Systematics of the avian family Alaudidae using multilocus and genomic data

The family Alaudidae,larks,comprises 93-100 species(depending on taxonomy)that are widely distributed across Africa and Eurasia,with single species extending their ranges to North and northernmost South America and Australia.A decade-old molecular phylogeny,comprising~80%of the species,revealed multiple cases of parallel evolution and large variation in rates of morphological evolution,which had misled taxonomists into creating many non-monophyletic genera.Here,we reconstruct the phylogeny of the larks,using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species(in total 133 taxa;not all loci available for all species).We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling(in total 51 samples of 44 taxa across 40 species).Our results confirm the previous findings of rampant morphological convergence and divergence,and reveal new cases of paraphyletic genera.We propose a new subfamily classification,and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae.Our study supports recently proposed species splits as well as some recent lumps,while also questioning some of the latter.This comprehensive phylogeny will form an important basis for future studies,such as comparative studies of lark natural history,ecology,evolution and conservation.

Phylogeography and diversification of Oriental weaverbirds(Ploceus spp.):A gradual increase of eurytopy

Weaverbirds are a speciose group of colorful passerines inhabiting the Old World Tropics.Nevertheless,the Oriental weaverbirds(Ploceus spp.),widespread across southern Asia,are much less diverse and restricted to a few ecological niches compared to their African counterpart.To investigate their phylogeography,we retrieved 101 samples of Baya Weaver(P.philippinus),Streaked Weaver(P.manyar),Black-Throated Weaver(P.benghalensis)and Asian Golden Weaver(P.hypoxanthus)along with GenBank sequences of Finn's Weaver(P.megarhynchus).We reconstructed the first molecular phylogeny based on a dataset consisting of both mitochondrial and nuclear genes,dating the most recent common ancestor of Oriental Ploceus to~11 mya.Subsequent speciation appears to have been a combination of divergence within the Indian subcontinent and dispersal across a barrier situated between the Indian subcontinent and the Indochinese region,which provided habitats with a varying degree of isolations and ultimately promoted divergences in allopatry.Two descendants of the earliest nodes,P.megarhynchus and P.hypoxanthus,are both rare and local,often found near large river systems,which perhaps reflects niche conservatism and a lack of adaptive potential.The three smaller species are all widespread,common and less habitat specific.The most recent divergence,between western and eastern P.philippinus populations,is supported by both phylogenetic and morphological evidence,pointing toward limited gene flow between them.However,a zone of intergradation may exist in Myanmar and Brahmaputra flood plains,thus preventing a recommendation for species level recognition without further study.

莺总科鸟类的系统分类进展评述(英文)

本文评述了莺总科鸟类的系统分类,并重点探讨科间、属内系统发育关系以及种级分类地位。基于已发表的 DNA 序列数据,对马岛莺科(Bernieridae)和柳莺科(Phylloscopidae)重新进行了分析。大量的分子水平的研究让我们对鸟类系统发育的认识有了很大提高。但是,由于一些主要进化分支(科)的快速分化,使得这些科之间的相互关系依然不明确。同样,分子标记和(或)鸣声及其他生活史资料在大量研究中的应用,大大提高了种级水平的分类可靠性。我们推测,随着人们运用现代的整合方法对新类群的不断研究,物种数量会不断增加。

Integrative taxonomy of the Russet Bush Warbler Locustella mandelli complex reveals a new species from central China

