Population structure in Mixornis tit-babblers across Sunda Shelf matches interfluvia of paleo-rivers.

Rivers constitute an important biogeographic divide in vast areas of tropical rainforest, such as the Amazon and Congo Basins. Southeast Asia's rainforests are currently fragmented across islands divided by sea, which has long obscured their extensive history of terrestrial connectivity as part of a vast (but now submerged) subcontinent - Sundaland - during most of the Quaternary. The role of paleo-rivers in determining population structure in Sundaic rainforests at a time when these forests were connected remains little understood. We examined the coloration of museum skins and used the genomic DNA of museum samples and freshly-collected blood tissue of a pair of Sundaic songbird species, the pin-striped and bold-striped tit-babblers (Mixornis gularis and M. bornensis, respectively), to assess the genetic affinity of populations on small Sundaic islands that have largely been ignored by modern research. Our genomic and morphological results place the populations from the Anambas and Natuna Islands firmly within M. gularis from the Malay Peninsula in western Sundaland, even though some of these islands are geographically much closer to Borneo, where M. bornensis resides. Our results reveal genetic structure consistent with the course of Sundaic paleo-rivers and the location of the interfluvia they formed, and add to a small but growing body of evidence that rivers would have been of equal biogeographic importance in Sundaland's former connected forest landscape as they are in Amazonia and the Congo Basin today.

When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae).

Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace's Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.

The Innovation Arena: A Method for Comparing Innovative Problem-Solving Across Groups.

Problem-solving tasks are commonly used to investigate technical, innovative behavior but a comparison of this ability across a broad range of species is a challenging undertaking. Specific predispositions, such as the morphological toolkit of a species or exploration techniques, can substantially influence performance in such tasks, which makes direct comparisons difficult. The method presented here was developed to be more robust with regard to such species-specific differences: the Innovation Arena presents 20 different problem-solving tasks. All tasks are presented simultaneously. Subjects are confronted with the apparatus repeatedly, which allows a measurement of the emergence of innovations over time - an important next step for investigating how animals can adapt to changing environmental conditions through innovative behavior. Each individual was tested with the apparatus until it ceased to discover solutions. After testing was concluded, we analyzed the video recordings and coded successful retrieval of rewards and multiple apparatus-directed behaviors. The latter were analyzed using a Principal Component Analysis and the resulting components were then included in a Generalized Linear Mixed Model together with session number and the group comparison of interest to predict the probability of success. We used this approach in a first study to target the question of whether long-term captivity influences the problem-solving ability of a parrot species known for its innovative behavior: the Goffin´s cockatoo. We found an effect in degree of motivation but no difference in the problem-solving ability between short- and long-term captive groups.

Wild Goffin's cockatoos flexibly manufacture and use tool sets.

The use of different tools to achieve a single goal is considered unique to human and primate technology. To unravel the origins of such complex behaviors, it is crucial to investigate tool use that is not necessary for a species' survival. These cases can be assumed to have emerged innovatively and be applied flexibly, thus emphasizing creativity and intelligence. However, it is intrinsically challenging to record tool innovations in natural settings that do not occur species-wide. Here, we report the discovery of two distinct tool manufacture methods and the use of tool sets in wild Goffin's cockatoos (Cacatua goffiniana). Up to three types of wooden tools, differing in their physical properties and each serving a different function, were manufactured and employed to extract embedded seed matter of Cerbera manghas. While Goffin's cockatoos do not depend on tool-obtained resources, repeated observations of two temporarily captive wild birds and indications from free-ranging individuals suggest this behavior occurs in the wild, albeit not species-wide. The use of a tool set in a non-primate implies convergent evolution of advanced tool use. Furthermore, these observations demonstrate how a species without hands can achieve dexterity in a high-precision task. The presence of flexible use and manufacture of tool sets in animals distantly related to humans significantly diversifies the phylogenetic landscape of technology and opens multiple avenues for future research. VIDEO ABSTRACT.

