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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. We focused on the genomic sequences of 43 birds from five populations to show that the Taiwan group split from its sister group in mainland China around 1–2 million years ago (Ma) and colonized the montane habitats of Taiwan at least twice around 0.03–0.22 Ma. The montane and lowland Taiwan populations diverged with gene flow between them, suggesting strong selection associated with different elevations. We found that the montane babblers had smaller beaks than the lowland ones, consistent with Allen's rule, and identified candidate genes—COL9A1 and SOX11—underlying the beak size changes. We also found that altitudinally divergent mutations were mostly located in noncoding regions and tended to accumulate in chromosomal inversions and autosomes. The altitudinally divergent mutations might regulate genes related to haematopoietic, metabolic, immune, auditory and vision functions, as well as cerebrum morphology and plumage development. The results reveal the genomic bases of morphological and physiological adaptation in this species to the low temperature, hypoxia and high UV light environment at high elevation. These findings improve our understanding of how ecological adaptation drives population divergence from the perspective of genomic architecture. [ABSTRACT FROM AUTHOR]

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. Here we assembled the genomes of a recently domesticated species—the society finch—and its parent species—the white‐rumped munia—to examine its domestication history. We applied genomic analyses to two society finch breeds and white‐rumped munias to test whether domestication of the former resulted from inbreeding or hybridization. The society finch showed longer and more runs of homozygosity and lower genomic heterozygosity than the white‐rumped munia, supporting an inbreeding origin in the former. Blocks of white‐rumped munia and other ancestry in society finch genomes showed similar genetic distance between the two taxa, inconsistent with the hybridization origin hypothesis. We then applied two Sequentially Markov Coalescent models—psmc and smc++—to infer the demographic histories of both. Surprisingly, the two models did not reveal a recent population bottleneck, but instead the psmc model showed a specious, dramatic population increase in the society finch. Subsequently, we used simulated genomes based on an array of demographic scenarios to demonstrate that recent inbreeding, not hybridization, caused the distorted psmc population trajectory. Such analyses could have misled our understanding of the domestication process. Our findings stress caution when interpreting the histories of recently domesticated species inferred by psmc, arguing that these histories require multiple analyses to validate. [ABSTRACT FROM AUTHOR]

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. Since oxytocin (OT) has been found to be involved in stress coping and auditory processing, we tested whether the OT sequence and brain expression pattern and content differ in wild munias and domesticated Bengalese finches. We sequenced the OT from 10 wild munias and 11 Bengalese finches and identified intra‐strain variability in both the untranslated and protein‐coding regions of the sequence, with all the latter giving rise to synonymous mutations. Several of these changes fall in specific transcription factor‐binding sites, and show either a conserved or a relaxed evolutionary trend in the avian lineage, and in vertebrates in general. Although in situ hybridization in several hypothalamic nuclei did not reveal significant differences in the number of cells expressing OT between the two strains, real‐time quantitative PCR showed a significantly higher OT mRNA expression in the cerebrum of the Bengalese finches relative to munias, but a significantly lower expression in their diencephalon. Our study thus points to a brain region‐specific pattern of neurochemical expression in domesticated and wild avian strains, which could be linked to domestication and the behavioral changes associated with it. [ABSTRACT FROM AUTHOR]

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, Ne, had been relatively stable (7500–9000) since 22,000 years ago; however, a recent brief yet severe bottleneck (Ne = 20) which we here estimated to occur around the 1940s wiped out >99% of its historical Ne in roughly three generations. Despite a >15‐fold population recovery since 1988, we found that black‐faced spoonbill population has higher levels of inbreeding (7.4 times more runs of homozygosity) than its sister species, the royal spoonbill (P. regia), which is not thought to have undergone a marked population contraction. Although the two spoonbills have similar levels of genome‐wide genetic diversity, our results suggest that selection on more genes was relaxed in the black‐faced spoonbill; moreover individual black‐faced spoonbills carry more putatively deleterious mutations (Grantham's score > 50), and may therefore express more deleterious phenotypic effects than royal spoonbills. Here we demonstrate the value of using genomic indices to monitor levels of genetic erosion, inbreeding and mutation load in species with conservation concerns. To mitigate the prolonged negative genetic effect of a population bottleneck, we recommend that all possible measures should be employed to maintain population growth of a threatened species. [ABSTRACT FROM AUTHOR]

