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Species delimitation of the white-tailed rubythroat Calliope pectoralis complex (Aves, Muscicapidae) using an integrative taxonomic approach
Journal of Avian Biology
Abstract
Our knowledge of the systematics and taxonomy of Asian birds has improved much in the last two decades, and the number of recognised species has increased significantly as a result of in-depth studies using an integrative taxonomic approach. The Sino-Himalayan mountains harbor a high level of passerine diversity. Several allopatric or parapatric taxa that are currently treated as subspecies of polytypic species within that region are likely to deserve full species status, and thus their taxonomic status needs to be revisited. Based on analyses of multilocus data, vocalizations and morphology, we propose that the white-tailed rubythroat Calliope pectoralis should be treated as two species, the Himalayan rubythroat C. pectoralis sensu stricto in the Tian Shan and Himalayan mountains, and the Chinese rubythroat C. tschebaiewi in the mountains of southwestern and north-central China. According to our dating analyses based on mitochondrial loci, these two species diverged approximately 2.2 million yr ago. We further found that C. tschebaiewi was paraphyletic to C. pectoralis sensu stricto in nuclear data, which demonstrates a state of mitonuclear discordance that warrants further work. Our results suggest that geographic changes and glacial cycles in the Pleistocene may have caused allopatric divergence in the C. pectoralis complex. Our study stresses the importance of applying an integrative taxonomy approach to fully unravel the true avian diversity in the Sino-Himalayan Mountains.
... Although morphological taxonomy has been well studied, estimations of evolutionary relationships among avian groups at various phylogenetic levels are still being improved by the input of more data and the use of more advanced analytical techniques (Hackett et al., 2008;Tobias et al., 2010). For example, the Plain-backed Thrush, Zoothera mollissima, comprises three species based on congruent support from both molecular and morphometric evidence (Alström et al., 2015), and the White-tailed Rubythroat, Calliope pectoralis, should be treated as two species based on analyses of an integrative taxonomic approach: the Himalayan Rubythroat C. pectoralis and the Chinese Rubythroat C. tschebaiewi (Liu et al., 2016). ...
... Regarding studies on species delimitation in birds, some taxa, before being considered conspecifics, were subsequently elevated to full species based on integrative evidence of phylogeny, morphology, and plumage coloration (Alström et al., , 2015Liu et al., 2016;Martens et al., 2004;Zhang et al., 2016). Our phylogenetic analyses, based on the species tree and BPP delimitation, indicated that the deep split first originated from S. and was followed by divergence between E. cia and N. ...
Species boundaries of birds across the Euro-Asian continent, especially the widely distributed passerines with multiple subspecies, are not completely resolved. The Rock Bunting complex, Emberiza cia and E. godlewskii, is subject to ongoing debate due to geographic variation in its morphology, and deep genetic splits. In this study, the phylogenetic relationships of the E. cia/godlewskii complex were evaluated based on multilocus coalescence methods combined with analyses of plumage color and morphological variation. Although the northern and southern populations of E. godlewski formed reciprocally monophyletic groups, the northern E. godlewskii clade is the sister group to E. cia, rendering E. godlewskii as currently defined paraphyletic. The significant differences in morphometry and plumage color reflectance are complementary and support the phenotypic validity of northern and southern E. godlewskii. Thus, we recommend the following taxonomic revisions: the northern and southern E. godlewskii subspecies should be recognized as different full species, such as E. godlewskii and E. yunnanensis, respectively. This resolves the issue that E. godlewskii, as currently defined, is paraphyletic. Our research provides direct evidence of cryptic species in old world buntings and highlights the underestimation of species diversity in birds in East Asia.
... These three markers were chosen as they remain relevant in studies on avian population structure (e.g. Liu et al., 2016;Dantas et al., 2019;Stervander, Ryan, Melo, & Hansson, 2019), as well as general avian taxonomy (Ericson, Klopfstein, Irestedt, Nguyen, & Nylander, 2014). We hypothesized that unsuitable lowland habitat between the geographically distinct mountain ranges would act as a barrier to effective dispersal between populations, resulting in genetic structuring aligned with the topography of the Cape Fold Belt. ...
... aurantius (1.5 %) was below most p -distance values for species-level distances of 3.3-12.8 % in passerines (Liu et al., 2016;Luo et al., 2014;Martens, Tietze, & Sun, 2005), although (Martens, Tietze, & Päckert, 2011) suggested sister-species can be <3 %. Similarly, our recorded ND2 p -distance result for C. frenatus -C. ...
Mountain habitats physically isolated from one another ("sky islands") represent a unique system for studying dispersal in seemingly isolated populations. The Cape Fold Belt of southwest South Africa forms a sky island archipelago of high-altitude mountain fynbos of which the Cape Rockjumper Chaetops frenatus is an avian-endemic. Continued contraction of habitat due to increasing temperatures may be causing further isolation of C. frenatus populations beyond their dispersal capacities, resulting in currently declining populations in warmer areas of their habitat. In this study, we sequenced two mitochondrial loci and one nuclear locus of 73 C. frenatus samples from 13 localities representing 8 mountain ranges. We found (1) low overall genetic diversity, (2) no evidence for geographically-based genetic structuring, and (3) no evidence for inbreeding within localities. While this may indicate birds are effectively dispersing, it may also indicate strong selective pressure is being placed on their specific genotype. Haplotype networks suggested that C. frenatus may have experienced a bottleneck or founder effect in their recent genetic pasta result supported by a significantly negative Tajima's D value. As the first avian genetic study to arise from a range-restricted species of the Cape Fold Belt sky islands, our results show no evidence that C. frenatus are unable to disperse across inhospitable lowland habitat, and thus may not experience isolation due to climate change. We thus potentially found further support that selective pressure in species with highly specialized habitat niches may have a stronger effect than dispersal limitations.
... However, we acknowledge that the Calandrella larks are poorly differentiated morphometrically (Figure 1), and we stress that other types of data, in combination with dense taxon sampling, are necessary for confident taxonomic revisions. Here, we lack substantive data from nuclear DNA markers, vocalizations, other behaviours, ecology etc., to take the fully integrative taxonomic approach [108][109][110] that is becoming more common, e.g., [111][112][113][114][115][116][117][118][119][120] and which we argue should be the gold standard. Yet, while we emphasize that taxonomic decisions should never rest on mitochondrial trees alone [101,106], we here make use of available morphometric data and evaluate a recent tool for single-locus molecular species delimitation [54], which has been used to propose avian taxonomic revisions based solely on mitochondrial data [121] or in combination with morphometry [65]. ...
... However, we acknowledge that the Calandrella larks are poorly di↵erentiated morphometrically (Figure 1), and we stress that other types of data, in combination with dense taxon sampling, are necessary for confident taxonomic revisions. Here, we lack substantive data from nuclear DNA markers, vocalizations, other behaviours, ecology etc., to take the fully integrative taxonomic approach [108][109][110] that is becoming more common, e.g., [111][112][113][114][115][116][117][118][119][120] and which we argue should be the gold standard. Yet, while we emphasize that taxonomic decisions should never rest on mitochondrial trees alone [101,106], we here make use of available morphometric data and evaluate a recent tool for single-locus molecular species delimitation [54], which has been used to propose avian taxonomic revisions based solely on mitochondrial data [121] or in combination with morphometry [65]. ...
Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.
... (2014) and Habel et al. (2015b). An understanding of how phenotype and song diverge in comparison to molecular markers, in isolated populations, would give greater insight into this rapidly evolving lineage (Jønsson et al. 2014), and provide more effective species delimitation (Dong et al. 2015;Liu et al. 2016;Wood et al. 2016). ...
... WhileAndersen et al. (2015b) significantly revised the taxonomy of this remarkable diversification, the morphological and ecological adaptations that led to the isolation of the different populations remain to be studied. While morphology and phylogenetics have co-varied in many taxa(Jablonski and Finarelli 2009;McKay et al. 2010;Dong et al. 2015;Liu et al. 2016) there are multiple examples of differing morphological and phylogenetic patterns, particularly in recently diverged island fauna(Cibois et al. 2007;Phillimore et al. 2008b;Saitoh et al. 2012). ...
As biodiversity loss reaches critical levels, greater knowledge of its distribution is needed to concentrate conservation efforts. Biodiversity can be measured at several levels, with the species typically the unit used in conservation planning. Attempts to set accurate conservation priorities face a number of prominent challenges; 1. species distributions are often poorly known, particularly in the tropics where the rate of biodiversity loss is highest, 2. the number of currently described species is known to be a huge underestimate, with many cryptic species awaiting formal description, and 3. much remains unknown about the drivers of speciation, particularly what adaptations are associated with population divergence in the early stages of the process. In this thesis I explore each of these main topics in a study system in South-east Sulawesi, in the biodiversity hotspot of the Wallacea region. I focus on the avifauna of the region, contributing to characterising the community composition of unstudied islands, assess the species status of island populations which have diverged from the mainland and provide insight into how adaptations to island life may drive population divergence.