Genomic investigation of colour polymorphism and phylogeographic variation among populations of black-headed bulbul (Brachypodius atriceps) in insular southeast Asia.

Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black-headed bulbul (Brachypodius atriceps) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Here, we generated a high-quality reference genome of a yellow individual and resequenced genomes of multiple individuals of both yellow and grey morphs to study the genetic basis of coloration and population history of the species. Using PCA and STRUCTURE analysis, we found the Maratua Island population (which is exclusively grey) to be distinct from all other B. atriceps populations, having been isolated c. 1.9 million years ago (Ma). In contrast, Bawean grey individuals (a subset of yellow and grey individuals on that island) are embedded within an almost panmictic Sundaic clade of yellow birds. Using FST and dxy to compare variable genomic segments between Maratua and yellow individuals, we located peaks of divergence and identified candidate loci involved in the colour polymorphism. Tests of selection among coding-proteins in high FST regions, however, did not indicate selection on the candidate genes. Overall, we report on some loci that are potentially responsible for the grey/yellow polymorphism in a species that otherwise shows little genetic diversification across most of its range.

Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild.

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.

Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity.

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.

High microphone signal-to-noise ratio enhances acoustic sampling of wildlife.

BACKGROUND: Automated sound recorders are a popular sampling tool in ecology. However, the microphones themselves received little attention so far, and specifications that determine the recordings' sound quality are seldom mentioned. Here, we demonstrate the importance of microphone signal-to-noise ratio for sampling sonant animals. METHODS: We tested 12 different microphone models in the field and measured their signal-to-noise ratios and detection ranges. We also measured the vocalisation activity of birds and bats that they recorded, the bird species richness, the bat call types richness, as well as the performance of automated detection of bird and bat calls. We tested the relationship of each one of these measures with signal-to-noise ratio in statistical models. RESULTS: Microphone signal-to-noise ratio positively affects the sound detection space areas, which increased by a factor of 1.7 for audible sound, and 10 for ultrasound, from the lowest to the highest signal-to-noise ratio microphone. Consequently, the sampled vocalisation activity increased by a factor of 1.6 for birds, and 9.7 for bats. Correspondingly, the species pool of birds and bats could not be completely detected by the microphones with lower signal-to-noise ratio. The performance of automated detection of bird and bat calls, as measured by its precision and recall, increased significantly with microphone signal-to-noise ratio. DISCUSSION: Microphone signal-to-noise ratio is a crucial characteristic of a sound recording system, positively affecting the acoustic sampling performance of birds and bats. It should be maximised by choosing appropriate microphones, and be quantified independently, especially in the ultrasound range.

The conservation value of admixed phenotypes in a critically endangered species complex.

In today's environmental crisis, conservationists are increasingly confronted with terminally endangered species whose last few surviving populations may be affected by allelic introgression from closely related species. Yet there is a worrying lack of evidence-based recommendations and solutions for this emerging problem. We analyzed genome-wide DNA markers and plumage variability in a critically endangered insular songbird, the Black-winged Myna (BWM, Acridotheres melanopterus). This species is highly threatened by the illegal wildlife trade, with its wild population numbering in the low hundreds, and its continued survival urgently depending on ex-situ breeding. Its three subspecies occur along a geographic gradient of melanism and are variably interpreted as three species. However, our integrative approach revealed that melanism poorly reflects the pattern of limited genomic differentiation across BWM subspecies. We also uncovered allelic introgression into the most melanistic subspecies, tertius, from the all-black congeneric Javan Myna (A. javanicus), which is native to the same islands. Based on our results, we recommend the establishment of three separate breeding programs to maintain subspecific traits that may confer local adaptation, but with the option of occasional cross-breeding between insurance populations in order to boost genetic diversity and increase overall viability prospects of each breeding program. Our results underscore the importance of evidence-based integrative approaches when determining appropriate conservation units. Given the rapid increase of terminally endangered organisms in need of ex-situ conservation, this study provides an important blueprint for similar programs dealing with phenotypically variable species.

