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  • 101.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Quan, Qing
    Song, Gang
    Zhang, Ruiying
    Gao, Bin
    Lei, Fumin
    Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya.2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 3, p. 705-20Article in journal (Refereed)
    Abstract [en]

    China's Southwest Mountainous Region in Eastern Himalaya is a ‘biodiversity hotspot’ of global interest for conservation. Yet little is known about what has driven this unique diversity. The dramatic topography of the Southwest Mountainous Region resulting from the tectonic uplift during the late Pliocene leads to dramatic ecological stratification, which creates physical barriers to migration and isolates organisms into different subregions and mountain systems. This agrees with the observation that the phylogeographical patterns found in four species of birds (Alcippe morrisonia, Stachyridopsis ruficeps, Parus monticolus and Aegithalos concinnus) distributed in this region are characterized by deep splits between lineages that coalesce between 0.8 and 2.1 Ma. Unlike other regions at this latitude, the Southwest Mountainous Region was largely unaffected by the Pleistocene glaciations. Genetically isolated populations of these birds could thus be maintained throughout the Pleistocene in these rather stable montane environments. In comparison, we found radically different phylogeographical patterns in populations of the same four species distributed in the adjacent lowland, the Central China region. This region has a distinctly different geological history with dramatic, climate-induced shifts in vegetation during the Pleistocene. Here, we found a considerably less geographical structure in the genetic variation and a much younger coalescence time (0.3-0.7 Ma). We also found evidence of genetic bottlenecks during the glacial periods and gene flow during the interglacial expansions. We conclude that the high genetic diversity in the Southwest Mountainous Region results from a long-term in situ diversification within these evolutionary isolated and environment stable montane habitats.

  • 102.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Song, Gang
    Gao, Bin
    Quan, Qing
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Lei, Fumin
    The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography2015In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 42, no 1, p. 179-192Article in journal (Refereed)
    Abstract [en]

    Aim: East Asia is known for its exceptionally high biological diversity and endemism. Various geological and climatic events during the Pliocene and Pleistocene have been invoked to explain this high endemism, and these processes have had different impacts on different organisms. Herein, we investigate the relative role of these historical processes in the genetic evidence for endemism of intraspecific lineages of two East Asian species: the grey-cheeked fulvetta (Alcippe morrisonia) and the red-headed tree babbler (Stachyridopsis ruficeps).

    Location: East Asia.

    Methods: We studied the genetic structure based on mitochondrial and nuclear DNA and evaluated the phylogeographical lineages using coalescent species tree approaches. The influences of different historical processes on diversification among phylogeographical lineages were analysed using coalescent models. We tested correlations between ecological divergence and phylogeographical splits.

    Results: The genetic structure analysis and species tree estimation revealed three deeply divergent lineages within both species. One lineage is endemic to the mountains of Southwest China and the other to Taiwan. Coalescent simulations suggested that lineage diversification mostly occurred during the late Pliocene. Within this time frame, uplift of the mountains of Southwest China and formation of the island of Taiwan are geological events consistent with the geographical isolation and ecological niche divergence of these phylogeographical lineages.

    Main conclusions: Our results suggest that the main driver of avian endemism in East Asia was the formation of new montane and island habitats following the uplift of the mountains of Southwest China and formation of the island of Taiwan in the Pliocene. However, the populations in the two regions were affected differently by the climatic oscillations during the Pleistocene. The mountains of Southwest China were climatically stable during glaciations,allowing populations to persist throughout the Pleistocene and maintain their genetic uniqueness. In contrast, glaciations resulted in lowered sea levels, allowing dispersal between the island of Taiwan and mainland China, thus obscuring the genetic endemism of the Taiwanese populations.

  • 103.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Tian, Shilin
    Han, Nanjian
    Zhao, Hongwei
    Gao, Bin
    Fu, Jun
    Cheng, Yalin
    Song, Gang
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zhang, Yong E.
    Wang, Dawei
    Quan, Qing
    Jiang, Zhi
    Li, Ruiquang
    Lei, Fumin
    Genetic responses to seasonalvariation in altitudinal stress: whole-genome resequencing ofgreat tit in eastern Himalayas2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 14256Article in journal (Refereed)
    Abstract [en]

    Species that undertake altitudinal migrations are exposed to a considerable seasonal variationin oxygen levels and temperature. How they cope with this was studied in a population of greattit (Parus major) that breeds at high elevations and winters at lower elevations in the easternHimalayas. Comparison of population genomics of high altitudinal great tits and those living inlowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (aminosugar, nucleotide sugar metabolism and insulin signaling pathways) and hypoxia response (PI3K-akt,mTOR and MAPK signaling pathways) in the high altitudinal population. The PI3K-akt, mTOR andMAPK pathways modulate the hypoxia-inducible factors, HIF-1α and VEGF protein expression thusindirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategiesobserved in high altitudinal great tits differ from those described in a closely related species onthe Tibetan Plateau, the sedentary ground tit (Parus humilis). This species has enhanced selectionin lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparativepopulation genomics also revealed selection for larger body size in high altitudinal great tits.