Environment plays an important role in the evolution of plumage coloration in birds and may also lead to sexual dichromatism if males and females face different selection pressures. Mountains exhibit varying ecological conditions along their elevation gradient that may impose divergent selection on elevationally widespread species, causing intraspecific plumage divergence. For example, UV light environments often vary between montane and lowland habitats, which could potentially cause differences in plumage UV reflection between birds occurring in the two types of habitats. However, few studies have examined the effects of elevation on plumage evolution. In this study, we quantified the plumage coloration of the Rufous‐capped Babbler Cyanoderma ruficeps from montane and lowland habitats on a mountainous island, Taiwan. We aimed to examine whether their plumage showed differences associated with changing ecological environments across the elevational gradient. The results supported that the plumage of babblers occupying montane habitats had higher UV‐reflectance and brightness than that of lowland birds, corresponding to the higher UV intensity in montane than lowland background light environments. The elevational differences were mainly found across the ventral parts of babblers that had relatively higher levels of UV reflectance compared with their dorsal parts. Alternatively, the brighter plumage, with higher UV‐reflectance in montane than lowland birds, might be mediated by physiological adaptation to other ecological factors, such as parasite pressures. The elevational differences in plumage UV‐reflectance and brightness were more dramatic in males than in females. However, we found significant sexual dichromatism in different body parts between montane and lowland babblers in which females had brighter or stronger UV‐associated coloration than males, suggesting that sexual selection has little impact on babbler plumage. Our study suggests the importance of elevational divergent selection associated with UV light or other ecological environments on avian plumage evolution. [ABSTRACT FROM AUTHOR]

Abstract Background The subtropical island of Taiwan is an area of high endemism and a complex topographic environment. Phylogeographic studies indicate that vicariance caused by Taiwan's mountains has subdivided many taxa into genetic phylogroups. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the evolutionary history of an endemic montane bird, Steere's Liocichla (Liocichla steerii), fit the general vicariant paradigm for a montane organism. Results We found that while mountains appear to channel gene flow they are not a significant barrier for Steere's Liocichla. Recent demographic expansion was evident, and genetic diversity was relatively high across the island, suggesting expansion from multiple areas rather than a few isolated refugia. Ecological niche modeling corroborated the molecular results and suggested that populations of Steere's Liocichla are connected by climatically suitable habitat and that there was less suitable habitat during the Last Glacial Maximum. Conclusions Genetic and ecological niche modeling data corroborate a single history--Steere's Liocichla was at lower density during the Last Glacial Maximum and has subsequently expanded in population density. We suggest that such a range-wide density expansion might be an overlooked cause for the genetic patterns of demographic expansion that are regularly reported. We find significant differences among some populations in FST indices and an admixture analysis. Though both of these results are often used to suggest conservation action, we affirm that statistically significant results are not necessarily biologically meaningful and we urge caution when interpreting highly polymorphic data such as microsatellites.

Abstract Background Combination of CHD (chromo-helicase-DNA binding protein)-specific polymerase chain reaction (PCR) with electrophoresis (PCR/electrophoresis) is the most common avian molecular sexing technique but it is lab-intensive and gel-required. Gender determination often fails when the difference in length between the PCR products of CHD-Z and CHD-W genes is too short to be resolved. Results Here, we are the first to introduce a PCR-melting curve analysis (PCR/MCA) to identify the gender of birds by genomic DNA, which is gel-free, quick, and inexpensive. Spilornis cheela hoya (S. c. hoya) and Pycnonotus sinensis (P. sinensis) were used to illustrate this novel molecular sexing technique. The difference in the length of CHD genes in S. c. hoya and P. sinensis is 13-, and 52-bp, respectively. Using Griffiths' P2/P8 primers, molecular sexing failed both in PCR/electrophoresis of S. c. hoya and in PCR/MCA of S. c. hoya and P. sinensis. In contrast, we redesigned sex-specific primers to yield 185- and 112-bp PCR products for the CHD-Z and CHD-W genes of S. c. hoya, respectively, using PCR/MCA. Using this specific primer set, at least 13 samples of S. c. hoya were examined simultaneously and the Tm peaks of CHD-Z and CHD-W PCR products were distinguished. Conclusion In this study, we introduced a high-throughput avian molecular sexing technique and successfully applied it to two species. This new method holds a great potential for use in high throughput sexing of other avian species, as well.