In Chapters 2 and 3 we filled in some of the gaps in the knowledge of the avifaunal distribution in South-east Sulawesi on the previously unsurveyed islands of Kabaena, Muna and Wawonii, identifying potentially important populations, particularly for the Endangered Milky Stork Mycteria cinerea. Chapters 4 and 5 evaluated the diversification of the ‘great speciator’ taxa of South-east Sulawesi, Zosterops white-eyes and Todiramphus kingfishers, lineages renowned for their wide range and propensity for speciation. We propose two new white-eye species, an isolated population descended from the widespread island coloniser the Lemon-bellied White-eye Zosterops chloris, and a single island endemic the ‘Wangi-wangi White-eye’. The ‘Wangi-wangi White-eye’ is a particularly intriguing new species, as its closest relatives are found >3000 km away in the Solomon Islands. Chapters 4 and 5 also flag up other populations for further taxonomic refinement, the Wakatobi Islands Collared Kingfisher Todiramphus chloris population and Runduma Island Lemon-bellied White-eye populations may represent endemic subspecies for South-east Sulawesi.
Chapters 4-7 investigated different morphological adaptations that are associated with island colonisation and the early stages of speciation. Chapter 5 suggested that a reduced dispersal ability, in comparison to source populations, may be a feature of populations of widespread island colonisers which become isolated. In Chapter 4 we discussed how potential differences in habitat, and associated increases in interspecific competition, may have driven a niche shift in Collared Kingfishers on the Wakatobi Islands. Chapter 6 outlined how Lemon-bellied White-eyes had a larger morphological niche volume and greater population density in allopatry from the Pale-bellied White-eye Zosterops consobrinorum, on both a small island and in urban areas. Reduced interspecific competition, and greater intraspecific competition in high density populations, likely led to the increase in niche volume seen in the Lemon-bellied White-eye populations. This chapter highlights the potential for urban areas to act as ecological islands for island colonising edge species in the Indo-Pacific. Chapter 7 looked at some of the effects of island colonisation on sexual dimorphism. Showed that Olive-backed Sunbirds Cinnyris jugularis on the small oceanic Wakatobi Islands showed greater sexual dimorphism and higher population density than those on the mainland and continental islands. There was no difference in the niche volume of males from Wakatobi and mainland populations, but females from the Wakatobi Islands had a smaller niche volume than those from the mainland. Potentially their niche volume has contracted to reduce intersexual competition in the high density populations of the Wakatobi Islands.
This thesis illustrates how studying the populations of Indo-Pacific island colonisers, particularly the ‘great speciator’ lineages, provides the opportunity to contribute both taxonomic revision and insight into the early stages of speciation. Their rapid speed of evolutionary change, ability to colonise islands and the frequency with which they are found in secondary sympatry makes ‘great speciators’ ideal groups in which to study speciation. This work is given impetus by the looming biodiversity crisis that threatens not just Southeast Asia, but the whole world. Much biodiversity, and the evolutionary lessons it can teach us, faces extinction before being formally recognised.
... Die Gebirgsart pectoralis mit vier Ssp. erwies sich morphologisch (was lange bekannt war), genetisch und akustisch als stark differenziert, so dass Liu et al. (2016) vorschlagen, C. pectoralis in zwei Arten aufzuspalten: C. pectoralis s. str. und C. tschebaiewi Przevalski, 1876. ...
... C. calliope und C. tschebaiewi kommen bei Gonghe in der Provinz Qinghai in Kontakt, vermischen sich aber nicht, zumal sich ihre bevorzugten Habitate unterscheiden. C. calliope besiedelt an dieser Stelle Laub-und Mischwälder in mittleren Höhenlagen, C. tschebaiewi lebt in Gebüsch der Subalpin-und der Alpinstufe (Liu et al. 2016). ...
This report is the twelfth of a series and presents the results of a comprehensive literature screening in search for new bird taxa described in 2016, namely new genera, species and subspecies worldwide. We tracked names of 16 new genera, six species and seven subspecies new to science, which were correctly described according to the International Code of Zoological Nomenclature. The new genera are within Psittaculidae, Thraupidae and Muscicapidae. The new species refer to Turdidae, Muscicapidae and Thraupidae; all are Passeriformes. In 2016, one species of Thraupidae was described twice by different authors. New subspecies were named within Rallidae (1), Psittaculidae (1), Acrocephalidae (1), Muscicapidae (2), Nectariniidae (1), Leiotrichidae (1; in addition to the 2015 report) und Pellorneidae (1; addition to 2015) und Maluridae (1). In several cases, the populations in question now considered to represent a new species were known since long. But only substantial studies of type specimens of related species, songs, genetics and/or ecology led to description of new formerly unrecognized species. The descriptions of most new taxa concern the Neotropics (eleven new genera, two new species, one new subspecies), Indo-Malaya (three new genera, one new species, two new subspecies, the latter as addenda to 2015) and the Afrotropics (2 new genera, 2 new species, 1 new subspecies). The distributional areas of new species often are minute, consequently also the size of the populations concerned. Due to their limited ranges, species new to science are often already endangered when detected or newly defined. In the North African/European fauna elevation to species rank is most prominent in populations of the finch genus Fringilla from the Canary Islands and of the flycatcher genus Muscicapa from Corsica in this report. In a sequence by family/genus/species/subspecies the newly described taxa have the following origins: Palaearctic (-/-/-/1), Neotropics (-/11/2/1), Indo-Malaya (-/3/1/2), Afrotropics (-/2/3/1) and Australian-Papua (-/-/-/2). Multiple splits of widely distributed species refer to Palaearctic and Southeast Asian flycatchers (Muscicapa, Calliope, Cyornis), an Southeast Asian bulbul (Pycnonotus) and an Indo-Malayan thrush (Zoothera). We suggest possible flaws in new descriptions and certain splits, regardless of the species concept addressed. In this respect, the Tobias concept for species delimitation is mentioned. However, this general report addresses documentation of new taxa, and is not a critical review of recent changes in bird taxonomy and bird descriptions.
... Die Gebirgsart pectoralis mit vier Ssp. erwies sich morphologisch (was lange bekannt war), genetisch und akustisch als stark differenziert, so dass Liu et al. (2016) vorschlagen, C. pectoralis in zwei Arten aufzuspalten: C. pectoralis s. str. und C. tschebaiewi Przevalski, 1876. ...
... C. calliope und C. tschebaiewi kommen bei Gonghe in der Provinz Qinghai in Kontakt, vermischen sich aber nicht, zumal sich ihre bevorzugten Habitate unterscheiden. C. calliope besiedelt an dieser Stelle Laub-und Mischwälder in mittleren Höhenlagen, C. tschebaiewi lebt in Gebüsch der Subalpin-und der Alpinstufe (Liu et al. 2016). ...
This report is the twelfth of a series and presents the results of a comprehensive literature screening in search for new bird taxa
described in 2016, namely new genera, species and subspecies worldwide. We tracked names of 16 new genera, six species and
seven subspecies new to science, which were correctly described according to the International Code of Zoological Nomenclature.
The new genera are within Psittaculidae, Thraupidae and Muscicapidae. The new species refer to Turdidae, Muscicapidae
and Thraupidae; all are Passeriformes. In 2016, one species of Thraupidae was described twice by different authors.
New subspecies were named within Rallidae (1), Psittaculidae (1), Acrocephalidae (1), Muscicapidae (2), Nectariniidae (1),
Leiotrichidae (1; in addition to the 2015 report) und Pellorneidae (1; addition to 2015) und Maluridae (1). In several cases,
the populations in question now considered to represent a new species were known since long. But only substantial studies of
type specimens of related species, songs, genetics and/or ecology led to description of new formerly unrecognized species. The
descriptions of most new taxa concern the Neotropics (eleven new genera, two new species, one new subspecies), Indo-Malaya
(three new genera, one new species, two new subspecies, the latter as addenda to 2015) and the Afrotropics (2 new genera,
2 new species, 1 new subspecies). The distributional areas of new species often are minute, consequently also the size of the
populations concerned. Due to their limited ranges, species new to science are often already endangered when detected or
newly defined. In the North African/European fauna elevation to species rank is most prominent in populations of the finch
genus Fringilla from the Canary Islands and of the flycatcher genus Muscicapa from Corsica in this report.
In a sequence by family/genus/species/subspecies the newly described taxa have the following origins: Palaearctic (-/-/-/1),
Neotropics (-/11/2/1), Indo-Malaya (-/3/1/2), Afrotropics (-/2/3/1) and Australian-Papua (-/-/-/2). Multiple splits of widely
distributed species refer to Palaearctic and Southeast Asian flycatchers (Muscicapa, Calliope, Cyornis), an Southeast Asian
bulbul (Pycnonotus) and an Indo-Malayan thrush (Zoothera). We suggest possible flaws in new descriptions and certain splits,
regardless of the species concept addressed. In this respect, the Tobias concept for species delimitation is mentioned. However,
this general report addresses documentation of new taxa, and is not a critical review of recent changes in bird taxonomy
and bird descriptions
... Total genomic DNA was extracted from feather or blood samples following standard protocols (Liu et al., 2016;Schweizer and Shirihai, 2013). A special protocol was applied for toe-pad samples from museum skins (Schweizer and Shirihai, 2013). ...
... Similar levels of divergence are often found in avian taxa treated at species level (e.g. Liu et al., 2016;Olsson et al., 2013;Qu et al., 2006;Schweizer and Shirihai, 2013). However, our geographic sampling within those subspecies and R. r. tibetana is rather limited, and it is not clear how these inter-taxa differences are related to intra-taxon variability. ...
