Convergent evolution of kidney sizes and supraorbital salt glands for birds living in saline habitats.

Only a small number of avian species inhabit salty environments. To understand how they adapted, we examined the evolution of kidney sizes, supraorbital salt glands (SSGs), and the utilization of salty habitats across 230 species spanning 25 avian orders. Phylogenetic analysis indicates that SSGs, large kidneys, and thriving in salty habitats emerged convergently in birds.

Weak gene-gene interaction facilitates the evolution of gene expression plasticity.

Background: Individual organisms may exhibit phenotypic plasticity when they acclimate to different conditions. Such plastic responses may facilitate or constrain the adaptation of their descendant populations to new environments, complicating their evolutionary trajectories beyond the genetic blueprint. Intriguingly, phenotypic plasticity itself can evolve in terms of its direction and magnitude during adaptation.

Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird.

Organisms often acquire physiological and morphological modifications to conquer ecological challenges when colonizing new environments which lead to their adaptive evolution. However, deciphering the genomic mechanism of ecological adaptation is difficult because ecological environments are often too complex for straightforward interpretation. Thus, we examined the adaptation of a widespread songbird-the rufous-capped babbler (Cyanoderma ruficeps)-to a relatively simple system: distinct environments across elevational gradients on the mountainous island of Taiwan.

Cryptic species in a colorful genus: Integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species.

Several cryptic avian species have been validated by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study, we investigated species limits in the genus Tarsiger, the bush robins, a group of montane forest specialists with high species richness in the Sino-Himalayan region. Based on comprehensive sampling of all 11 subspecies of the six currently recognized species, we applied an integrative taxonomic approach by combining multilocus, acoustic, plumage and morphometric analyses.

Oxytocin variation and brain region-specific gene expression in a domesticated avian species.

The Bengalese finch was domesticated more than 250 years ago from the wild white-rumped munia (WRM). Similar to other domesticated species, Bengalese finches show a reduced fear response and have lower corticosterone levels, compared to WRMs. Bengalese finches and munias also have different song types.

Domestication obscures genomic estimates of population history.

Domesticated species are valuable models to examine phenotypic evolution, and knowledge on domestication history is critical for understanding the trajectories of evolutionary changes. Sequentially Markov Coalescent models are often used to infer domestication history. However, domestication practices may obscure the signal left by population history, affecting demographic inference.

Not out of the woods yet: Signatures of the prolonged negative genetic consequences of a population bottleneck in a rapidly re-expanding wader, the black-faced spoonbill Platalea minor.

The long-term persistence of a population which has suffered a bottleneck partly depends on how historical demographic dynamics impacted its genetic diversity and the accumulation of deleterious mutations. Here we provide genomic evidence for the genetic effect of a recent population bottleneck in the endangered black-faced spoonbill (Platalea minor) after its rapid population recovery. Our data suggest that the bird's effective population size, N , had been relatively stable (7500-9000) since 22,000 years ago; however, a recent brief yet severe bottleneck (N  = 20) which we here estimated to occur around the 1940s wiped out >99% of its historical N in roughly three generations.

Egg recognition abilities of tit species in the Paridae family: do Indomalayan tits exhibit higher recognition than Palearctic tits?

Recent studies have shown that the closely related cinereous tit ( ) and green-backed tit ( ) in China display strong egg recognition ability in contrast to tit species in Europe, which lack such ability. However, egg recognition in other populations of cinereous and green-backed tits and additional Paridae species still requires further research. Here, we compared the egg recognition abilities of cinereous tits across China, green-backed tits ( ) in Taiwan, China, and five other species from the Paridae family, including the marsh tit ( ), varied tit ( ), willow tit ( ), coal tit ( ), and ground tit ( ).

Strict allopatric speciation of sky island Pyrrhula erythaca species complex.

Increasing evidence of post-divergence gene flow between taxa is shifting our understanding on the mode of speciation. A fundamental question arises concerning the circumstances under which strict allopatric speciation still holds true. Sky island populations might undergo reduced gene flow by niche conservatism to highland habitats and follow divergence in an allopatric manner.

The Making of a Flight Feather: Bio-architectural Principles and Adaptation.

The evolution of flight in feathered dinosaurs and early birds over millions of years required flight feathers whose architecture features hierarchical branches. While barb-based feather forms were investigated, feather shafts and vanes are understudied. Here, we take a multi-disciplinary approach to study their molecular control and bio-architectural organizations.

To Trim or Not to Trim: Effects of Read Trimming on the De Novo Genome Assembly of a Widespread East Asian Passerine, the Rufous-Capped Babbler ( Blyth).

Trimming low quality bases from sequencing reads is considered as routine procedure for genome assembly; however, we know little about its pros and cons. Here, we used empirical data to examine how read trimming affects assembled genome quality and computational time for a widespread East Asian passerine, the rufous-capped babbler ( Blyth). We found that scaffolds assembled from raw reads were always longer than those from trimmed ones, whereas computational times for the former were sometimes much longer than the latter.

Frequent detection of anticoagulant rodenticides in raptors sampled in Taiwan reflects government rodent control policy.

Anticoagulant rodenticides (ARs) are known to cause extensive secondary exposure in top predators in Europe and North America, but there remains a paucity of data in Asia. In this study, we collected 221 liver samples from 21 raptor species in Taiwan between 2010 and 2018. Most birds were recovered from rescue organizations, but some free-ranging individuals were obtained from bird-strike prevention measures at airports.