Using an Innovation Arena to compare wild-caught and laboratory Goffin's cockatoos.

The ability to innovate, i.e., to exhibit new or modified learned behaviours, can facilitate adaptation to environmental changes or exploiting novel resources. We hereby introduce a comparative approach for studying innovation rate, the 'Innovation Arena' (IA), featuring the simultaneous presentation of 20 interchangeable tasks, which subjects encounter repeatedly. The new design allows for the experimental study of innovation per time unit and for uncovering group-specific problem-solving abilities - an important feature for comparing animals with different predispositions and life histories. We applied the IA for the first time to investigate how long-term captivity affects innovative capacities in the Goffin's cockatoo, an avian model species for animal innovation. We found that fewer temporarily-captive wild birds are inclined to consistently interact with the apparatus in comparison to laboratory-raised birds. However, those that are interested solve a similar number of tasks at a similar rate, indicating no difference in the cognitive ability to solve technical problems. Our findings thus provide a contrast to previous literature, which suggested enhanced cognitive abilities and technical problem-solving skills in long-term captive animals. We discuss the impact and discrepancy between motivation and cognitive ability on innovation rate. Our findings contribute to the debate on how captivity affects innovation in animals.

A lost world in Wallacea: Description of a montane archipelagic avifauna.

Birds are the best-known animal class, with only about five or six new species descriptions per year since 1999. Integrating genomic and phenotypic research with arduous fieldwork in remote regions, we describe five new songbird species and five new subspecies from a small area near Sulawesi, Indonesia, all collected in a single 6-week expedition. Two factors contributed to the description of this large number of species from such a small geographic area: (i) Knowledge of Quaternary Period land connections helped pinpoint isolated islands likely to harbor substantial endemism and (ii) studying accounts of historic collectors such as Alfred Wallace facilitated the identification of undercollected islands. Our findings suggest that humans' understanding of biogeographically complex regions such as Wallacea remains incomplete.

A striking new species of leaf warbler from the Lesser Sundas as uncovered through morphology and genomics.

Leaf warblers (Aves; Phylloscopidae) are a diverse clade of insectivorous, canopy-dwelling songbirds widespread across the Old World. The taxonomy of Australasian leaf warblers is particularly complex, with multiple species-level divergences between island taxa in the region requiring further scrutiny. We use a combination of morphology, bioacoustics, and analysis of thousands of genome-wide markers to investigate and describe a new species of Phylloscopus leaf warbler from the island of Rote in the Lesser Sundas, Indonesia. We show that this new Rote Leaf Warbler is morphologically and genomically highly distinct from its congenerics, but do not find vocal differentiation between different island taxa. We discuss the behaviour and ecology of this highly distinctive new species, and make recommendations about its conservation status. We believe this constitutes the first description of a novel bird species that is partly based on insights from massive amounts of genome-wide DNA markers.

Birds of primary and secondary forest and shrub habitats in the peat swamp of Berbak National Park, Sumatra.

Background: Tropical lowland rainforests are threatened by deforestation and degradation worldwide. Relatively little research has investigated the degradation of the forests of South-east Asia and its impact on biodiversity, and even less research has focused on the important peat swamp forests of Indonesia, which experienced major losses through severe fires in 2015. Methods: We acoustically sampled the avifauna of the Berbak National Park in 2013 in 12 sites split in three habitats: primary swamp forest, secondary swamp forest, and shrub swamp, respectively representing non-degraded, previously selectively logged, and burned habitats. We analysed the species richness, abundance, vocalisation activity, and community composition across acoustic counts, sites, feeding guilds and IUCN Red List categories. We also analysed community-weighted means of body mass, wing length, and distribution area. Results: The avifauna in the three habitats was remarkably similar in richness, abundance and vocalisation activity, and communities mainly differed due to a lower prevalence of understory insectivores (Old-World Babblers, Timaliidae) in shrub swamp. However primary forest retained twice as many conservation-worthy species as shrub swamp, which harboured heavier, probably more mobile species, with larger distributions than those of forest habitats. Conclusions: The National Park overall harboured higher bird abundances than nearby lowland rainforests. Protecting the remaining peat swamp forest in this little-known National Park should be a high conservation priority in the light of the current threats coming from wildlife trade, illegal logging, land use conversion, and man-made fires.