Aim: Pleistocene climate and associated environmental changes have influenced phylogeographic patterns of many species. These not only depend on a species' life history but also vary regionally. Consequently, populations of widespread species that occur in several biomes might display different evolutionary trajectories. We aimed to identify regional drivers of diversification in the common pheasant, a widely distributed ecological generalist. Location: Asia. Taxon: Common pheasant Phasianus colchicus. Methods: Using a comprehensive geographical sampling of 204 individuals from the species' entire range genotyped at seven nuclear and two mitochondrial loci, we reconstructed spatio‐temporal diversification and demographic history of the common pheasant. We applied Bayesian phylogenetic inference to describe phylogeographic structure, generated a species tree and inferred demographic history within and migration between lineages. Moreover, to establish a taxonomic framework, we conducted a species delimitation analysis. Results: The common pheasant diversified during the Late Pleistocene into eight distinct lineages. It originated at the edge of the Qinghai–Tibetan plateau and spread to East and Central Asia. Only the widely distributed lowland lineage of East Asia displayed recent range expansion. Greater phylogeographic structure was identified elsewhere, with lineages showing no sign of recent demographic changes. One lineage in south‐central China is the result of long‐term isolation within a climatically stable but topographically complex region. In lineages from arid Central Asia and China, range expansions were impeded by repeated population fragmentation during dry glacial periods and by recent aridification. Main conclusions: Spatio‐temporal phylogeographic frameworks of widespread taxa such as the common pheasant provide valuable opportunities to identify divergent drivers of regional diversification. Our results suggest that diversification and population histories in the eight distinct evolutionary lineages were shaped by regionally variable effects of past climate and associated environmental changes. The evolutionary history of the common pheasant is best reflected by its being split into three species. [ABSTRACT FROM AUTHOR]

We re‐evaluated the taxonomy of the Striated Prinia Prinia crinigera–Brown Prinia P. polychroa complex using molecular, morphological and vocal analyses. The extensive seasonal, sexual, age‐related, geographical and taxon‐specific variation in this complex has never before been adequately studied. As no previous genetic or vocal analyses have focused on this group, misinterpretation of taxonomic signals from limited conventional morphological study alone was likely. Using mitochondrial and nuclear DNA, we found that P. crinigera sensu lato (s.l.) comprises two non‐sister groups of taxa (Himalayan crinigera and Chinese striata groups) that differ substantially morphologically and vocally and that are broadly sympatric in Yunnan Province, China. Prinia polychroa cooki (Myanmar) and P. p. rocki (southern Vietnam) are each morphologically, vocally and genetically distinct. Thai, Cambodian and Laotian populations formerly ascribed to P. p. cooki are morphologically and vocally most similar to and most closely related to Javan P. p. polychroa, and require a new name, proposed here. Prinia p. bangsi of Yunnan is part of the crinigera group rather than of P. polychroa, and hence there is no evidence for sympatry between P. polychroa s.l. and P. crinigera s.l., nor of the occurrence of P. polychroa in mainland China or Taiwan. We recommend the recognition of five species in the complex, with the following suggestions for new English names: Himalayan Prinia P. crinigera sensu stricto (s.s.; with subspecies striatula, crinigera, yunnanensis and bangsi); Chinese Prinia P. striata (subspecies catharia, parumstriata and striata); Burmese Prinia P. cooki (monotypic); Annam Prinia P. rocki (monotypic) and Deignan's Prinia P. polychroa s.s. (subspecies Javan polychroa and the new Southeast Asian taxon). This study underlines the importance of using multiple datasets for the elucidation of diversity of cryptic bird species and their evolutionary history and biogeography. [ABSTRACT FROM AUTHOR]