  • 104.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Zhao, Hongwei
    Han, Naijian
    Zhou, Guangyu
    Song, Gang
    Gao, Bin
    Tian, Shilin
    Zhang, Jinbo
    Zhang, Ruiying
    Meng, Xuehong
    Zhang, Yuan
    Zhang, Yong
    Zhu, Xiaojia
    Wang, Wenjuan
    Lambert, David
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Subramanian, Sankar
    Yeung, Carol
    Zhu, Hongmei
    Jiang, Zhi
    Li, Ruiqiang
    Lei, Fumin
    Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.2013In: Nature communications, ISSN 2041-1723, Vol. 4, p. 2071-Article in journal (Refereed)
    Abstract [en]

    The ground tit (Parus humilis) is endemic to the Tibetan plateau. It is a member of family Paridae but it was long thought to be related to the ground jays because of their morphological similarities. Here we present the ground tit's genome and re-sequence two tits and one ground jay, to clarify this controversially taxonomic status and uncover its genetic adaptations to the Tibetan plateau. Our results show that ground tit groups with two tits and it diverges from them between 7.7 and 9.9 Mya. Compared with other avian genomes, ground tit shows expansion in genes linked to energy metabolism and contractions in genes involved in immune and olfactory perception. We also found positively selected and rapidly evolving genes in hypoxia response and skeletal development. These results indicated that ground tit evolves basic strategies and 'tit-to-jay' change for coping with the life in an extreme environment.

  • 105.
    Sangster, George
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Roselaar, Cees S.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G. P.
    Swedish Museum of Natural History, Research Division.
    Sillem’s Mountain Finch Leucosticte sillemi is a valid species of rosefinch (Carpodacus, Fringillidae)2016In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 158, no 1, p. 184-189Article in journal (Refereed)
  • 106. Sodhi, Navjot S.
    et al.
    Astuti, Dwi
    Diesmos, Arvin C.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fernandopulle, Neil
    Kotagama, Sarath
    Kudavidanege, Enoka
    Lim, Haw Chuan
    Lee, Benjamin
    Lim, Susan L. H.
    Lin, Yangchen
    Lohman, David J.
    Meckvichai, Wina
    Miranda, Hector
    Moyle, Robert G.
    Ong, Perry
    Pan, Khang Aun
    Prawiradilaga, Dewi
    Rahman, Mustafa Abdul
    Rahmani, Asad
    Sheldon, Frederick H.
    Stoeckle, Mark Y.
    Sulandari, Sri
    Wang, Luan Keng
    Winker, Kevin
    Barcoding Indo-Malayan birds2007In: The Raffles bulletin of zoology, ISSN 0217-2445, Vol. 55, no 2, p. 397-398Article in journal (Other academic)
  • 107. Song, Gang
    et al.
    Zhang, Ruiying
    Qu, Yanhua
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Wang, Zhiheng
    Kristin, Anton
    Alström, Per
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Lambert, David M
    Fjeldså, Jon
    Lei, Fumin
    A zoogeographical boundary between the Palaearctic and Sino-Japanese realms documented by consistent north/south phylogeographical divergences in three woodland birds in eastern China2016In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 43, p. 2099-2112Article in journal (Refereed)
    Abstract [en]

    Aim.The location of zoogeographical boundaries in eastern China has longbeen the subject of debate. To identify any north/south genetic divergence between the Palaearctic and Sino-Japanese realms proposed by previous studies, we conducted a comparative phylogeographical study involving three passerine species with wide latitudinal distributions in eastern China.Location. Eastern China.Methods.Two mitochondrial genes and three nuclear introns were amplified and sequenced. Population structures were analysed using intra-specific phylogeny,tcs networks, AMOVA and structure inferences. We tested for evidence of genetic barriers based on pairwise differences. Lineage divergences, demographic dynamics and gene flow between lineages were estimated using Bayesian methods.Results. A congruent north/south phylogeographical divergence was identified for three species. A geographical barrier was inferred at c.40°N in easternChina. The population sizes of the northern and southern lineages have both been stable through the late Pleistocene, while multiple divergences were inferred during the early and middle Pleistocene.Main conclusions. Our results suggest a general phylogeographical break in north-eastern China, coinciding with the Palaearctic/Sino-Japanese boundary. Physical blocking of the Yan Mountains and fragmentation of suitable habitat during glacial stages between the north and south probably acted together to provide long-lasting barrier effects. Our comparative phylogeographical approach demonstrates that the Palaearctic/Sino-Japanese boundary may represent a gene-flow barrier even within widespread species.

