discovery of new species continues to the present day. Despite this, we hypothesized that our current knowledge of phylogenetic diversity (PD) may be almost complete because new discoveries may be less phylogenetically distinct than past discoveries. Focusing on birds, which are well studied, we generated a robust phylogenetic tree for most extant species by combining existing published trees and calculated each discovery's marginal contribution to known PD since the first formal species descriptions in 1758. We found that PD contributions began to plateau in the early 1900s, about half a century earlier than species richness. Relative contributions of each phylogenetic order to known PD shifted over the first 150 years, with a growing contribution of the hyper-diverse perching birds (Passeriformes) in particular, but after the early 1900s this has remained relatively stable. Altogether, this suggests that our knowledge of the evolutionary history of extant birds is mostly complete, with few discoveries of high evolutionary novelty left to be made, and that conclusions of studies using avian phylogenies are likely to be robust to future species discoveries.

SummaryThe Straw-headed BulbulPycnonotus zeylanicusis one of South-East Asia’s most threatened songbirds due to relentless demand for the regional cage-bird trade. The species was recently uplisted from ‘Endangered’ to ‘Critically Endangered’ only two years after its previous uplisting. Intriguingly, populations in highly urbanised Singapore appear relatively secure. However, the last Singaporean density estimates, derived from traditional census methods, were obtained nearly two decades ago in 2001. A recent population estimate in 2016 was derived from the census work in 2001 coupled with relative abundance indices from population trends. We thus performed systematic field surveys using the distance sampling method, estimating 573 ± 185 individuals nation-wide, with a break-down of 217 ± 81 on the main island of Singapore and 356 ± 104 birds on the satellite of Pulau Ubin. Taken together, the total population estimate reported here comprises 22.9–57.3% of the global wild population, underscoring the importance of Singapore as a stronghold for the species. In spite of its apparently secure status in Singapore, the species remains susceptible to local and foreign trapping pressures. Based on our assessment, we propose a number of local and regional conservation measures to ensure the continued survival of populations in Singapore.

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.

Southeast Asian avifauna is under threat from both habitat loss and illegal poaching, yet the region’s rich biodiversity remains understudied. Here, we uncover cryptic species-level diversity in the Sunda Blue Robin (Myiomela diana), a songbird complex endemic to Javan (subspecies diana) and Sumatran (subspecies sumatrana) mountains. Taxonomic inquiry into these populations has previously been hampered by a lack of DNA material and the birds’ general scarcity, especially sumatrana which is only known from few localities. We demonstrate fundamental bioacoustic differences in courtship song paired with important distinctions in plumage saturation and tail length that combine to suggest species-level treatment for the two taxa. Treated separately, both taxa are independently threatened by illegal poaching and habitat loss, and demand conservation action. Our study highlights a case of underestimated avifaunal diversity that is in urgent need of revision in the face of imminent threats to species survival.

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.

The red junglefowl Gallus gallus is the ancestor of the domestic chicken and arguably the most important bird species on Earth. Continual gene flow between domestic and wild populations has compromised its gene pool, especially since the last century when human encroachment and habitat loss would have led to increased contact opportunities. We present the first combined genomic and morphological admixture assessment of a native population of red junglefowl, sampled from recolonized parts of its former range in Singapore, partly using whole genomes resequenced from dozens of individuals. Crucially, this population was genomically anchored to museum samples from adjacent Peninsular Malaysia collected ~110–150 years ago to infer the magnitude of modern domestic introgression across individuals. We detected a strong feral–wild genomic continuum with varying levels of domestic introgression in different subpopulations across Singapore. Using a trait scoring scheme, we determined morphological thresholds that can be used by conservation managers to successfully identify individuals with low levels of domestic introgression, and selected traits that were particularly useful for predicting domesticity in genomic profiles. Our study underscores the utility of combined genomic and morphological approaches in population management and suggests a way forward to safeguard the allelic integrity of wild red junglefowl in perpetuity.

The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species. Here we report a chromosome-level genome assembly for the mangrove horseshoe crab (Carcinoscorpius rotundicauda) using PacBio reads and Hi-C data. The assembly spans 1.67 Gb with contig N50 of 7.8 Mb and 98% of the genome assigned to 16 chromosomes. The genome contains five Hox clusters with 34 Hox genes, the highest number reported in any invertebrate. Detailed analysis of the genome provides evidence that suggests three rounds of whole-genome duplication (WGD), raising questions about the relationship between WGD and species radiation. Several gene families, particularly those involved in innate immunity, have undergone extensive tandem duplication. These expanded gene families may be important components of the innate immune system of horseshoe crabs, whose amebocyte lysate is a sensitive agent for detecting endotoxin contamination., Horseshoe crabs have been morphologically stable across evolutionary time. Here, the authors generate a chromosome-level assembly for the mangrove horseshoe crab, with implications for innate immunity, and challenging assumptions about the role of genome duplication in adaptive radiation.