Species not only responded idiosyncratically to past climate changes, there were also regionally contrasting effects on spatio-temporal diversification patterns. Studies of closely related species appear to be a particularly promising comparative approach to disentangle such regionally differential impacts. In this study, we undertook a comprehensive geographic sampling to investigate the evolutionary history of the Holarctic Sand Martin Riparia riparia and the chiefly Central and East Asian Pale Martin R. diluta. Previous phylogenetic studies using only a limited geographic sampling, particularly for the latter, revealed the two to be genetically distinct, with the former showing only a shallow genetic structure in mitochondrial DNA. Based on one mitochondrial, one autosomal and one Z-linked nuclear marker, we confirmed the shallow genetic structure in R. riparia even when including the morphologically relatively distinct subspecies R. r. shelleyi from the Nile Valley in Egypt and probably the Middle East. On the other hand the different subspecies of R. diluta, i.e. R. d. diluta from Central Asia, R. d. indica from the northwestern Indian Subcontinent, R. d. tibetana from the Tibetan Plateau and R. d. fohkienensis from southwestern China, were found to be genetically distinct. Their diversification started before the Early to Middle Pleistocene Transition, which was followed by a pronounced succession of glacial and interglacial periods. These rather old divergence events contrast with the lack of any strong phylogeographic structure in R. riparia. Strongly structured populations and regional diversification have been reported in different forest passerine families of South-East Asia. Here we demonstrate, however, that species characteristic of open-country habitats such as R. diluta might display a similar pattern. Morphometric analyses of 120 individuals revealed no clear differences between the different subspecies of R. diluta. Given their similarity also in plumage features, we refrain from proposing any splits despite their marked genetic differentiation, pending further studies and particularly the discovery of potential secondary contact zones.
... At the intraspecific level, ample research in this region has focused on exploring the role of glacial climatic oscillations in population formation or identifying geographic barriers related to differentiation across plant and animal taxa (Chen et al. 2011;Wang et al. 2013Wang et al. , 2018Zuo et al. 2015;Liu et al. 2016a). Great strides have been made in DNA sequencing technology during the past 2 decades, helping to provide more comprehensive insights into species differentiation and population demography by utilizing whole-genome data Davey et al. 2011;Ellegren et al. 2012;Lamichhaney et al. 2015). ...
Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai–Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.
... Therefore, we also searched associated literature and museum vouchers for species with recent splits proposed. In this way, we identified more sequences, for example, Ficedula luzoniensis from Ficedula hyperythra (Moyle et al., 2015), Ficedula riedeli from Ficedula dumetoria (Outlaw and Voelker, 2006), Calliope tschebaiewi from Calliope pectoralis (Liu et al., 2016), Cyornis pelingensis from Cyornis colonus (Garg et al., 2018), and Copsychus superciliaris from Copsychus luzoniensis (Lim et al., 2010). These sequences were added into the supermatrix to represent their corresponding species. ...
The Old World flycatchers, robins and chats (Aves, Muscicapidae) are a diverse songbird family with over three hundred species. Despite continuous efforts over the past two decades, there is still no comprehensive and well-resolved species-level phylogeny for Muscicapidae. Here we present a supermatrix phylogeny that includes all 50 currently recognized genera and ca. 92% of all the species, built using data from up to 15 mitochondrial and 13 nuclear loci. In addition to assembling nucleotide sequences available in public databases, we also extracted sequences from the genome assemblies and raw sequencing reads from GenBank and included a few unpublished sequences. Our analyses resolved the phylogenetic position for several previously unsampled taxa, for example, the Grand Comoro Flycatcher Humblotia flavirostris, the Collared Palm Thrush Cichladusa arquata, and the Taiwan Whistling-Thrush Myophonus insularis, etc. We also provide taxonomic recommendations for genera that exhibit paraphyly or polyphyly. Our results suggest that Muscicapidae diverged from Turdidae (thrushes and allies) in the early Miocene, and the most recent common ancestors for the four subfamilies (Muscicapinae, Niltavinae, Cossyphinae and Saxicolinae) all arose around the middle Miocene.
... Several recent integrative taxonomic studies on Sino-Himalayan birds have proposed treatment of certain allopatric or parapatric subspecies as full species (Alström et al., , 2008Liu et al., 2016a), while other studies have described cryptic new taxa (Alström et al., , 2016. Based on reconstruction of evolutionary histories and relationships of forest songbird species in the region, one of the emerging biogeographical patterns is that lineage splits may be a consequence of colonization events from other biotas, e.g. from the northern Palearctic boreal regions and subtropical regions of southeast Asia (Johansson et al., 2007;Päckert et al., 2012;Price et al., 2014). ...
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. Our results reveal that the isolated north-central Chinese populations of Tarsiger cyanurus, described as the subspecies albocoeruleus but usually considered invalid, is distinctive in genetics and vocalisation, but only marginally differentiated in morphology. We also found the Taiwan endemic T. indicus formosanus to be distinctive in genetics, song and morphology from T. i. indicus and T. i. yunnanensis of the Sino-Himalayan mountains. Moreover, Bayesian species delimitation using BPP suggests that both albocoeruleus and formosanus merit full species status. We propose their treatment as 'Qilian Bluetail' T. albocoeruleus and 'Taiwan Bush Robin' T. formosanus, respectively.
... However, there are still few studies addressing phenotypic and song evolution, processes key to species isolation (Uy et al., 2009), although see Phillimore et al. (2008), Baker (2012), Potvin (2013), Husemann et al. (2014) and Habel et al. (2015b). An understanding of how phenotype and song diverge in comparison to the molecular markers, in isolated populations, would give greater insight into this rapidly evolving lineage (Jønsson et al., 2014) and provide more effective species delimitation (Dong et al., 2015;Liu et al., 2016;Wood et al., 2016). ...
Research in the Indo-Pacific region has contributed massively to the understanding of speciation. White-eyes (Aves: Zosteropidae: Zosterops), a lineage containing both widespread ‘supertramp’ species and a high proportion of island endemics, have provided invaluable models. Molecular tools have increased speciation research, but delimiting species remains problematic. We investigated the evolutionary history of Zosterops species in south-east Sulawesi using mitochondrial DNA, morphometric, song and plumage analyses, to draw species limits and assess which techniques offer best resolution. Our investigation revealed a novel Zosterops species, >3000 km from its closest relative. Additionally, we demonstrated unanticipated diversity in the alleged ‘supertramp’ Zosterops chloris and propose the Wakatobi Islands subspecies (Z. c. flavissimus) to be given full species status. Furthermore, we provide the first molecular and phenotypic assessment of the Sulawesi endemic Zosterops consobrinorum. While local populations of this species vary in either genetics or morphometrics, none show consistency across measures. Therefore, we propose no change to Zosterops consobrinorum taxonomy. This study gives insight into one of the great Indo-Pacific radiations and demonstrates the value of using multiple lines of evidence for taxonomic review.
... While Andersen et al. (2015b) significantly revised the taxonomy of this remarkable diversification, the morphological and ecological adaptations that led to the isolation of the different populations remain to be studied. While morphology and phylogenetics have co-varied in many taxa (Jablonski & Finarelli 2009, McKay et al. 2010, Dong et al. 2015, Liu et al. 2016) there are multiple examples of differing morphological and phylogenetic patterns, particularly in recently diverged island fauna (Cibois et al. 2007, Phillimore et al. 2008, Saitoh et al. 2012). ...
The Collared Kingfisher species complex is the most widespread of the ‘great speciator’ lineages of the Indo‐Pacific. They have shown a remarkable ability to spread and diversify. As a result of this rapid diversification Todiramphus species are often found in secondary sympatry. In South‐east Sulawesi, Indonesia, two Todiramphus species are present, the breeding resident Collared Kingfisher Todiramphus chloris and the over‐wintering migratory Sacred Kingfisher Todiramphus sanctus. We investigated the effect of isolation on these closely related species by comparing their populations on mainland Sulawesi and its larger continental islands, with populations on the small, oceanic Wakatobi Islands. Within our wider analysis we provide further support for the distinctiveness of the Sulawesi Collared Kingfisher population, perhaps isolated by the deep water barrier of Wallace's Line. Within Sulawesi we found that populations of Collared Kingfisher on the Wakatobi had diverged from those on mainland Sulawesi, differing both in morphology and mitochondrial DNA. In contrast there was no divergence between Sacred Kingfisher populations in either morphology or mitochondrial DNA. We propose that a difference in habitat occupied by Collared Kingfisher populations between the mainland and continental islands versus oceanic islands, has caused this divergence. Mainland Collared Kingfishers are predominately found inland, while Wakatobi Collared Kingfishers are also found in coastal habitats. The larger body size of Wakatobi Collared Kingfisher populations may be a result of increased competition with predominantly coastal Sacred Kingfisher populations. The uniform nature of Sacred Kingfisher populations in this region likely reflects their consistent habitat choice (coastal mangrove) and their migratory nature. The demands of their breeding range are likely to have an even stronger selective influence than their Sulawesi wintering range, limiting their scope for divergence. These results provide insight into the adaptability of the widespread Todiramphus lineage and provide evidence of the need for further taxonomic revision of Collared Kingfisher populations. This article is protected by copyright. All rights reserved.
... Moreover, several Sino-Himalayan taxa have been elevated from subspecies to species rank in recent years based on integrative studies of morphology, vocalizations, DNA, and sometimes also other traits, which have indicated lineage separation (e.g. Martens et al. 2004, 2016, Liu et al. 2016. As diagnosable trait differences may not evolve under certain scenarios of speciation (Barley et al. 2013) and tail, and might possibly be treated as a distinct species in case of further evidence from acoustic data. ...