Pleistocene land bridges act as semipermeable agents of avian gene flow in Wallacea.

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.

Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation.

The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment,and we argue againstproliferation of taxonomic names,and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.

The effects of Pleistocene climate change on biotic differentiation in a montane songbird clade from Wallacea.

The role of Pleistocene Ice Age in tropical diversification is poorly understood, especially in archipelagos, in which glaciation-induced sea level fluctuations may lead to complicated changes in land distribution. To assess how Pleistocene land bridges may have facilitated gene flow in tropical archipelagos, we investigated patterns of diversification in the rarely-collected rusty-bellied fantail Rhipidura teysmanni (Passeriformes: Rhipiduridae) complex from Wallacea using a combination of bioacoustic traits and whole-genome sequencing methods (dd-RADSeq). We report a biogeographic leapfrog pattern in the vocalizations of these birds, and uncover deep genomic divergence among island populations despite the presence of intermittent land connections between some. We demonstrate how rare instances of genetic introgression have affected the evolution of this species complex, and document the presence of double introgressive mitochondrial sweeps, highlighting the dangers of using only mitochondrial DNA in evolutionary research. By applying different tree inference approaches, we demonstrate how concatenation methods can give inaccurate results when investigating divergence in closely-related taxa. Our study highlights high levels of cryptic avian diversity in poorly-explored Wallacea, elucidates complex patterns of Pleistocene climate-mediated diversification in an elusive montane songbird, and suggests that Pleistocene land bridges may have accounted for limited connectivity among montane Wallacean biota.

Evolutionary and ecological forces influencing population diversification in Bornean montane passerines.

The mountains of Borneo are well known for their high endemicity and historical role in preserving Southeast Asian rainforest biodiversity, but the diversification of populations inhabiting these mountains is poorly studied. Here we examine the genetic structure of 12 Bornean montane passerines by comparing complete mtDNA ND2 gene sequences of populations spanning the island. Maximum likelihood and Bayesian phylogenetic trees and haplotype networks are examined for common patterns that might signal important historical events or boundaries to dispersal. Morphological and ecological characteristics of each species are also examined using phylogenetic generalized least-squares (PGLS) for correlation with population structure. Populations in only four of the 12 species are subdivided into distinct clades or haplotype groups. Although this subdivision occurred at about the same time in each species (ca. 0.6-0.7Ma), the spatial positioning of the genetic break differs among the species. In two species, northeastern populations are genetically divergent from populations elsewhere on the island. In the other two species, populations in the main Bornean mountain chain, including the northeast, are distinct from those on two isolated peaks in northwestern Borneo. We suggest different historical forces played a role in shaping these two distributions, despite commonality in timing. PGLS analysis showed that only a single characteristic-hand-wing index-is correlated with population structure. Birds with longer wings, and hence potentially more dispersal power, have less population structure. To understand historical forces influencing montane population structure on Borneo, future studies must compare populations across the entirety of Sundaland.

Measuring the impact of the pet trade on Indonesian birds.