Habitat fragmentation is a major extinction driver. Despite dramatically increasing fragmentation across the globe, its specific impacts on population connectivity across species with differing life histories remain difficult to characterize, let alone quantify. Here, we investigate patterns of population connectivity in six songbird species from Singapore, a highly fragmented tropical rainforest island. Using massive panels of genome‐wide single nucleotide polymorphisms across dozens of samples per species, we examined population genetic diversity, inbreeding, gene flow and connectivity among species along a spectrum of ecological specificities. We found a higher resilience to habitat fragmentation in edge‐tolerant and forest‐canopy species as compared to forest‐dependent understorey insectivores. The latter exhibited levels of genetic diversity up to three times lower in Singapore than in populations from contiguous forest elsewhere. Using dense genomic and geographic sampling, we identified individual barriers such as reservoirs that effectively minimize gene flow in sensitive understorey birds, revealing that terrestrial forest species may exhibit levels of sensitivity to fragmentation far greater than previously expected. This study provides a blueprint for conservation genomics at small scales with a view to identifying preferred locations for habitat corridors, flagging candidate populations for restocking with translocated individuals and improving the design of future reserves.

Management of biological invasions and conservation activity in the fight against habitat fragmentation both require information on how ongoing dispersal of organisms is affected by the environment. However, there are few landscape genetic computer programs that map resistance to dispersal at small spatiotemporal scales. To facilitate such analyses, we present an r package named ResDisMapper for the mapping of resistance to dispersal at small spatiotemporal scales, without the need for prior knowledge on environmental features or intensive computation. Based on the concept of isolation by distance (IBD), ResDisMapper calculates resistance using deviations of each pair of samples from the general IBD trend (IBD residuals). The IBD residuals are projected onto the studied area, which allows construction and visualization of a fine-scale map of resistance based on spatial accumulation of positive or negative IBD residuals. In this study, we tested ResDisMapper with both simulated and empirical data sets and compared its performance with two other popular landscape genetic programs. Overall, we found that ResDisMapper can map resistance with relatively high accuracy. The latest version of the package and associated documentation are available on Github (https://github.com/takfung/ResDisMapper).

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.

Brush cuckoos of the Cacomantis variolosus complex, which range from Southeast Asia to Australia and the Solomon Islands, have undergone much taxonomic upheaval. Here we examine 389 vocal recordings, 832 skins, and records of brood parasitism and habitat partitioning to shed light on their species and subspecies taxonomy. Bioacoustic analysis revealed seven distinct vocal groups. Among morphological markers, shape and proportions of the tail were found to be supporting indicators, in addition to plumage tone and pattern. Integration of the resulting data set distinguished six species-level taxa within the complex: sepulcralis in the Philippines and Sundaland east to central Nusa Tenggara, virescens in Sulawesi and the Sula Archipelago, aeruginosus in the Moluccas, variolosus in east Nusa Tenggara, the Moluccas, north and east Australia, New Guinea and Bismarck Archipelago, blandus in the Admiralty Islands, and addendus in the Solomon Islands. Our review of infra-specific differentiation among species leads us to distinguish 13 subspecies. All taxa identified are listed in a summary classification of the complex. Taxon diversity is greatest in the Moluccas, where two habitat-partitioned species and five allopatric subspecies occur, of which one species and three subspecies are endemic to this region.

Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowlGallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20–50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity ofG.gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.

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.