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. Our genetic results suggested that Horornis fortipes is composed of at least three independently evolving lineages, which diverged 1.1–1.8 million years ago. However, these lineages have hardly diverged in song or morphometrics and only very slightly in plumage. Our result indicate that there are three incipient species in Horonis fortipes complex diverged in central Himalayas and Hengduan Mountains, but not between the continent and Taiwan island.
A survey of recent taxonomic studies of birds that included acoustic trait analyses reveals that most studies have not archived the sound recordings that support their conclusions, despite the current availability of online, publicly available collections of bird sounds. In addition, bird sound recordings have often been cited without unique accession numbers that permit unambiguous sample identification and in considerably less detail than other types of samples, such as museum specimens or genetic samples. Both this lack of data openness and the way acoustic samples have been cited undermine the methodological rigor that otherwise characterizes many of these studies, and much invaluable biological data are likely to be lost over time if bird sound recordings are not archived in long-term collections. I suggest that these problems can be easily addressed by embracing the open data movement and adopting some best practices that are widely used in other fields. Just as study skins and DNA sequences are required to be deposited in publicly available collections such as natural history museums and the GenBank, respectively, sound recordings used in taxonomic studies with acoustic trait analyses should be archived in publicly available collections as a condition for publication of associated results. Authors of taxonomic studies involving sounds should archive their sound recordings and provide unique accession numbers for sound recordings examined, and journals and reviewers should ensure that authors have done so. By embracing the open data movement, research studying avian acoustic signals is expected to become more transparent, reproducible, and useful.
For the first time we propose a hypothesis of hybrid origin of Calliope pectoralis from two species, C. calliope and C. obscura, based on the new molecular genetic data and phenotypic characters. We examined 80 samples of C. calliope and one sample of С. pectoralis tschebaiewi. We discovered that products of the cytochrome b gene, as well as three transport RNAs, ND6, and a control region (3.2 kb) were heterogeneous in 22 specimens of C. calliope. The result of cloning of these amplicons produced two clone variants: the cytochrome b gene of C. calliope and the nuclear pseudogene homologous to the cytochrome b gene of C. pectoralis (96% match). Computer assisted phylogenetic analysis of the connections between the cloned sequences for the mtDNA cytochrome b gene and its nuclear copies revealed a distribution into two clades: C. calliope and C. pectoralis. This can be explained by an intergenomic recombination event, namely, a transfer of C. calliope’s nuclear copy of the cytochrome b gene into a mitochondrial genome of a hybrid female that later became the founder of the C. pectoralis species. According to morphological features, the second species involved in hybridization with C. calliope was probably C. obscura, since it is the only species of the Calliope genus that has a black breast and black outer tail feathers with white bases similar to those of C. pectoralis.
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.
A recent study of New World orioles (Icterus spp.), which traced a large number of plumage characters onto a mitochondrial DNA phylogeny, reported high frequencies of evolutionary convergence and reversal of plumage characters (Omland and Lanyon 2000). Although those results are consistent with other smaller scale studies that have documented plumage homoplasy, the mitochondrial genome is inherited as a single linkage group, so mitochondrial data represent only one gene tree. The mitochondrial (mt) DNA tree may not reflect the true evolutionary history of a lineage; therefore, it remains possible that the plumage characters could reflect the true species phylogeny. Other rapidly evolving regions of DNA can provide independent phylogenetic hypotheses useful for evaluating mitochondrial gene trees. A novel phylogenetic marker, a region of the nuclear gene ornithine decarboxylase (ODC) spanning from exon 6 to exon 8, was sequenced in 10 oriole species. The resultant nuclear gene tree reconstructs the same three major oriole clades as the mtDNA tree (Omland et al. 1999), supporting the conclusion that plumage evolution in the New World orioles has been highly homoplastic. Although most phylogenetic studies that have employed introns report greatest resolution at the genus or family level, ODC appears to offer some degree of phylogenetic resolution for infrageneric analyses. However, that intron has clearly not sorted to monophyly within or between closely related species.
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.
We used an integrative approach, incorporating analyses of morphology, vocalizations and a molecular marker, to re-evaluate species limits in the L. mandelli complex.
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.
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.
We investigated external morphology, molecular genetics and bioacoustics of the Chinese leaf warblers Phylloscopus fuscatus, P. fuligiventer, P. affinis, P. armandii and P. subaffinis, a set of predominantly high-altitude species of open bushy habitats. Phylloscopus fuscatus and P. fuligiventer were found to be sister taxa; the current subspecies of P. fuscatus appeared to be paraphyletic. P. fuscatus weigoldi (Qinghai) is excluded from P. fuscatus and transferred to P. fuligiventer as a subspecies (formerly E Himalayas/SE Tibet only). Several individuals of nominate fuscatus carrying private haplotypes were found in China during the breeding season and may locally breed there (Shaanxi, Gansu). Genotyping of type specimens of P. fuscatus robustus yielded a composite type series including nominate fuscatus. A lectotype of taxon robustus is designated since the holotype was lost in World War II. – Phylloscopus affinis falls into three distinct population groups which differ by exhibiting marked molecular genetic distance values, in coloration and in vocalisations. Central Asian Phylloscopus griseolus is firmly nested in the P. affinis clade. The Himalayan (incl. SE Tibet) populations of P. affinis on the one hand and the Chinese populations (Yunnan, Sichuan, Qinghai, Gansu) on the other are differentiated on the species level. For the latter populations a new name is introduced (P. occisinensis nov. sp.). The Himalayan population group itself is subdivided into a western (P. affinis perflavus nov. ssp.) and an eastern group (nominate affinis). – Phylloscopus armandii generally is subdivided into a larger northern (nominate armandii) and a smaller southern Chinese population (ssp. perplexus). Their cytb and 16S distance values are remarkably high but subspecies status is retained because of only subtle morphological differences and a lack of acoustic divergence. – Phylloscopus subaffinis is unstructured with respect to cytb and 16S genes throughout China.
Volume 1 covers the Non-passerines (4072 spp. in pp. i-l, 1-461). Joel Cracraft provided and explained the sequence of families. Fourteen colleagues participated in this work which draws extensively on recent molecular studies, is very extensively footnoted and includes 2877 references. The reference list is on an accompanying CD which includes maps, a gazetteer and appendices 5 to 9 (the previous four being in the book).
The systematics of the avian superfamily Sylvioidea are reviewed, focusing on studies of relationships among families and within genera, more superficially on taxonomic studies at the species level. For the families Bernieridae and Phylloscopidae, new analyses based on already published sequence data are presented. Our understanding of relationships has been vastly improved in recent years due to a large number of molecular studies. However, the relationships among the different families remain largely obscured, probably mainly as a result of rapid divergence of the different primary lineages (families). Also, species level taxonomy has been much improved in recent years due to a large number of studies applying molecular markers and/or vocalizations and other life-history data. It seems likely that the number of species will continue to increase, as new groups are being studied with modern integrative methods.
The Chinese endemic breeders Blackthroat Calliope obscura and Firethroat C. pectardens are two of the world’s rarest and least known ‘chats’ (Muscicapidae). They have been considered colour morphs of the same species (Firethroat, by priority), although they are nowadays usually treated as separate species. The taxonomic status of these two taxa is here investigated based on analyses of mitochondrial and nuclear DNA, vocalisations and reassessed distributions. Phylogenetic analysis confirms that they are sisters. Their genetic divergence (cytochrome b 6.4%, GTR+Γ+I corrected) is comparable to several other species pairs of ‘chats’. Discriminant function analysis of songs correctly classified 88% of the recordings. The breeding ranges appear to be mainly parapatric. Based on congruent differences in morphology, songs and molecular markers, it is concluded that Blackthroat and Firethroat are appropriately treated as separate species.
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.
We used morphological, vocal and molecular (one mitochondrial and two nuclear loci) data to re-evaluate the taxonomic status of the taxa acanthizoides, concolor, and brunnescens in the Cettia acanthizoides (J. Verreaux, 1871) complex. We conclude that all three are valid taxa, and that acanthizoides of China and concolor of Taiwan are best treated as conspecific, whereas brunnescens of the Himalayas is better considered as a separate species. The degree of morphological, vocal, and genetic differentiation is variably congruent among all taxa; the recently separated acanthizoides and concolor differ slightly in plumage and structure but are indistinguishable in vocalizations, whereas the earlier diverged brunnescens and acanthizoides/concolor differ only slightly more in morphology but to a much greater degree in vocalizations. We stress the essential nature of taxonomic revisions as a prerequisite for the biodiversity estimates required for conservation planning. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 437–452.
Introduction
Incomplete lineage sorting and hybridization are two major nonexclusive causes of haplotype sharing between species. Distinguishing between these two processes is notoriously difficult as they can generate similar genetic signatures. Previous studies revealed that the mitochondrial DNA (mtDNA) differentiation between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus) was extremely low, even lower than intraspecific differentiation in some other long-tailed tits. Using a combination of multilocus and coalescent analyses, we explored the causes of the anomalous lack of mtDNA differentiation between the two species.