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. Phylogenetic reconstruction and ecological niche models (ENMs) showed that the Eurasian nuthatch contained six parapatric lineages that diverged within 2 Myr and did not share identical climatic niches. However, the niche discrepancy between these distinct lineages was relatively conserved compared with the environmental differences between their ranges and thus was unlikely to drive lineage divergence. The ENMs of southern lineages tended to cross‐predict with their neighbouring lineages whereas those of northern lineages generally matched with their abutting ranges. The coalescence‐based analyses revealed more stable populations for the southern lineages than the northern ones during the last glaciation cycle. In contrast to the overlapping ENMs, the smaller parapatric distribution suggests that the southern lineages might have experienced competitive exclusion to prevent them from becoming sympatric. On the other hand, the northern lineages have expanded their ranges and their current abutting distribution might have resulted from lineages adapting to different climatic conditions in allopatry. This study suggests that niche evolution may affect lineage distribution in different ways across latitude. [ABSTRACT FROM AUTHOR]

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 Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella 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. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo-/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials-contrary to the usual view that glacial periods resulted mainly in fragmentations. [ABSTRACT FROM AUTHOR]

Although tropical and subtropical Asia harbour a high level of species diversity, their species richness can be underestimated because species which are in fact distinct have not been separately identified. In this study, we delimit Bambusicola thoracica into two full species, the Chinese bamboo partridge ( B. thoracica) in continental Asia and the Taiwanese bamboo partridge ( B. sonorivox) on the island of Taiwan, using coalescent-based multilocus division and diagnosable vocalization patterns. Isolation-with-migration analysis indicated that the two bamboo partridges diverged approximately 1.8 million years ago, with gene flow present most probably during the early stages of their divergence. This conclusion supports the hypothesis that diverging lowland lineages spread across the Asian mainland, and continental islands have more opportunities for secondary contact than highland ones when the sea level was low. Our results imply that conservation of biodiversity in tropical and subtropical Asia could be hindered by overlooking numerous 'hidden' species and highlight the importance of re-examining the taxonomic statuses of species in this region traditionally defined as polytypic. [ABSTRACT FROM AUTHOR]

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. In this study, we applied both a character-based and a coalescent-based approaches to delimit species in a closely related avian complex, the light-vented/Taiwan bulbul ( Pycnonotus sinensis/ Pycnonotus taivanus). Population aggregation analyses of plumage, mitochondrial and 13 nuclear intron character data sets produced conflicting species hypotheses with plumage data suggesting three species, mitochondrial data suggesting two species, and nuclear intron data suggesting one species. Such conflict is expected among recently diverged species, and by integrating all sources of data, we delimited three species verified with independently congruent character evidence as well as a more weakly supported fourth species identified by a single character. Attempts to validate species hypothesis using Bayesian Phylogenetics and Phylogeography ( BPP), a coalescent-based method of species delimitation, revealed several issues that can seemingly affect statistical support for species recognition. We found that θ priors had a dramatic impact on speciation probabilities, with lower values consistently favouring splitting and higher values consistently favouring lumping. More resolved guide trees also resulted in overall higher speciation probabilities. Finally, we found suggestive evidence that BPP is sensitive to the divergent effects of nonrandom mating caused by intraspecific processes such as isolation-with-distance, and therefore, BPP may not be a conservative method for delimiting independently evolving population lineages. Based on these concerns, we questioned the reliability of BPP results and based our conclusions about species limits exclusively on character data. [ABSTRACT FROM AUTHOR]

A total of 594 ticks were collected from the environment, dogs, cattle, goats, small mammals, birds, a turtle, a snake, a bat and a human. Morphological identification of 509 ticks resulted in the listing of the following species: Rhipicephalus sanguineus, Rhipicephalus haemaphysaloides, Rhipicephalus microplus, Haemaphysalis warburtoni, Haemaphysalis phasiana, Haemaphysalis campanulata, Ixodes acutitarsus and Amblyomma geoemydae. [ABSTRACT FROM AUTHOR]