We describe a colorful and distinctive new species of tanager from the lower slopes of the Andes of southeastern Peru and western Bolivia. The species was first noted from southeastern Peru in 2000, but little of its natural history was uncovered until the 2011 discovery of a breeding population in deciduous forest in an intermontane valley, the Machariapo valley, in Bolivia. This species appears to be an intratropical migrant, breeding in deciduous forest during the rainy season (November–March) and spending the dry season dispersed along the lower slopes of the Andes, apparently favoring Guadua bamboo-dominated habitats in both seasons. Phylogenetic evidence suggests this tanager is embedded within a clade of thraupids that includes Ramphocelus, Coryphospingus, Loriotus, Tachyphonus, and related genera in the subfamily Tachyphoninae. Within this subfamily, the new species falls in a clade with two monotypic genera, Eucometis penicillata (Gray-headed Tanager) and Trichothraupis melanops (Black-goggled Tanager). There is strong support for a sister relationship between the new tanager and T. melanops, but because all three species in this clade are highly distinctive phenotypically, we propose erecting a new genus and species name for the new tanager. LAY SUMMARY We discovered a new species of tanager, from the foothills of the Andes mountains in Peru and Bolivia, which we name the Inti Tanager. The name “Inti” is the Quechua (a language indigenous to the region) word that means “sun,” referring to the bright yellow color of the bird. Unlike most new bird species discovered recently, which typically differ only subtly from their closest relatives, this species is so different in appearance and genetics that we also described a new genus just for it. The tanager family, to which the new species belongs, is one of the largest bird families in the world (with about 377 species), restricted almost entirely to the American tropics and including many beautifully colorful species. We uncovered a surprising piece of natural history about the Inti Tanager: it migrates from its breeding grounds in a little-explored valley in Bolivia to “winter” along the lower slopes of the Andes in Peru. Such migration within the tropics is rare within the tanagers. That this unique, bright yellow bird could have gone unnoticed by ornithologists until recently attests to the remoteness of the areas where it lives and to the importance of continued biological surveys off-the-grid in South America.

Intracontinental biotic divisions across the vast Palaearctic region are not well-characterized. Past research has revealed patterns ranging from a lack of population structure to deep divergences along varied lines of separation. Here we compared biogeographic patterns of two Palaearctic shorebirds with different habitat preferences, Whimbrel (Numenius phaeopus) and Eurasian curlew (N. arquata). Using genome-wide markers from populations across the Palaearctic, we applied a multitude of population genomic and phylogenomic approaches to elucidate population structure. Most importantly, we tested for isolation by distance and visualized barriers and corridors to gene flow. We found shallow Palaearctic population structure in subpolar bog and tundra-breeding whimbrels, consistent with other species breeding at a similarly high latitude, indicating connectivity across the tundra belt, both presently and during southward shifts in periods of global cooling. In contrast, the temperate grassland-breeding Eurasian curlew emerged in three distinct clades corresponding to glacial refugia. Barriers to gene flow coincided with areas of topographic relief in the central Palaearctic for whimbrels and further east for Eurasian curlews. Our findings highlight the interplay of historic and ecological factors in influencing present-day population structure of Palaearctic biota.

We here describe a new species of Myzomela honeyeater from the Lesser Sunda island of Alor (southeast Indonesia). The new species is phylogenetically most closely related to Myzomela kuehni from the adjacent island of Wetar and most closely resembles that species in plumage. However, it differs in important morphological, bioacoustic and ecological characteristics. The discovery of a new bird species on Alor is of great biogeographic importance and elevates this island to the status of an Endemic Bird Area. The new Alor Myzomela is restricted to montane eucalypt woodland mostly above 900 m elevation and is currently known from few sites across the island. Based on its occurrence records and human population trends in the highlands of Alor Island, we recommend classification under the IUCN threat status endangered.

Background The taxonomy of the Collared Owlet (Glaucidium brodiei) species complex is confused owing to great individual variation in plumage colouration seemingly unrelated to their distribution. Although generally recognised as a single species, vocal differences among the subspecies have been noted by field recordists. However, there is no study assessing the vocal differences among these four subspecies. Methods We obtained 76 sound recordings of the G. brodiei species complex comprising all four subspecies. We conducted bioacoustic examinations using principal component analysis and the Isler criterion to quantitatively test species boundaries within the G. brodiei complex. In addition, we compared plumage colouration among 13 specimens of the G. brodiei complex deposited at the Natural History Museum at Tring, UK and the Lee Kong Chian Natural History Museum, Singapore to ascertain the presence of plumage differences across taxa. Results We found the Bornean and Sumatran populations vocally similar to each other, but distinctly different from the mainland and Taiwan populations. The vocal pattern seems to corroborate plumage distinctions in the colouration of neck collars: the Bornean and Sumatran taxa share a white neck collar, whereas the continental and Taiwan taxa share a rufous neck collar. Conclusions We propose the taxonomic elevation of the Sumatran and Bornean populations to species level as Sunda Owlet G. sylvaticum, with one subspecies on Sumatra (G. s. sylvaticum) and Borneo (G. s. borneense) each. Our study corroborates the importance of bioacoustics in ascertaining species boundaries in non-passerines, and emphasises the significance of incorporating multiple species delimitation approaches when making taxonomic decisions.