Results
The mtDNA divergence between the two species was shallow, while the nuclear DNA (nuDNA) divergence was considerably deeper. The IMa analyses based on the mtDNA dataset suggested relatively high gene flow from A. fuliginosus to A. bonvaloti, while negligible gene flow in the opposite direction. In contrast to mtDNA, the migration rates at autosomal and Z-linked nuDNA loci were negligible or much lower. The NEWHYBRIDS analysis assigned all individuals except one to pure parental species with high posterior probability. The Bayesian skyline plot showed that both species underwent population expansions during the Last Glacial Maximum (LGM), and the ecological niche modelling suggested that their ranges overlapped more during the LGM than at present.
Conclusions
We suggest that historical hybridization, in combination with selective sweep and/or genetic drift might be the main causes of the extremely low mtDNA differentiation between the two species. The hybridization probably occurred mainly between A. fuliginosus females and A. bonvaloti males. The LGM distribution expansion might have facilitated hybridization, while the post-LGM distribution contraction could have facilitated some mtDNA sorting. Ongoing hybridization between the two species might be very limited, but further studies with more samples from the contact zone are needed to test this conclusion.
Speciation generally involves a three-step process-range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations. Speciation relies on cycling through these three steps and each may limit the rate at which new species form. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions, set an ultimate limit on speciation. Based on a phylogeny for all 358 species distributed along the eastern elevational gradient, here we show that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later. These results are consistent with competition for niche space limiting species accumulation. Even the elevation dimension seems to be approaching ecological saturation, because the closest relatives both inside the assemblage and elsewhere in the Himalayas are on average separated by more than five million years, which is longer than it generally takes for reproductive isolation to be completed; also, elevational distributions are well explained by resource availability, notably the abundance of arthropods, and not by differences in diversification rates in different elevational zones. Our results imply that speciation rate is ultimately set by niche filling (that is, ecological competition for resources), rather than by the rate of acquisition of reproductive isolation.
The Qinghai-Tibet Plateau (QTP) is well known for being of great importance in the evolution of montane species due to its unique geological history and landform configuration, climate complexity, and diversified habitats. The effect of environmental changes since the Quaternary on species diversification, population genetic structure, and demography under environmental change can be studied using phylogenetic and phylogeographical approaches. Birds are the most well-studied group of all terrestrial vertebrates with regard to their response to climatic changes over time. Herein, we briefly review the species diversification of birds in response to the uplift of the QTP, focusing on summarizing the different phylogeographical patterns of birds on the Plateau, its southeastern margin, and the Eastern Himalayas and the reasons underlying these patterns. Speciation was found to be closely related to the uplift of the QTP, with different patterns of intraspecific processes: (1) no divergence within a single refuge was identified in a restricted semi-continuous area of the eastern margin of the Plateau; (2) two divergent lineages with separated refugia were located at the south-eastern and north-eastern margins of the plateau; and (3) multiple divergent lineages within subregions were found in the Eastern Himalayas. Glacial movements and induced climate change are considered to be key factors in shaping these different patterns. The species distributed mainly in the heavily ice-covered platform regions of the Plateau experienced population expansion following the retreat of the extensive glaciations, whereas the species distributed on the ice-free edges of the plateau maintained their population size at a stable level. Demographic stresses on the edge species might have been mitigated by the milder climate in comparison to their platform-distributed counterparts. Various behavioral and ecological characteristics, including dispersal capacity, habitat preference, and elevation specificity, along with evolutionary history might have helped to shape these different phylogeographical patterns.
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., morphological, molecular, behavioral, ecological, etc.). However, although most taxonomic descriptions have been based on morphology, some key morphological features, such as color, are rarely quantified and incorporated into integrative taxonomic studies. In this article, we applied a new method of ultraviolet digital photography to measure plumage variation in a color-variable avian species complex, the varied tit (Sittiparus varius). Plumage measurements corroborated species limits defined by morphometric, mitochondrial DNA, and nuclear DNA disjunctions and provided the only evidence for distinguishing two recently evolved species. Importantly, color quantification also provided a justification for lumping putative taxa with no evidence of evolutionary independence. Our revised taxonomy thus refines conservation units for listing and management and clarifies the primary units for evolutionary studies. Species tree analyses, which applied the newly delimited species as operational taxonomic units, revealed a robust phylogenetic hypothesis for the group that establishes a foundation for future biogeographic analyses. This study demonstrates how digital photography can be used to incorporate color character variation into integrative taxonomies, which should lead to more informed, more rigorous, and more accurate assessments of biodiversity. [Color, digital photography, integrative taxonomy, Sittiparus varius, species delimitation, varied tit.] © 2014 The Author(s) 2014. All rights reserved. For Permissions, please email: [email protected]
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Analysis of one of the most comprehensive datasets to date of the largest passerine bird clade, Passerida, identified 10 primary well-supported lineages corresponding to Sylvioidea, Muscicapoidea, Certhioidea, Passeroidea, the 'bombycillids' (here proposed to be recognized as Bombycilloidea), Paridae/Remizidae (proposed to be recognized as Paroidea), Stenostiridae, Hyliotidae, Regulidae (proposed to be recognized as Reguloidea) and spotted wren-babbler Spelaeornis formosus. The latter was found on a single branch in a strongly supported clade with Muscicapoidea, Certhioidea and Bombycilloidea, although the relationships among these were unresolved. We conclude that the spotted wren-babbler represents a relict basal lineage within Passerida with no close extant relatives, and we support the already used name Elachura formosa and propose the new family name Elachuridae for this single species.
We analyzed passerine biodiversity and phylogeography in the Sino-Himalayan region with respect to neighboring areas, especially the Siberian taiga zone to the north and tropical Asia southeast of the Himalayas and mountainous parts of southwest China. Fresh results, informative about evolutionary processes in that area, were obtained mainly by the application of new methods in passerine systematics, acoustic and molecular genetic markers. It became evident that species with areas in the Himalayas and southwest China and, in addition, often with disjunct areas in Siberia, actually belong to swarms of closely related, mostly allopatric species. In many cases these differ markedly in vocalizations and are deeply split according to molecular genetic markers. External morphology of the constituent taxa quite often remained surprisingly homogeneous and thus resulted in traditional subspecies status of single populations at best. Other such well-differentiated taxa were often overlooked and only discovered by molecular genetic techniques. Within the Himalayas, contrary to current thinking, intra-range differentiation is well developed in some taxa but still largely unresolved because of deficient sampling along the Himalayan chain. Both subspecies and allopatric species are also concerned here. Apparently, the Himalayas were mostly settled from the east following intra-range diversification. Immigration from the west into the Himalayas was a much rarer event and, impeded by the monsoons, immigrants reached just west Nepal and, with respect to evolutionary history, did not diverge further. Himalayan endemic passerines are few and mainly confined to the western part. © 2011 by The American Ornithologists' Union. All rights reserved.
Based on distinctive morphological and vocal characters we describe a new species of lowland tailorbird Orthotomus from dense humid lowland scrub in the floodplain of the Mekong, Tonle Sap and Bassac rivers of Cambodia. Genetic data place it in the O. atrogularis-O. ruficeps-O. sepium clade. All data suggest that the new species is most closely related to O. atrogularis, from which genetic differences are apparently of a level usually associated with subspecies. However the two taxa behave as biological species, existing locally in sympatry and even exceptionally in syntopy, without apparent hybridisation. The species is known so far from a small area within which its habitat is declining in area and quality. However, although birds are found in a number of small habitat fragments (including within the city limits of Phnom Penh), most individuals probably occupy one large contiguous area of habitat in the Tonle Sap floodplain. We therefore recommend it is classified as Near Threatened on the IUCN Red List. The new species is abundant in suitable habitat within its small range. Further work is required to understand more clearly the distribution and ecology of this species and in particular its evolutionary relationship with O. atrogularis.
The Blackthroat (or Blackthroated Blue Robin) Calliope obscura (previously Luscinia obscura) is one of the world’s rarest “robins”. It is extremely poorly known, with only a handful of records since it was firstly described in the 1890s. In 2011–2012, a series of field investigations were carried out in nature reserves in the Qinling Mountains, Shaanxi Province, China. During these surveys, a total of 14 males were found in 2011 and 24 males and 2 females in 2012 in the national nature reserves of Foping and Changqing. Based on these observations, we here describe the Blackthroat’s vocalizations and habitat choice and review its distribution and conservation status. We also provide some notes on the plumage, especially of the female, and the nesting behaviour of this species. The present report confirms that the Blackthroat breeds on the southern slope of the Qinling Mountains in large, dense expanses of dwarf bamboo with scattered coniferous and broadleaved trees above 2,100 m. Our observations suggest that it is more numerous than previously believed, although it appears to be highly localized. The locally dense populations found in 2011 and 2012 and the vast expanses of suitable habitat suggest that the breeding population might be healthy.
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements our RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
Mountains host greater avian diversity than lowlands at the same latitude due to their greater diversity of habitats stratified along an elevation gradient. Here we test whether this greater ecological heterogeneity promotes sympatric speciation. We selected accentors (Prunellidae), an avian family associated with mountains of the Palearctic, as a model system. Accentors differ in their habitat/elevation preferences and south-central Siberia and Himalayan regions each host 6 of the 13 species in the family. We used sequences of the mtDNA ND2 gene and the intron 9 of the Z chromosome specific ACO1 gene to reconstruct a complete species-level phylogeny of Prunellidae. The tree based on joint analysis of both loci was used to reconstruct the family's biogeographic history and to date the diversification events. We also analyzed the relationship between the node age and sympatry, to determine the geographic mode of speciation in Prunellidae. Our data suggest a Miocene origin of Prunellidae in the Himalayan region. The major division between alpine species (subgenus Laiscopus) and species associated with shrubs (subgenus Prunella) and initial diversification events within the latter happened within the Himalayan region in the Miocene and Pliocene. Accentors colonized other parts of the Palearctic during the Pliocene-Pleistocene transition. This spread across the Palearctic resulted in rapid diversification of accentors. With only a single exception dating to 0.91 Ma, lineages younger than 1.5 Ma are allopatric. In contrast, sympatry values for older nodes are >0. There was no relationship between node age and range symmetry. Allopatric speciation (not to include peripatric) is the predominant geographic mode of speciation in Prunellidae despite the favorable conditions for ecological diversification in the mountains and range overlaps among species.