  • 108. Sundberg, Per
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Bachmann, Lutz
    Zoologica Scripta in the dynamic field of systematics2013In: Zoologica Scripta, Vol. 42, no 6, p. 551-552Article in journal (Other academic)
  • 109. Sundberg, Per
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Bachmann, Lutz
    Slagsvold, Tore
    Jacobson, Carl-Olof
    Untitled2007In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 36, no 3, p. 229-230Article in journal (Other academic)
  • 110. Zhang, Fucheng
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zhou, Zhonghe
    Description of a new enantiornithine bird from the Early Cretaceous of Hebei, northern China2004In: Canadian journal of earth sciences (Print), ISSN 0008-4077, E-ISSN 1480-3313, Vol. 41, no 9, p. 1097-1107Article in journal (Refereed)
    Abstract [en]

    This paper describes a new enantiornithine fossil bird, Vescornis hebeiensis, nov. sp. from the Early Cretaceous of China. We refer Vescornis to the crown clade Euenantiornithes based on several characteristics observed in the thoracic girdle and wing. Vescornis also exhibits characteristics that separate it from other enantiornithine birds, such as the short alular phalanx, the vestigial manual claws, and the well-developed and long foot claws. These features suggest an adaptation towards an improved flight capability, while the ability of Vescornis to climb is reduced compared with many other enantiornithine birds.

  • 111. Zhang, Ruiying
    et al.
    Song, Gang
    Qu, Yanhua
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Alström, Per
    Ramos, Raül
    Xing, Xiaoying
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fjeldså, Jon
    Wang, Haitao
    Yang, Xiaojun
    Kristin, Anton
    Shestopalov, Alexander M
    Choe, Jae Chun
    Lei, Fumin
    Comparative phylogeography of two widespread magpies: importance of habitat preference and breeding behavior on genetic structure in China.2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, no 2, p. 562-72Article in journal (Refereed)
    Abstract [en]

    Historical geological events and climatic changes are believed to have played important roles in shaping the current distribution of species. However, sympatric species may have responded in different ways to such climatic fluctuations. Here we compared genetic structures of two corvid species, the Azure-winged Magpie Cyanopica cyanus and the Eurasian Magpie Pica pica, both widespread but with different habitat dependence and some aspects of breeding behavior. Three mitochondrial genes and two nuclear introns were used to examine their co-distributed populations in East China and the Iberian Peninsula. Both species showed deep divergences between these two regions that were dated to the late Pliocene/early Pleistocene. In the East Chinese clade of C. cyanus, populations were subdivided between Northeast China and Central China, probably since the early to mid-Pleistocene, and the Central subclade showed a significant pattern of isolation by distance. In contrast, no genetic structure was found in the East China populations of P. pica. We suggest that the different patterns in the two species are at least partly explained by ecological differences between them, especially in habitat preference and perhaps also breeding behavior. These dissimilarities in life history traits might have affected the dispersal and survival abilities of these two species differently during environmental fluctuations.

  • 112. Zuccon, Dario
    et al.
    Cibois, Alice
    Pasquet, Eric
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Nuclear and mitochondrial sequence data reveal the major lineages of starlings, mynas and related taxa.2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 41, no 2, p. 333-44Article in journal (Refereed)
    Abstract [en]

    We investigated the phylogenetic relationships among the major lineages of the avian family Sturnidae and their placement within the Muscicapoidea clade using two nuclear (RAG-1 and myoglobin) and one mitochondrial gene (ND2). Among Muscicapoidea, we recovered three clades corresponding to the families Cinclidae, Muscicapidae and Sturnidae (sensu [Sibley, C.G., Monroe Jr., B.L., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT]). Within the sturnoid lineage Mimini and Sturnini are sister groups, with Buphagus basal to them. We identified three major lineages of starlings: the Philippine endemic genus Rhabdornis, an Oriental-Australasian clade (genera Scissirostrum, Gracula, Mino, Ampeliceps, Sarcops, Aplonis), and an Afrotropical-Palaearctic clade (all African taxa, Sturnus and Acridotheres). We discuss the biogeographic implications of our findings and suggest an Asiatic origin for this family. The congruence between the age of major clades, estimated by NPRS, and palaeoclimatic data present evidence for the role of climatic changes in shaping present day distribution of the group.