The southern river terrapin, Batagur affinis is one of the world's 25 most endangered freshwater turtle species. The major portion of the global population is currently found in peninsular Malaysia, with the only remnant Indochinese population in southern Cambodia. For more than a decade, wild nests in this remnant Cambodian population have been fenced and hatchlings reared in captivity. Here we amplified 10 microsatellite markers from all 136 captive individuals, obtained 2,658 presumably unlinked and neutral single nucleotide polymorphisms from 72 samples with ddRAD‐seq, and amplified 784 bp of mtDNA from 50 samples. Our results reveal that the last Indochinese population comprised only four kinship groups as of 2012, with all offspring sired from

In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by “speciation reversal” or by mitochondrial capture through genetic introgression. Here, we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological, and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of “ghost introgression” as the cause of DMD, and we suggest that “ghost introgression” may be a widely overlooked phenomenon in nature.

Background Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced genetic differentiation across the region by investigating phylogeographic patterns in the Pitta sordida species complex. Results We generated a de novo genome and compared population genomics of 29 individuals of Pitta sordida from the entire distributional range and we reconstructed phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset and single nucleotide polymorphisms (SNPs). We found deep divergence between an eastern and a western group of taxa across Indo-Australasia. Within both groups we have identified major lineages that are geographically separated into Philippines, Borneo, western Sundaland, and New Guinea, respectively. Although these lineages are genetically well-differentiated, suggesting a long-term isolation, there are signatures of extensive gene flow within each lineage throughout the Pleistocene, despite the wide geographic range occupied by some of them. We found little evidence of hybridization or introgression among the studied taxa, but forsteni from Sulawesi makes an exception. This individual, belonging to the eastern clade, is genetically admixed between the western and eastern clades. Geographically this makes sense as Sulawesi is not far from Borneo that houses a population of hooded pittas that belongs to the western clade. Conclusions We found that geological vicariance events cannot explain the current genetic differentiation in the Pitta sordida species complex. Instead, the glacial-interglacial cycles may have played a major role therein. During glacials the sea level could be up to 120 m lower than today and land bridges formed within both the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and faunal elements. The geographic distribution of hooded pittas shows the importance of overwater, “stepping-stone” dispersals not only to deep-sea islands, but also from one shelf to the other. The most parsimonious hypothesis is an Asian ancestral home of the Pitta sordida species complex and a colonization from west to east, probably via Wallacea. Electronic supplementary material The online version of this article (10.1186/s12862-019-1481-5) contains supplementary material, which is available to authorized users.

Despite the ongoing taxonomic revolution incorporating multiple species delimitation methods, knowledge gaps persist in the taxonomy of comparatively well-studied animal groups such as birds. Morph ...

The Lesser Sundas Region continues to be widely unexplored even in such relatively well-known animal groups as birds (Aves). We report the results of an ornithological expedition from November through December 2015 to Timor, Alor and Rote islands along with some opportunistic observations made in that area between 2006 to 2015, providing details on numerous first records of bird species outside their previously known geographic or elevational ranges observed or otherwise recorded during this expedition. Our results underscore the fragmentary nature of our knowledge of the composition of the avifauna of the Lesser Sunda Islands, and demonstrate that there continues to be a large volume of significant new records and range extensions of birds on these islands.

Endangerment and extinction of threatened populations can often be accelerated by genomic contamination through infiltration with alien alleles. With a growing anthropogenic footprint, many such hybridization events are human-mediated. The Milky Stork (Mycteria cinerea) is one such species whose genomic composition is threatened by human-mediated hybridization with its sister taxon, the Painted Stork (Mycteria leucocephala). A comprehensive investigation of the stork population in Singapore using three complementary population-genomic approaches revealed a large proportion of hybrids that have undergone several generations of genomic leakage from Painted Storks and fall along a genetic cline that closely mirrors a phenotypic cline from pure Milky to pure Painted. Although originating from a limited number of introduced Painted Storks, these hybrids are now an integral part of both the wild and captive Singaporean and southern peninsular Malaysian stork population. Genetically informed conservation management including the isolation of hybrids in captivity and a strict removal of hybrids from the wild along with a release of genetically pure Milky Storks is imperative for continued survival. Similar approaches must become routine in endangered species conservation as human-mediated hybridization increases in volume.