Avian faunas vary greatly among montane areas; those at high latitudes are biologically impoverished, whereas those of some low-latitude mountains are biologically very complex. Their high level of species richness is caused by the aggregation of many small-ranged species, which has been difficult to explain from purely macroecological models focusing on contemporary ecological processes. Because the individual mountain tracts harbor species that represent different evolutionary trajectories, it seems plausible to relate these species assemblages to high persistence (or absence of extinction) in addition to high levels of speciation. The distribution of small-ranged species is concentrated near tropical coasts, where moderation of the climate in topographically complex areas creates cloud forests and stable local conditions. The stability underpins specialization and resilience of local populations, and thereby the role of these places as cradles of biodiversity.
We demonstrate the importance of using multiple criteria in species delimitations, whatever the conceptual base for species delimitation. We do this by studying plumage, biometrics, egg coloration, song, mitochondrial DNA and habitat/altitudinal distribution in the Spotted Bush Warbler Bradypterus thoracicus (Blyth) complex, and by conducting playback experiments. Taxa that we suggest are best treated as separate species [B. thoracicus (Blyth), B. davidi (La Touche) and B. kashmirensis (Sushkin)] differ in most or all of these aspects, particularly in song and mitochondrial DNA, while those that we treat as subspecies (suschkini) or synonyms (przevalskii) differ slightly and only in morphology. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154, 291–307.
Developments in several fields of study (including bio-acoustics and the analysis of DNA) together with reappraisals of the nature of species have impacted significantly on avian taxonomy. The BOU's Taxonomic Subcommittee has developed guidelines for the application of species limits to sympatric, parapatric, allopatric and hybridizing taxa. These are published here to assist researchers understand the rationale behind the committee's taxonomic recommendations relating to the British List.
A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized leastsquares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.311.7, 13.31.5, 10.91.2, 3.70.6, and 2.70.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a protochimpanzee after the former had developed bipedalism.
The statistical rigor of species delimitation has increased dramatically over the past decade. Coalescent theory provides powerful models for population genetic inference, and is now increasingly important in phylogenetics and speciation research. By applying probabilistic models, coalescent-based species delimitation provides clear and objective testing of alternative hypotheses of evolutionary independence. As acquisition of multilocus data becomes increasingly automated, coalescent-based species delimitation will improve the discovery, resolution, consistency, and stability of the taxonomy of species. Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification.
Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relation to, for instance, complex introgression scenarios involving many species. Here, we report remarkably widespread mitonuclear discordance between about 15 mitochondrial and 4 nuclear Brachionus calyciflorus groups identified using different species delimitation approaches. Using coalescent-, Bayesian admixture-, and allele sharing-based methods with DNA sequence or microsatellite data, we provide strong evidence in support of hybridization as a driver of the observed discordance. We then describe our combined molecular, morphological, and ecological approaches to resolving phylogenetic conflict and inferring species boundaries. Species delimitations based on the ITS1 and 28S nuclear DNA markers proved a more reliable predictor of morphological variation than delimitations using the mitochondrial COI gene. A short-term competition experiment further revealed systematic differences in the competitive ability between two of the nuclear-delimited species under six different growth conditions, independent of COI delimitations; hybrids were also observed. In light of these findings, we discuss the failure of the COI marker to estimate morphological stasis and morphological plasticity in the B. calyciflorus complex. By using B. calyciflorus as a representative case, we demonstrate the potential of integrative taxonomy to guide species delimitation in the presence of mitonuclear phylogenetic conflicts.
Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relation to, for instance, complex introgression scenarios involving many species. Here, we report remarkably widespread mitonuclear discordance between about 15 mitochondrial and four nuclear Brachionus calyciflorus groups identified using different species delimitation approaches. Using coalescent-, Bayesian admixture-, and allele sharing-based methods with DNA sequence or microsatellite data, we provide strong evidence in support of hybridization as a driver of the observed discordance. We then describe our combined molecular, morphological, and ecological approaches to resolving phylogenetic conflict and inferring species boundaries. Species delimitations based on the ITS1 and 28S nuclear DNA markers proved a more reliable predictor of morphological variation than delimitations using the mitochondrial COI gene. A short-term competition experiment further revealed systematic differences in the competitive ability between two of the nuclear-delimited species under six different growth conditions, independent of COI delimitations; hybrids were also observed. In light of these findings, we discuss the failure of the COI marker to estimate morphological stasis and morphological plasticity in the B. calyciflorus complex. By using B. calyciflorus as a representative case, we demonstrate the potential of integrative taxonomy to guide species delimitation in the presence of mitonuclear phylogenetic conflicts.
Aim
Montane regions like the Sino‐Himalayas constitute global diversity hotspots. Various mechanisms such as in situ adaptive divergence, speciation following immigration or allopatric diversification in complex landscapes have been proposed to account for the exceptional diversity found in a particular clade in a montane setting. We investigated macroevolutionary patterns to test these different hypotheses in the continental radiation of a Sino‐Himalayan bird group, the parrotbills (Paradoxornithidae).
Location
Sino‐Himalayan region, Indo‐Burma.
Methods
We used phylogenetic comparative methods based on a multilocus, time‐calibrated phylogeny to reconstruct patterns of lineage diversification, biogeographical history, morphological evolution as well as of climate niche history using ecological niche modelling.
Results
The radiation of parrotbills started c. 12 Ma, diversifying at an apparent constant rate over time. The biogeographical history appears to be complex, within‐region speciation in mountains was restricted to China. Size evolution was concentrated in the early phase of parrotbill radiation, whereas morphological shape evolution did not differ from Brownian motion. We found no indication for niche conservatism, with climate niche evolution occurring throughout the radiation of parrotbills.
Conclusions
Parrotbills diversified within a time span of increased regional orogenesis and associated strong climate change. While the south‐west and central Chinese mountains were revealed to be a species pump, with in situ allopatric diversification triggered by complex topography and high habitat turnover, the diversity in the Himalayas was chiefly the result of immigration. Evidence for continuous ecological specialization and for the absence of climate niche conservatism could be interpreted as the consequence of ongoing climate‐ and habitat‐induced ecological opportunities. The radiation of parrotbills demonstrates the influence of multiple drivers of diversification in a single group due to the dynamic geological and palaeoclimatic history of the Sino‐Himalayan region and illustrates the complex nature of continental radiations.
Studies of the geomorphology and stratigraphy in the upper reaches of the Yellow River during the late Cenozoic demonstrate that the period of 30-3.4Ma is charactered by a relatively stable tectonic setting, a persistently hot climate and a wide distribution of inland basins. This long-term stable environment resulted in a planation surface, the main surface on the Qinghai-Xizang (Qingzang) Plateau, on which red earth crust and karst are formed. Since 3.4 Ma, the Qingzang Plateau was uplifted as a whole massif accompanied by the dissection and disintegration of the main surface, termination of deposition and deformation of stratigraphy in red basins, increasing relief and commencing accumulation of inland molasse formation mainly of conglomerate. Subsequent strong uplift of the Qingzang Plateau at 2.5Ma and 1.7-1.66Ma led to cormation of the basic geomorphological configuration of the Qingzang Plateau and occurrence of the Yellow River. These three strong uplifts of the Qingzang Plateau between 3.4 Ma and 1.7-1.66Ma was therefore, named the Qingzang movement and divided correspondingly into three phases A, B and C. After the appearance of the Yellow River, the Qingzang Plateau continued uplifting intermittently, resulting in 8 valley terraces dated to 1.63, 1.5, 1.2, 0.8, 0.6, 0.15, 0.05, and 0.01 Ma, which also record the whole process of headward erosion of the Yellow River.
The taxonomy of the Narcissus Flycatcher Ficedula narcissina-Yellow-rumped Flycatcher Ficedula zanthopygia complex from East Asia has long been debated. Most authors recognize two species: F. narcissina, with the subspecies narcissina (most of Japan and Sakhalin Island), owstoni (south Japanese islands) and elisae (northeast China) and F. zanthopygia (monotypic), although species status has been proposed for elisae and sometimes for owstoni. Here, we revise the taxonomy of this complex based on an integrative approach utilizing morphology, songs and mitochondrial and nuclear DNA for all taxa. All taxa were diagnosably different in plumage, and there were also structural differences among them, although the northernmost populations of owstoni (sometimes recognized as jakuschima and shonis) were somewhat intermediate in plumage, structure and male plumage maturation between southern populations of owstoni and narcissina. All taxa had different songs, and a discriminant function analysis of four song variables correctly classified 100% of all songs. A strongly supported phylogeny was recovered based on three mitochondrial genes and three nuclear introns (total of 3543 bp), revealing a sister relationship between F. zanthopygia and the other taxa, between F. n. narcissina and F. n. owstoni, and between F. n. elisae and F. n. narcissina + F. n. owstoni. The corrected COI distances among the three F. narcissina subspecies ranged from 2.8% (narcissina-owstoni) to 8.2% (narcissina-elisae). We suggest that the congruent differences in multiple independent traits and the deep genetic divergences among the four taxa in the F. narcissina-F. zanthopygia complex support treatment of all of these taxa as separate species. However, we acknowledge the paucity of data for F. owstoni and recommend further studies of this taxon. We suggest listing both F. elisae and F. owstoni, which have small and fragmented populations, as globally threatened.