Population divergence and gene flow in two East Asian shorebirds on the verge of speciation.

Genetic isolation of populations over evolutionary time leads to the formation of independent species. We examined a pair of shorebirds - the Kentish Plover Charadrius alexandrinus and the enigmatic White-faced Plover C. dealbatus - which display strong plumage differentiation, yet show minimal genetic divergence based on previous mitochondrial and microsatellite work.

Standing genetic variation as the predominant source for adaptation of a songbird.

What kind of genetic variation contributes the most to adaptation is a fundamental question in evolutionary biology. By resequencing genomes of 80 individuals, we inferred the origin of genomic variants associated with a complex adaptive syndrome involving multiple quantitative traits, namely, adaptation between high and low altitudes, in the vinous-throated parrotbill () in Taiwan. By comparing these variants with those in the Asian mainland population, we revealed standing variation in 24 noncoding genomic regions to be the predominant genetic source of adaptation.

The niches of nuthatches affect their lineage evolution differently across latitude.

Ecological niche evolution can promote or hinder the differentiation of taxa and determine their distribution. Niche-mediated evolution may differ among climatic regimes, and thus, species that occur across a wide latitudinal range offer a chance to test these heterogeneous evolutionary processes. In this study, we examine (a) how many lineages have evolved across the continent-wide range of the Eurasian nuthatch (Sitta europaea), (b) whether the lineages' niches are significantly divergent or conserved and (c) how their niche evolution explains their geographic distribution.

From the Himalayas to a continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex.

As species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespread in the Sino-Himalayan region. We also examined the vocal and morphometric divergence within this complex.

Tick-borne pathogens in ticks collected from birds in Taiwan.

Background: A variety of human diseases transmitted by arthropod vectors, including ticks, are emerging around the globe. Birds are known to be hosts of ticks and can disperse exotic ticks and tick-borne pathogens. In Taiwan, previous studies have focused predominantly on mammals, leaving the role of birds in the maintenance of ticks and dissemination of tick-borne pathogens undetermined.

Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family.

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of was present in the Sino-Himalayan Mountains or these mountains and Central Asia-Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid-Pliocene to early Pleistocene.

Himalayan black bulbuls (Hypsipetes leucocephalus niggerimus) exhibit sexual dichromatism under ultraviolet light that is invisible to the human eye.

Sexual dichromatism is a key proxy for the intensity of sexual selection. Studies of dichromatism in birds may, however, have underestimated the intensity and complexity of sexual selection because they used museum specimens alone without taking colour-fading into account or only measured conspicuous visual traits in live animals. We investigated whether the Himalayan black bulbul (Hypsipetes leucocephalus nigerrimus), which is sexually monomorphic to the human eye, exhibits sexual dichromatism distinguishable by a spectrometer.

Incipient speciation with gene flow on a continental island: Species delimitation of the Hainan Hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves).

Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation.

Was the exposed continental shelf a long-distance colonization route in the ice age? The Southeast Asia origin of Hainan and Taiwan partridges.

Research on island biotas has greatly contributed to the development of modern evolutionary and biogeographic theories. Until now, most studies have suggested that continental islands received their biotas directly from the adjacent mainland. However, only a few studies have indicated that species on continental islands might originate from other distantly non-adjacent regions.

Incorporating color into integrative taxonomy: analysis of the varied tit (Sittiparus varius) complex in East Asia.

Species designations are critically important scientific hypotheses that serve as the foundational units in a wide range of biological subdisciplines. A growing realization that some classes of data fail to delimit species under certain conditions has led to increasingly more integrative taxonomies, whereby species discovery and hypothesis testing are based on multiple kinds of data (e.g.

An empirical comparison of character-based and coalescent-based approaches to species delimitation in a young avian complex.

The process of discovering species is a fundamental responsibility of systematics. Recently, there has been a growing interest in coalescent-based methods of species delimitation aimed at objectively identifying species early in the divergence process. However, few empirical studies have compared these new methods with character-based approaches for discovering species.

Inferring the geographic mode of speciation by contrasting autosomal and sex-linked genetic diversity.

When geographic isolation drives speciation, concurrent termination of gene flow among genomic regions will occur immediately after the formation of the barrier between diverging populations. Alternatively, if speciation is driven by ecologically divergent selection, gene flow of selectively neutral genomic regions may go on between diverging populations until the completion of reproductive isolation. It may also lead to an unsynchronized termination of gene flow between genomic regions with different roles in the speciation process.

High-throughput gender identification of three Columbidae species using melting curve analysis.

The objective was to perform high-throughput gender identification of three Columbidae species (Columba livia, Columba pulchricollis, and Streptopelia tranquebarica). Although the chromo-helicase-DNA binding protein (CHD)-based Griffiths P2/P8 primer set resolved the amplicon products of these species in 3% agarose gel electrophoresis, it was unsuitable for molecular gender identification using the melting curve analysis (MCA) curve for high-throughput analysis. After sequencing the CHD-Z and CHD-W genes for these species, we redesigned a female-specific CHD-W primer (dove-W) and a female/male (or CHD-Z/CHD-W)-common primer (dove-ZW) to combine with the Griffiths P2 primer to generate two PCR amplicons with different lengths (P2/dove-W and P2/dove-ZW for 252- and 104-bp, respectively).