The ornithological world has 4 global checklists (as of early 2020). While 3 follow the results of peer-reviewed research at varying pace and conservatism, the HBW/BirdLife checklist, which is adopted by the global Red List authority, has implemented Tobias et al.’s (2010) 7-point scoring system to overhaul global ornithological treatment. Critically received in some academic quarters, this scoring system is lauded by other ornithologists for its simplicity and reproducibility, a claim that remains to be tested. We subjected 26 ornithologists to a set of 48 bird skins belonging to 20 controversial taxonomic complexes and observed a wide variance in scoring results, in most cases straddling anywhere from far below to above the species threshold of the 7-point rule and casting doubt on claims of high reproducibility. For a detailed assessment of genuine taxonomic discord, we compared the taxonomic coverage of the avifauna of the Indonesian Archipelago (comprising ~1,400 species) between the HBW/BirdLife checklist, other major authorities, and the peer-reviewed literature. We detected that controversial treatments supported by the 7-point rule but at odds with the peer-reviewed literature predominantly refer to lumps, not splits, which are the usual subject of modern taxonomic quarrels. Notably, the method tends to unite morphologically (and sometimes vocally) cryptic forms into single larger species because of its inability to accommodate molecular and massive bioacoustic datasets that would indicate otherwise. On the other hand, the 7-point rule has produced numerous novel proposals for splits that may or may not be corroborated by future peer-reviewed inquiry. We recommend the 7-point rule as one of the multiple unofficial exploratory tools to flag cases of potentially cryptic species requiring further inquiry, but we advise against its adoption by other taxonomic authorities and the ornithological community.

Heavily managed wildlife may suffer from genetic homogenization and reshuffling of locally adapted genotypes with non-native ones. This phenomenon often affects natural populations by reducing their evolutionary potential and speeding up the ongoing biodiversity crisis. For decades, the red-legged partridge (Alectoris rufa), an intensively managed gamebird of conservation concern and considerable socio-economic importance, has been subjected to extensive releases of farm-reared hybrids with the chukar partridge (Alectoris chukar) and translocations irrespective of subspecific affinity. These practices have led to serious concerns that the genetic integrity and biogeographic structure of most red-legged partridge populations are irreversibly affected, as suggested by previous studies based on few genetic markers. Using over 168 000 genome-wide loci and a sampling across the entireA. rufarange, we detected unexpectedly limited and spatially uneven chukar introgression as well as significant intraspecific structure. We demonstrate that species widely feared to have irretrievably lost their genetic identity are likely to be much less affected by unsuitable management practices than previously assumed. Our results spell the need for a radical re-think on animal conservation, possibly restoring native status to populations long treated as compromised. Our study exemplifies how the application of innovative conservation-genomic methods is key to solving wildlife management problems dealing with introgressive hybridization worldwide.

We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa , the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity . Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.

Archipelagoes serve as important ‘natural laboratories’ which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a ‘great speciator’, comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.

BackgroundThe Elegant Pitta (Pitta elegans) complex displays a remarkable diversity of morphological and bioacoustic traits across five taxa currently recognized as subspecies. They differ in plumage characteristics (such as red versus black belly patches; supercilium color and extent; and white versus black throats), in lifestyle (resident versus migratory) and in vocalizations. We investigated the morphological, bioacoustic and ecological differences across all taxa after recent studies demostrated the importance of these traits in recognizing biological species limits across pittas.MethodsMorphometric analysis was carried out by measuring tarsus, wing, tail and bill lengths of 15 specimens at the Natural History Museum, UK, and plumages were inspected across 106 unique individuals from four different repositories. Bioacoustic analysis was based on 134 range-wide sound recordings. Two types of calls, territorial calls and alarm calls, were analyzed using different sets of parameters. Principal component analysis and the Isler Criterion were applied to the measurements. Playback trials were conducted to explore the levels of response of each taxon to the call types of the other taxa.ResultsThe territorial call ofconcinnaexhibits a distinct two-element motif, whileelegans,mariaandvirginalisutter a three-element motif in which the first two elements are given in quick succession. On the other hand,vigorsii, produces both two-element and three-element motifs with longer breaks in between elements. As further corroborated by the playback trials, the three taxaelegans,virginalisandmariaform a tight vocal cluster, whereas eachconcinnaandvigorsiiare distinct. The alarm call turned out to be less diagnostic even though most taxa did roughly separate into different vocal clusters. Morphometric analysis failed to produce strong differences, but plumage distinctions among multiple taxa are pronounced.ConclusionsWe suggest splitting the Elegant Pitta into three biological species based on bioacoustic and—less so—plumage evidence: (1) Temminck’s Elegant PittaP. elegans(including subspecieselegans,virginalisandmaria), (2) Wallace’s Elegant PittaP. concinna(monotypic), and (3) Banda Elegant PittaP. vigorsii(monotypic).