The volume is broadly split into two main sections. The firsts consists of seven introductory chapters: biodiversity and priority setting; identifying endemic bird areas; global analyses; the prioritization of endemic brid areas; the conservation relevance of endemic bird areas; endemic bird areas as targets for conservation action; and regional introductions. The second, and larger part of the text looks at the endemic bird areas in detail. The section is split into six subsections, by region: North and Central America; Africa, Europe and the Middle East; continental Asia; SE Asian Islands, New Guinea and Australia; and the Pacific Islands. Within each regional subsection the endemic areas are detailed, providing information on : general characteristics; restricted-range species; threats and conservation; and location maps.
Biodiversity is unevenly distributed on Earth and hotspots of biodiversity are often associated with areas that have undergone orogenic activity during recent geological history (i.e. tens of millions of years). Understanding the underlying processes that have driven the accumulation of species in some areas and not in others may help guide prioritization in conservation and may facilitate forecasts on ecosystem services under future climate conditions. Consequently, the study of the origin and evolution of biodiversity in mountain systems has motivated growing scientific interest. Despite an increasing number of studies, the origin and evolution of diversity hotspots associated with the Qinghai-Tibetan Plateau (QTP) remains poorly understood. We review literature related to the diversification of organisms linked to the uplift of the QTP. To promote hypothesis-based research, we provide a geological and palaeoclimatic scenario for the region of the QTP and argue that further studies would benefit from providing a complete set of complementary analyses (molecular dating, biogeographic, and diversification rates analyses) to test for a link between organismic diversification and past geological and climatic changes in this region. In general, we found that the contribution of biological interchange between the QTP and other hotspots of biodiversity has not been sufficiently studied to date. Finally, we suggest that the biological consequences of the uplift of the QTP would be best understood using a meta-analysis approach, encompassing studies on a variety of organisms (plants and animals) from diverse habitats (forests, meadows, rivers), and thermal belts (montane, subalpine, alpine, nival). Since the species diversity in the QTP region is better documented for some organismic groups than for others, we suggest that baseline taxonomic work should be promoted.
Aim
Although global species richness patterns appear consistent across taxa and continents, patterns are elusive at smaller spatial scales. At regional/subcontinental scales, climatic, environmental and taxon‐specific contingencies are likely to interact to modify general richness patterns. We develop a biogeographical paradigm for the H imalayan range as representative of regions at similar spatial scales, and where historical climate fluctuations might interact with species ecology to drive species richness patterns.
Location
H imalayan range, A sia
Methods
We obtained a cell × species presence–absence matrix for babblers and murid rodents in 1° latitude × 1° longitude cells in the H imalayan range. We investigated nestedness in species richness patterns in these taxa along a distance gradient from the species‐rich eastern towards the relatively depauperate west. We also investigated the relationship between species autecology and westward extent along the H imalaya. Climate data were obtained from published sources.
Results
Himalayan babbler and murid assemblages are nested along an east–west axis, with assemblages in westward cells tending to be subsets of assemblages immediately to the east. Distance westward from the eastern H imalaya was related positively to altitudinal mobility of babbler assemblages, while body size increased with distance westward for murid assemblages.
Main conclusions
The eastern H imalaya, which was not glaciated over during glacial maxima, was a potential refugium for babbler and murid species. Following glacial retreat, species could have recolonized the H imalaya westwards to different extents based on ecological traits (size, altitudinal migration) determining ability to deal with the more seasonal west. This produces both (1) a nested species richness pattern, and (2) correlations between ‘filtering’ autecological traits and distance. Such patterns should be replicated in other regions with historical climatic refugia; investigating nestedness along distance gradients from refugia would be a powerful tool in mapping biogeographical history, especially in separating historical effects from currently proposed energy‐productivity relationships.
True rosefinches (Aves: Carpodacus) are restricted to Eurasia, and 19 out of 25 species occur in the Sino-
Himalayas, making this the likely centre of origin. To test this hypothesis, suggested species splits had to be
evaluated and potential further cryptic diversity unravelled. A taxon-complete dated molecular phylogeny was
reconstructed using maximum-likelihood and Bayesian methods. Maximum-parsimony and likelihood approaches
were applied to deduce ancestral areas. Rosefinches, including the widespread Carpodacus erythrinus (Pallas,
1770), originated in south-west China (and the Himalayas) 14 Mya, and gave rise to a smaller clade consisting of
C. erythrinus, Haematospiza sipahi (Hodgson, 1836), and Chaunoproctus ferreorostris (Vigors, 1829), and a larger
clade with 22 species. The latter split into four major lineages through vicariance during the uplift of the
Himalayas. The suggested species splits of dubius from Carpodacus thura Bonaparte & Schlegel, 1850, formosanus
from Carpodacus vinaceus Verreaux, 1871, grandis from Carpodacus rhodochlamys Brandt, 1843, verreauxii from
Carpodacus rodopeplus (Vigors, 1831) (even polyphyletic) could be supported, whereas the suggested split of
severtzovi from Carpodacus rubicilla (Güldenstädt, 1775) appears to be too young, and should be considered
intraspecific. On the other hand, the central Asian lineage of Carpodacus synoicus Temminck, 1825 deserves
species rank [Carpodacus stolickae (Hume, 1874)]. The Carpodacus eos/pulcherrimus complex consists of four
lineages, pulcherrimus/argyrophrys and davidianus [Carpodacus pulcherrimus s.s. (Moore, 1856)], and eos and
waltoni [Carpodacus waltoni (Sharpe, 1905)].
The Quaternary climatic history of the Qinghai–Tibetan Plateau is reconstructed using Quaternary glacial geologic data. Four major glaciations are recognized: the Xixiabangma, Naynayxungla, Guxiang (the Penultimate), and Baiyu (the Last) Glaciation. These are dated at about 800–1170, 500–720, 130–300, and 10–70ka, respectively. These correspond to marine oxygen isotopic stages (MIS) 20∼36, 14∼18, 6∼8, and 2∼4. The most extensive glaciation occurred during the Naynayxungla Glaciation when there were many large ice caps, glacier complexes and great valley glaciers, covering a total area ⩾500,000km2. The Guxiang Glaciation (Stage 6) was characterized by valley glaciers, while during the Baiyu Glaciation (Stages 2–4) the glaciers were more restricted in extent and covered a total area of ∼350,000km2. These data show that glaciation become less extensive throughout the Quaternary and may have been the result of variations in climate in response to changing patterns of insolation related to changes in the Earth's orbit.
Aim Zoogeographic patterns in the Himalayas and their neighbouring Southeast Asian mountain ranges include elevational parapatry and ecological segregation, particularly among passerine bird species. We estimate timings of lineage splits among close relatives from the north Palaearctic, the Sino-Himalayan mountain forests and from adjacent Southeast Asia. We also compare phylogeographic affinities and timing of radiation among members of avian communities from different elevational belts.
Location East Asia.
Methods We reconstructed molecular phylogenies based on a mitochondrial marker (cytochrome b) and multilocus data sets for seven passerine groups: Aegithalidae, Certhiidae (Certhia), Fringillidae (Pyrrhula), Paridae (Periparus), Phylloscopidae, Regulidae and Timaliidae (Garrulax sensu lato). Molecular dating was carried out using a Bayesian approach applying a relaxed clock in beast. Time estimates were inferred from three independent calibrations based on either a fixed mean substitution rate or fixed node ages. The biogeographic history of each group was reconstructed using a parsimony-based approach.
Results Passerine radiation in Southeast Asia can be divided into roughly three major phases of separation events. We infer that an initial Miocene radiation within the Southeast Asian region included invasions of (sub)tropical faunal elements from the Indo-Burmese region to the Himalayan foothills and further successive invasions to Central Asia and Taiwan towards the early Pliocene. During two further Pliocene/Pleistocene phases, the subalpine mountain belt of the Sino-Himalayas was initially invaded by boreal species with clear phylogenetic affinities to the north Palaearctic taiga belt. Most terminal splits between boreal Himalayan/Chinese sister taxa were dated to the Pleistocene.
Main conclusions Extant patterns of elevational parapatry and faunal transition in the Sino-Himalayas originated from successive invasions from different climatic regions. The initiation of Southeast Asian passerine diversification and colonization of the Himalayan foothills in the mid-Miocene coincides with the postulated onset of Asian monsoon climate and the resulting floral and faunal turnovers. Patterns of elevational parapatry were established by southward invasions of boreal avifaunal elements to the subalpine Sino-Himalayan forest belt that were strongly connected to climate cooling towards the end of the Pliocene. Current patterns of allopatry and parapatry in boreal species (groups) were shaped through Pleistocene forest fragmentation in East Asia.
