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.

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.

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.

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.

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 () 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.

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 is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular.

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.

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).

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.

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.

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.

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

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. We acoustically sampled the avifauna of the Berbak National Park in 2013 in 12 plots split in three habitats: primary swamp forest, secondary swamp forest, and shrub swamp, respectively representing non-degraded, previously selectively logged, and burned habitats.

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.

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.

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.

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.

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.

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.

Averting biodiversity collapse in tropical forest protected areas.

The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon. With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses.

Deforestation and avian extinction on tropical landbridge islands.

There are few empirical data, particularly collected simultaneously from multiple sites, on extinctions resulting from human-driven land-use change. Southeast Asia has the highest deforestation rate in the world, but the resulting losses of biological diversity remain poorly documented. Between November 2006 and March 2008, we conducted bird surveys on six landbridge islands in Malaysia and Indonesia.

Improved COI barcoding primers for Southeast Asian perching birds (Aves: Passeriformes).

The All Birds Barcoding Initiative aims to assemble a DNA barcode database for all bird species, but the 648-bp 'barcoding' region of cytochrome c oxidase subunit I (COI) can be difficult to amplify in Southeast Asian perching birds (Aves: Passeriformes). Using COI sequences from complete mitochondrial genomes, we designed a primer pair that more reliably amplifies and sequences the COI barcoding region of Southeast Asian passerine birds. The 655-bp region amplified with these primers overlaps the COI region amplified with other barcoding primer pairs, enabling direct comparison of sequences with previously published DNA barcodes.

The importance of protected areas for the forest and endemic avifauna of Sulawesi (Indonesia).

Protected areas are critical for the conservation of residual tropical forest biodiversity, yet many of these are being deforested by humans both within and outside of their administrative boundaries. Therefore, it is critical to document the significance of protected areas for conserving tropical biodiversity, particularly in mega-diverse Southeast Asia. We evaluated the importance of protected areas (national parks [NP], nature reserves [NR], and wildlife reserves [WR]) in preserving avifaunal diversity, particularly the endemic and forest species, on the island of Sulawesi.

Long-term avifaunal impoverishment in an isolated tropical woodlot.

Long-term (> 50 years) extinction patterns and processes in isolated tropical forest patches are poorly understood. Considering that forest fragments are rapidly becoming the common feature of most tropical landscapes, data on the long-term conservation value of such fragments are urgently needed. We report on avifaunal turnover in a tropical woodlot (Bogor Botanical Gardens; 86 ha; 54% native and 46% introduced plants; mean 83,649 visitors/month) that has been surveyed several times before and after its isolation in 1936.