The trade in wild animals involves one-third of the world's bird species and thousands of other vertebrate species. Although a few species are imperiled as a result of the wildlife trade, the lack of field studies makes it difficult to gauge how serious a threat it is to biodiversity. We used data on changes in bird abundances across space and time and information from trapper interviews to evaluate the effects of trapping wild birds for the pet trade in Sumatra, Indonesia. To analyze changes in bird abundance over time, we used data gathered over 14 years of repeated bird surveys in a 900-ha forest in southern Sumatra. In northern Sumatra, we surveyed birds along a gradient of trapping accessibility, from the edge of roads to 5 km into the forest interior. We interviewed 49 bird trappers in northern Sumatra to learn which species they targeted and how far they went into the forest to trap. We used prices from Sumatran bird markets as a proxy for demand and, therefore, trapping pressure. Market price was a significant predictor of species declines over time in southern Sumatra (e.g., given a market price increase of approximately $50, the log change in abundance per year decreased by 0.06 on average). This result indicates a link between the market-based pet trade and community-wide species declines. In northern Sumatra, price and change in abundance were not related to remoteness (distance from the nearest road). However, based on our field surveys, high-value species were rare or absent across this region. The median maximum distance trappers went into the forest each day was 5.0 km. This suggests that trapping has depleted bird populations across our remoteness gradient. We found that less than half of Sumatra's remaining forests are >5 km from a major road. Our results suggest that trapping for the pet trade threatens birds in Sumatra. Given the popularity of pet birds across Southeast Asia, additional studies are urgently needed to determine the extent and magnitude of the threat posed by the pet trade.

Functional traits determine heterospecific use of risk-related social information in forest birds of tropical South-East Asia.

In birds and mammals, mobbing calls constitute an important form of social information that can attract numerous sympatric species to localized mobbing aggregations. While such a response is thought to reduce the future predation risk for responding species, there is surprisingly little empirical evidence to support this hypothesis. One way to test the link between predation risk reduction and mobbing attraction involves testing the relationship between species' attraction to mobbing calls and the functional traits that define their vulnerability to predation risk. Two important traits known to influence prey vulnerability include relative prey-to-predator body size ratio and the overlap in space use between predator and prey; in combination, these measures strongly influence prey accessibility, and therefore their vulnerability, to predators. Here, we combine community surveys with behavioral experiments of a diverse bird assemblage in the lowland rainforest of Sumatra to test whether the functional traits of body mass (representing body size) and foraging height (representing space use) can predict species' attraction to heterospecific mobbing calls. At four forest sites along a gradient of forest degradation, we characterized the resident bird communities using point count and mist-netting surveys, and determined the species groups attracted to standardized playbacks of mobbing calls produced by five resident bird species of roughly similar body size and foraging height. We found that (1) a large, diverse subcommunity of bird species was attracted to the mobbing calls and (2) responding species (especially the most vigorous respondents) tended to be (a) small (b) mid-storey foragers (c) with similar trait values as the species producing the mobbing calls. Our findings from the relatively lesser known bird assemblages of tropical Asia add to the growing evidence for the ubiquity of heterospecific information networks in animal communities, and provide empirical support for the long-standing hypothesis that predation risk reduction is a major benefit of mobbing information networks.

A new species of Muscicapa flycatcher from Sulawesi, Indonesia.

The Indonesian island of Sulawesi, a globally important hotspot of avian endemism, has been relatively poorly studied ornithologically, to the extent that several new bird species from the region have been described to science only recently, and others have been observed and photographed, but never before collected or named to science. One of these is a new species of Muscicapa flycatcher that has been observed on several occasions since 1997. We collected two specimens in Central Sulawesi in 2012, and based on a combination of morphological, vocal and genetic characters, we describe the new species herein, more than 15 years after the first observations. The new species is superficially similar to the highly migratory, boreal-breeding Gray-streaked Flycatcher Muscicapa griseisticta, which winters in Sulawesi; however, the new species differs strongly from M. griseisticta in several morphological characters, song, and mtDNA. Based on mtDNA, the new species is only distantly related to M. griseisticta, instead being a member of the M. dauurica clade. The new species is evidently widely distributed in lowland and submontane forest throughout Sulawesi. This wide distribution coupled with the species' apparent tolerance of disturbed habitats suggests it is not currently threatened with extinction.