Un estudio reciente de Icterus, que analizó la evolución de un gran número de caracteres del plumaje sobre una filogenia basada en ADN mitocondrial, documentó una alta frecuencia de convergencias y reversiones evolutivas en caracteres del plumaje (Omland y Lanyon 2000). Aunque esos resultados son consistentes con otros estudios a menor escala que han reportado homoplasia en el plumaje, el genoma mitocondrial se hereda como un solo grupo de ligamiento, por lo que los datos mitocondriales representan sólo un árbol génico. Como el árbol de ADN mitocondrial podría no reflejar la verdadera historia evolutiva de un grupo, es aún posible que los caracteres de plumaje reflejen la filogenia real de las especies. Otras regiones de ADN que evolucionan rápidamente pueden proveer hipótesis filogenéticas independientes de utilidad para evaluar los árboles de genes mitocondriales. Un marcador filogenético nuevo, una región del gen nuclear ODC (“ornithine decarboxylase”) que va del exón 6 al exón 8, fue secuenciada para 10 especies de Icterus. El árbol resultante del gen nuclear reconstruye los mismos tres clados principales de Icterus que el árbol de ADNmt (Omland et al. 1999), apoyando la conclusión de que la evolución del plumaje en Icterus ha sido altamente homoplásica. Aunque la mayoría de los estudios que han empleado intrones documentan una resolución máxima al nivel de género o familia, ODC parece ofrecer algún grado de resolución filogenética para análisis infragenéricos. Sin embargo, este intrón claramente no se ha separado hasta la monofilia entre o dentro de especies estrechamente relacionadas.
The phylogeny of all species and nearly all subspecies of Seicercus and representatives of all subgenera in Phylloscopus was estimated based on two mitochondrial genes. According to the gene tree, and supported by non-molecular data, Seicercus belongs in three separate clades. Two of these include only taxa currently classified as Seicercus, while the third comprises S. xanthoschistos and P. occipitalis. These results suggest that both Seicercus and Phylloscopus are paraphyletic. The gene tree suggests two more cases of non-monophyly: (1) the ‘S. burkii complex’ is separated into two different clades, one of which also includes S. affinis and S. poliogenys; (2) two populations of S. affinis intermedius are more closely related to S. affinis ocularis than to a third population of intermedius. A recent proposal to split the ‘S. burkii complex’ into six species is corroborated, as is the recognition of the taxon cognitus as a colour morph of S. affinis intermedius. Our study also revealed unexpectedly large genetic divergences between three different populations of the monotypic S. poliogenys, indicating the presence of cryptic species. Our results underscore the importance of dense sampling at the specific and infraspecific levels in intrageneric phylogenetic studies.
The present study evaluated the degree of differentiation between closely-related species of Blyth's leaf warbler complex (Phylloscopus reguloides s.l.) and white-tailed leaf warbler complex (Phylloscopus davisoni s.l.) by molecular (cytochrome b and 16S rRNA) and bioacoustic markers (sonagraphic analysis of songs). Molecular phylogenetic results corroborate the recently suggested splittings of the two former taxa into three and two species, respectively. By contrast to previous opinion, differentiation of territorial songs parallels the genetic diversification in both groups. In the P. reguloides group, all recently established species can be distinguished by a characteristic song pattern. Regularly structured songs composed of repeated two- or three-note syllables were found in all species of the group, whereas trill songs with single notes repeated are unique to Phylloscopus claudiae. The phylogenetic relationships of Phylloscopus occipitalis are ambiguous among different molecular trees, but song pattern clearly corroborates a close relationship to the P. reguloides group. In the white-tailed leaf warbler group, songs are irregularly structured and often descending in frequency with exception of P. davisoni and Phylloscopus ogilviegranti disturbans. Song pattern corroborates the genetic affiliation of Phylloscopus hainanus and Phylloscopus xanthoschistos to the molecular white-tailed leaf warbler clade. All target species correspond to distinct acoustic clusters resulting from discriminant analysis of several spectral and structural song parameters. Linear correlation between genetic and acoustic differentiation (pairwise p-distances versus difference of discriminant functions) is significant within both groups, except for one case, in which discriminant function 1 was correlated with a spectral parameter (minimum frequency) only. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 584–600.
We sequenced a part of the mitochondrial cytochrome-b gene from the seven treecreeper species, including 18 subspecies, to reconstruct the phylogeny of the genus Certhia. Species status of all seven species could be affirmed. Certhia discolor, C. himalayana, C. nipalensis, and C. tianquanensis, the species with relatively small distribution ranges in southeast Asia and simple territorial song, are found at the base of all phylogenetic trees, although without good support. A comparatively recent sister species of C. tianquanensis is C. nipalensis, replacing C. discolor as closest relative. Certhia familiaris, C. brachydactyla and C. americana form a derived set of species (again only weak support). The closest relative of C. americana is C. brachydactyla. The C. familiaris subtree is deeply split into two well-defined population groups: a Eurasian group including populations in northern China (Qinling range northward and all Eurasia) and a Sino-Himalayan group (Himalayas and China excluding northern China). In accordance with acoustic characters, the three subspecies hodgsoni, mandellii and khamensis of the Sino-Himalayan group are combined and elevated to species rank: Certhia hodgsoni. Certhia discolor manipurensis is deeply split from nominate discolor as well, and is also promoted to species level. Within C. brachydactyla (western palearctic) and within C. hodgsoni (Himalayas, China) several populations form well-supported separate lineages that diverged quite recently and represent subspecies level. In all other species, molecular–genetic and vocal characters support traditional species delimitation.
Combining nuclear (nuDNA) and mitochondrial DNA (mtDNA) markers has improved the power of molecular data to test phylogenetic and phylogeographic hypotheses and has highlighted the limitations of studies using only mtDNA markers. In fact, in the past decade, many conflicting geographic patterns between mitochondrial and nuclear genetic markers have been identified (i.e. mito-nuclear discordance). Our goals in this synthesis are to: (i) review known cases of mito-nuclear discordance in animal systems, (ii) to summarize the biogeographic patterns in each instance and (iii) to identify common drivers of discordance in various groups. In total, we identified 126 cases in animal systems with strong evidence of discordance between the biogeographic patterns obtained from mitochondrial DNA and those observed in the nuclear genome. In most cases, these patterns are attributed to adaptive introgression of mtDNA, demographic disparities and sex-biased asymmetries, with some studies also implicating hybrid zone movement, human introductions and Wolbachia infection in insects. We also discuss situations where divergent mtDNA clades seem to have arisen in the absence of geographic isolation. For those cases where foreign mtDNA haplotypes are found deep within the range of a second taxon, data suggest that those mtDNA haplotypes are more likely to be at a high frequency and are commonly driven by sex-biased asymmetries and/or adaptive introgression. In addition, we discuss the problems with inferring the processes causing discordance from biogeographic patterns that are common in many studies. In many cases, authors presented more than one explanation for discordant patterns in a given system, which indicates that likely more data are required. Ideally, to resolve this issue, we see important future work shifting focus from documenting the prevalence of mito-nuclear discordance towards testing hypotheses regarding the drivers of discordance. Indeed, there is great potential for certain cases of mitochondrial introgression to become important natural systems within which to test the effect of different mitochondrial genotypes on whole-animal phenotypes.
Mitochondrial control region sequences from European populations of the blue tit Parus caeruleus were used to reveal the Pleistocene history and the post-glacial recolonization of Europe by the species. The southern subspecies, P. c. ogliastrae was found to represent a stable population with isolation-by-distance structure harboring a lot of genetic variation, and the northern subspecies P. c. caeruleus a recently bottlenecked and expanded population. We suggest that after the last Ice Ages, the subspecies have colonized Europe from two different southern refuges following previously proposed general recolonization routes from the Balkans to northern and Central Europe, and from the Iberian Peninsula north- and eastwards. The two subspecies form a wide secondary contact zone extending from southern Spain to southern France.
Babblers, family Timaliidae, have long been subject to debate on systematic position, family
limits and internal taxonomy. In this study, we use five molecular regions to estimate the
relationships among a large proportion of genera traditionally placed in Timaliidae. We
find good support for five main clades within this radiation, and propose a new classification,
dividing the babblers into the families Sylviidae and Timaliidae. Within the latter family,
four subfamilies are recognized: Zosteropinae, Timaliinae, Pellorneinae and Leiothrichinae.
Several taxa, previously not studied with molecular data, are phylogenetically placed within
Sylviidae or Timaliidae. This is, however, not the case for the genus Pnoepyga, for which we
propose the family name Pnoepygidae fam. n.
Species are the fundamental units of biology, ecology and conservation, and progress in these fields is therefore hampered by widespread taxonomic bias and uncertainty. Numerous operational techniques based on molecular or phenotypic data have been designed to overcome this problem, yet existing procedures remain subjective or inconsistent, particularly when applying the biological species concept. We address this issue by developing quantitative methods for a classic technique in systematic zoology, namely the use of divergence between undisputed sympatric species as a yardstick for assessing the taxonomic status of allopatric forms. We calculated mean levels of differentiation in multiple phenotypic characters – including biometrics, plumage and voice – for 58 sympatric or parapatric species-pairs from 29 avian families. We then used estimates of mean divergence to develop criteria for species delimitation based on data-driven thresholds. Preliminary tests show that these criteria result in relatively few changes to avian taxonomy in Europe, yet are capable of extensive reassignment of species limits in poorly known tropical regions. While we recognize that species limits are in many cases inherently arbitrary, we argue that our system can be applied to the global avifauna to deliver taxonomic decisions with a high level of objectivity, consistency and transparency.