  • 113.
    Zuccon, Dario
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    A multi-gene phylogeny disentangles the chat-flycatcher complex (Aves: Muscicapidae)2010In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 39, no 3, p. 213-224Article in journal (Refereed)
  • 114. Zuccon, Dario
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Molecular and morphological evidences place the extinct New Zealand endemic Turnagra capensis in the Oriolidae.2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 62, no 1, p. 414-26Article in journal (Refereed)
    Abstract [en]

    The affinities of Piopio Turnagra capensis, an extinct New Zealand passerine, remain poorly known. It has been included into or associated with several bird families (Calleatidae, Cracticidae, Pachycephalidae, Ptilonorhynchidae, Turdidae), often on tenuous grounds. We reassessed Turnagra phylogenetic relationships using nuclear and mitochondrial sequences and a set of morphological and behavioural traits. Molecular and phenotypic characters strongly suggest a novel hypothesis, congruently placing Turnagra in Oriolidae, a highly dispersive corvoid family distributed from the Austro-Papuan landmass to Eurasia and Africa, but missing from the Pacific islands. We show also that the published molecular support to link Turnagra with Ptilonorhynchidae was biased by the use of incorrect genetic data and weak analyses.

  • 115. Zuccon, Dario
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    The Monticola rock-thrushes: phylogeny and biogeography revisited.2010In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 55, no 3, p. 901-10Article in journal (Refereed)
    Abstract [en]

    We investigated the phylogenetic relationships within the Monticola rock-thrushes, an open-habitat genus inhabiting a large part of the Old World. Our results support one Oriental clade and one clade including African, Malagasy and Eurasian taxa. The biogeographic reconstruction obtained with the dispersal-vicariance analysis suggested Southern Africa plus Palearctic as the Monticola ancestral area. Our phylogenetic hypothesis suggests also some taxonomic changes. The polytypic Monticola solitarius includes two reciprocally monophyletic clades that should be recognized as full species, M. solitarius s.s. and M. philippensis. With the exclusion of the south-western population, M. imerinus, all other Malagasy rock-thrush populations should be merged in the monotypic, albeit polymorphic, M. sharpei. The genus Thamnolaea is shown to be non-monophyletic, with T. semirufa being part of the Monticola radiation, while T. cinnamomeiventris is related to other chat species inhabiting open-habitats. We demonstrate that a previous phylogenetic hypothesis for the rock-thrushes was flawed by the inclusion of contaminated sequences obtained from study-skins and we suggest some working guidelines to improve the reliability of the sequences obtained from old or degraded DNA.

  • 116.
    Zuccon, Dario
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    The phylogenetic position of the Black-collared Bulbul Neolestes torquatus2010In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 152, no 2, p. 386-392Article in journal (Refereed)
  • 117.
    Zuccon, Dario
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Pasquet, Eric
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Phylogenetic relationships among Palearctic-Oriental starlings and mynas (genera Sturnus and Acridotheres: Sturnidae)2008In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 37, no 5, p. 469-481Article in journal (Refereed)
  • 118. Zuccon, Dario
    et al.
    Prŷs-Jones, Robert
    Rasmussen, Pamela C
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    The phylogenetic relationships and generic limits of finches (Fringillidae).2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 62, no 2, p. 581-96Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships among the true finches (Fringillidae) have been confounded by the recurrence of similar plumage patterns and use of similar feeding niches. Using a dense taxon sampling and a combination of nuclear and mitochondrial sequences we reconstructed a well resolved and strongly supported phylogenetic hypothesis for this family. We identified three well supported, subfamily level clades: the Holoarctic genus Fringilla (subfamly Fringillinae), the Neotropical Euphonia and Chlorophonia (subfamily Euphoniinae), and the more widespread subfamily Carduelinae for the remaining taxa. Although usually separated in a different family-group taxon (Drepanidinae), the Hawaiian honeycreepers are deeply nested within the Carduelinae and sister to a group of Asian Carpodacus. Other new relationships recovered by this analysis include the placement of the extinct Chaunoproctus ferreorostris as sister to some Asian Carpodacus, a clade combining greenfinches (Carduelis chloris and allies), Rhodospiza and Rhynchostruthus, and a well-supported clade with the aberrant Callacanthis and Pyrrhoplectes together with Carpodacus rubescens. Although part of the large Carduelis-Serinus complex, the poorly known Serinus estherae forms a distinct lineage without close relatives. The traditionally delimited genera Carduelis, Serinus, Carpodacus, Pinicola and Euphonia are polyphyletic or paraphyletic. Based on our results we propose a revised generic classification of finches and describe a new monotypic genus for Carpodacus rubescens.

123 101 - 118 of 118
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