Wu, H.-C., Lin, R.-C., Hung, H.-Y., Yeh, C.-F., Chu, J.-H., Yang, X.-J., Yao, C.-J., Zou, F.-S., Yao, C.-T., Li, S.-H. & Lei, F.-M. (2011). Molecular and morphological evidences reveal a cryptic species in the Vinaceous Rosefinch Carpodacus vinaceus (Fringillidae; Aves). - Zoologica Scripta, 40, 468-478. The Vinaceous Rosefinch ( Carpodacus vinaceus) is endemic in East Asia with two recognized subspecies - C. v. vinaceus, distributed along the eastern edge of the Tibetan Plateau and the Himalayas, and C. v. formosanus, restricted to Taiwan's Central Mountain Range. As reflected in a controversial taxonomic history, this vastly disjunctive distribution pattern suggests that the subspecies, having been isolated from each other for a long time, might have diverged, challenging the current taxonomic treatment and calling for possible species delimitation. Sequences of two mitochondrial fragments (mtDNA) and two Z-linked nuclear loci (zDNA) were used to reconstruct the intraspecific phylogeny of C. vinaceous. The mtDNA tree shows that the two subspecies of the vinaceous rosefinch form two exclusively monophyletic clades. All but one zDNA sequences from the nominate subspecies and C. v. formosanus also formed exclusively monophyletic clades (the exceptional zDNA sequence from C. v. vinaceous formed a weakly supported clade with two outgroup species). Moreover, by conducting quantitative comparisons of morphometric traits and male plumage coloration, we found that the two subspecies exhibit distinguishable morphological differences. All the evidence therefore suggests that C. v. formosanus is a cryptic species and that its taxonomic status should be restored to full species. Molecular dating suggests that the two sibling rosefinches split 1.7 ± 0.2 million years ago, providing a point estimate for the historical connectivity of biota between eastern Tibet-Himalayas and montane Taiwan. [ABSTRACT FROM AUTHOR]

Several recent studies have found instances of cryptic sexual dichromatism within avian taxa. Although this dichromatism has been found in plumage produced through a variety of proximate mechanisms, little is known about how dichromatism varies across these types of plumage within a single species. We used a reflectance spectrometer to measure colour within the Green-backed Tit Parus monticolus, a species which displays multiple types of pigment and structural colours. We found significant differences in spectral measurements corresponding to hue, chroma, and brightness between male and female carotenoid, melanin, structural white, grey and structural blue plumage. The only plumage that did not appear to show sexual dichromatism was the olive plumage of the back. These findings suggest that the mechanism(s) producing cryptic dichromatism in the Green-backed Tit are non-specific and act across multiple types of plumage, rather than within a single type, such as carotenoid-based or structurally produced. [ABSTRACT FROM AUTHOR]

We isolated 20 anonymous nuclear loci (8556 bp in total) from the Taiwan Hwamei ( Garrulax taewanus), an endemic songbird of Taiwan. A panel of nine to 15 individuals with unknown relationship was used to characterize polymorphism of these loci. We identified 46 single nucleotide polymorphic sites (SNPs) in 15 polymorphic loci. Frequency of SNPs was one per every 186 bp in average. Nucleotide diversity, θ, ranged from 0.00054 to 0.00371 per locus. We also tested cross-species applicability of these loci on 17 species from eight different passerine families. All 20 loci could be successfully amplified (ranged from one to 16 species, mean = 7.9 species). [ABSTRACT FROM AUTHOR]

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 (Cyanoderma ruficeps 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. Nevertheless, assembly completeness showed little difference among the trimming strategies. One should determine the optimal trimming strategy based on what the assembled genome will be used for. For example, to identify single nucleotide polymorphisms (SNPs) associated with phenotypic evolution, applying PLATANUS to gently trim reads would yield a reference genome with a slightly shorter scaffold length (N50 = 15.64 vs. 16.89 Mb) than the raw reads, but would save 75% of computational time. We also found that chromosomes Z, W, and 4A of the rufous-capped babbler were poorly assembled, likely due to a recently fused, neo-sex chromosome. The rufous-capped babbler genome with long scaffolds and quality gene annotation can provide a good system to study avian ecological adaptation in East Asia. [ABSTRACT FROM AUTHOR]

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. We measured the reflectance (within both the human visual perceptive and the ultraviolet ranges) of two carotenoid-based parts and eight dull and melanin-based parts for each individual live bird or museum skin sampled. According to an avian model of colour discrimination thresholds, we found that males exhibited perceptibly redder beaks, brighter tarsi and darker plumage than did females. This suggests the existence of multiple cryptic sexually dichromatic traits within this species. Moreover, we also observed detectable colour fading in the museum skin specimens compared with the live birds, indicating that sexual dichromatism could be underestimated if analysed using skin specimens alone. [ABSTRACT FROM AUTHOR]