Background: The Russet Bush Warbler Locustella(previously Bradypterus) mandelli complex occurs in mountains in the eastern Himalayas, southern China, Vietnam, the Philippines, and Indonesia. The taxonomy has been debated,with one(L. seebohmi) to four(L. seebohmi, L. mandelli, L. montis and L. timorensis) species having been recognised.Methods: We used an integrative approach, incorporating analyses of morphology, vocalizations and a molecular marker, to re-evaluate species limits in the L. mandelli complex.Results: We found that central Chinese L. mandelli differed from those from India through northern Southeast Asia to southeast China in plumage, morphometrics and song. All were easily classified by song, and(wing + culmen)/tail ratio overlapped only marginally. Both groups were reciprocally monophyletic in a mitochondrial cytochrome b(cytb) gene tree, with a mean divergence of 1.0 ± 0.2%. They were sympatric and mostly altitudinally segregated in the breeding season in southern Sichuan province. We found that the Mt Victoria(western Myanmar) population differed vocally from other L. mandelli, but no specimens are available. Taiwan Bush Warbler L. alishanensis was sister to the L. mandelli complex, with the most divergent song. Plumage, vocal and cytb evidence supported the distinctness of the south Vietnamese L. mandelli idonea. The Timor Bush Warbler L. timorensis, Javan Bush Warbler L.montis and Benguet Bush Warbler L. seebohmi differed distinctly in plumage, but among-population song variation in L. montis exceeded the differences between some populations of these taxa, and mean pairwise cytb divergences were only 0.5–0.9%. We also found that some L. montis populations differed morphologically.Conclusions: We conclude that the central Chinese population of Russet Bush Warbler represents a new species,which we describe herein, breeding at mid elevations in Sichuan, Shaanxi, Hubei, Hunan and Guizhou provinces.The taxonomic status of the other allopatric populations is less clear. However, as they differ to a degree comparable with that of the sympatric L. mandelli and the new species, we elevate L. idonea to species status, and retain L. seebohmi and L. montis as separate species, the latter with timorensis as a subspecies. Further research should focus on different populations of L. montis and the Mt Victoria population of L. mandelli.

Integrative taxonomy of the Plain-backed Thrush(Zoothera mollissima)complex(Aves,Turdidae)reveals cryptic species,including a new species

Background: The Plain-backed Thrush Zoothera mollissima breeds in the Himalayas and mountains of central China. It was long considered conspecific with the Long-tailed Thrush Zoothera dixoni, until these were shown to be broadly sympatric.Methods: We revise the Z. mollissima–Z. dixoni complex by integrating morphological, acoustic, genetic(two mitochondrial and two nuclear markers), ecological and distributional datasets.Results: In earlier field observations, we noted two very different song types of "Plain-backed" Thrush segregated by breeding habitat and elevation. Further integrative analyses congruently identify three groups: an alpine breeder in the Himalayas and Sichuan, China("Alpine Thrush"); a forest breeder in the eastern Himalayas and northwest Yunnan(at least), China("Himalayan Forest Thrush"); and a forest breeder in central Sichuan("Sichuan Forest Thrush"). Alpine and Himalayan Forest Thrushes are broadly sympatric, but segregated by habitat and altitude, and the same is probably true also for Alpine and Sichuan Forest Thrushes. These three groups differ markedly in morphology and songs. In addition, DNA sequence data from three non-breeding specimens from Yunnan indicate that yet another lineage exists("Yunnan Thrush"). However, we find no consistent morphological differences from Alpine Thrush, and its breeding range is unknown. Molecular phylogenetic analyses suggest that all four groups diverged at least a few million years ago, and identify Alpine Thrush and the putative "Yunnan Thrush" as sisters, and the two forest taxa as sisters. Cytochrome b divergences among the four Z. mollissima sensu lato(s.l.) clades are similar to those between any of them and Z. dixoni, and exceed that between the two congeneric outgroup species. We lectotypify the name Oreocincla rostrata Hodgson, 1845 with the Z. mollissima sensu stricto(s.s.) specimen long considered its type. No available name unambiguously pertains to the Himalayan Forest Thrush.Conclusions: The Plain-backed Thrush Z. mollissima s.l. comprises at least three species: Alpine Thrush Z. mollissima s.s., with a widespread alpine breeding distribution; Sichuan Forest Thrush Z. griseiceps, breeding in central Sichuan forests; and Himalayan Forest Thrush, breeding in the eastern Himalayas and northwest Yunnan(at least), which is described herein as a new species. "Yunnan Thrush" requires further study.

Taxonomy of the White-browed Shortwing(Brachypteryx montana)complex on mainland Asia and Taiwan:an integrative approach supports recognition of three instead of one species

Background: The White-browed Shortwing(Brachypteryx montana) is widespread from the central Himalayas to the southeast Chinese mainland and the island of Taiwan, the Philippines and Indonesia. Multiple subspecies are recognised, and several of these have recently been suggested to be treated as separate species based on differences in morphology and songs.Methods: We here analyse plumage, morphometrics, songs, two mitochondrial and two nuclear markers, and geographical distributions of the two mainland Asian taxa B. m. cruralis and B. m. sinensis and the Taiwan Residents B. m. goodfellowi.Results: We conclude that these differ congruently in morphology, songs and DNA. Male B. m. goodfellowi is the most divergent in plumage(sexually monomorphic, unlike the two others; male similar to female), and B. m. cruralis and B. m. sinensis differ in male plumage maturation. The song of B. m. cruralis is strongly divergent from the others, whereas the songs of B. m. sinensis and B. m. goodfellowi are more similar to each other. Brachypteryx m. sinensis and B. m. goodfellowi are sisters, with an estimated divergence time 4.1 million years ago(mya; 95% highest posterior distribution [HPD] 2.8–5.5 mya), and B. m. cruralis separated from these two 5.8 mya(95% HPD 4.1–7.5 mya). We also report notable range extensions of B. m. sinensis as well as sympatry between this taxon and B. m. cruralis in Sichuan Province, China. Brachypteryx m. montana from Java is found to be more closely related to Lesser Shortwing(B. leucophris) and Rusty-bellied Shortwing(B. hyperythra) than to the mainland Asian and Taiwan Residents taxa.Conclusion: Our data support a recent proposal to treat the three mainland Asian and Taiwan Residents taxa as three species, separate from B. montana sensu stricto: B. cruralis(central Himalayas to south central China and south Vietnam), B. sinensis(north central to southeastern part of China's Mainland) and B. goodfellowi(Taiwan Island).

分子证据表明苏拉威西岛特有鸟种苏拉山鸫(Geomalia heinrichi)属于地鸫属(Zoothera)(鸫科,鸟纲)(英文)

苏拉威西地区特有鸟种苏拉山鸫(Geomalia heinrichi)的分类地位,是属于画眉科还是鸫科,长期以来一直备受争议。基于线粒体细胞色素 b 基因、细胞核肌红蛋白内含子 2 以及鸟氨酸脱羧酶内含子 6–7 基因,我们估计了鸫科 43 个分类群的系统发育关系。结果表明,苏拉山鸫是地鸫属的一个分支,并具有较高的支持率。我们建议将 Geomalia 并入地鸫属(Zoothera),并命名为 Zoothera heinrichi。

Taxonomic status of grey-headed Yellow Wagtails breeding in western China

Background:Field studies from 2011 onwards have demonstrated the presence of a breeding population of Yellow Wagtails(Motacilla flava)in the Xinjiang Uygur Autonomous Region,China that is phenotypically distinct from known subspecies occurring in Asia.Here we describe the plumages and vocalisations of this population and discuss its taxonomic status.Methods:The analysis of plumage is based on field studies and photos available online.Recordings of vocalisations are compared with recordings from other Yellow Wagtail populations,and differences are analysed based on sonograms.Mitochondrial DNA from one individual is compared to other Yellow Wagtail taxa.Results:Unlike M.flava subspecies breeding in or near Xinjiang,males in the studied population show a blue-grey head without prominent white supercilium,being most similar to the widely disjunct M.f.cinereocapilla.They differ from the similarly widely allopatric M.f.thunbergi,which might occur as a migrant or vagrant in Xinjiang,by on average cleaner yellow breast and more extensive white on the throat,and from the widely disjunct M.f.plexa and M.f.macronyx,which might also occur on migration in that area,by softer contact calls and slower pace of song.Females are similar to female M.f.feldegg in plumage.The mitochondrial ND2 tree shows the single sample from Xinjiang to be nested in the clade of western Yellow Wagtail taxa.Conclusion:We discuss whether the Xinjiang breeding population could represent an intergrade between subspecies breeding nearby,or whether it is better regarded as a separate as yet unrecognized subspecies.We argue that the localization of its apparent range in relation to other subspecies along with fairly consistent male and female plumages suggest that it is more likely to represent an undescribed taxon,but conclude that more research is needed to firmly establish its status.