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  • 1
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    Great journey of Great Tits (Parus major group): Origin, diversification and historical demographics of a broadly distributed bird lineage
    Wiley ; 2020
    In:  Journal of Biogeography Vol. 47, No. 7 ( 2020-07), p. 1585-1598
    Details
    In: Journal of Biogeography, Wiley, Vol. 47, No. 7 ( 2020-07), p. 1585-1598
    Abstract: The Pleistocene glacial cycles play a prominent role in shaping phylogeographical patterns of organisms, while few studies have focused on the regional difference of glacial effects. By acquiring comprehensive knowledge of the origin, diversification and historical demography of an intensively studied passerine species complex, Great Tit, we aim to test the regional variation of the Late Pleistocene glaciation impacts on this widely distributed bird lineage. Location Eurasia and associated peninsulas and archipelagos. Taxa Parus major species complex. Methods Phylogeny, divergence times and demographic dynamics were estimated with Bayesian methods. Population structure, genetic diversity and correlation between genetic and physical distances were estimated based on mtDNA variation. Glacial‐to‐present distributional changes were assessed via ecological niche modelling (ENM). Results Five major clades (Central Asia, Eastern Asia, Eastern Himalaya, Northern and Western Eurasia and Southern Asia) were detected, with divergence times ranging 1.57–0.50 million years ago. Genetic diversity values and Bayesian skyline plots suggest that the three eastern clades had a deeper population history. A more complex geographic structure was observed in East Asia. Demographic expansion during the last glacial cycle was indicated for all five clades. ENM results showed broad conservatism of traits related to climate tolerances, and generally broader and more continuous distributional patterns under glacial conditions. Main Conclusions The Great Tit complex probably originated in Southeast Asia. Geographic barriers, such as the deserts of Central Asia and the Qinghai–Tibet Plateau appear to be related to the lineage divergence. Late Pleistocene climate cycles influenced both demographic dynamics and divergence, especially in terms of east–west differences in relation to geographic complexity.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    URL: Article
    DOI: 10.1111/jbi.v47.7
    DOI: 10.1111/jbi.13863
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020428-0
    detail.hit.zdb_id: 188963-1
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  • 2
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    Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late‐Pleistocene demographic expansion across the Northern Hemisphere
    Wiley ; 2018
    In:  Journal of Avian Biology Vol. 49, No. 2 ( 2018-02)
    Details
    In: Journal of Avian Biology, Wiley, Vol. 49, No. 2 ( 2018-02)
    Abstract: Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli . Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica .
    Type of Medium: Online Resource
    ISSN: 0908-8857 , 1600-048X
    URL: Issue
    URL: Article
    DOI: 10.1111/jav.2018.v49.i2
    DOI: 10.1111/jav.01612
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2028018-X
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  • 3
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    A zoogeographical boundary between the Palaearctic and Sino‐Japanese realms documented by consistent north/south phylogeographical divergences in three woodland birds in eastern China
    Wiley ; 2016
    In:  Journal of Biogeography Vol. 43, No. 11 ( 2016-11), p. 2099-2112
    Details
    In: Journal of Biogeography, Wiley, Vol. 43, No. 11 ( 2016-11), p. 2099-2112
    Abstract: The location of zoogeographical boundaries in eastern China has long been 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 eastern China. 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.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    URL: Article
    DOI: 10.1111/jbi.2016.43.issue-11
    DOI: 10.1111/jbi.12758
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2020428-0
    detail.hit.zdb_id: 188963-1
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  • 4
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    The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography
    Wiley ; 2015
    In:  Journal of Biogeography Vol. 42, No. 1 ( 2015-01), p. 179-192
    Details
    In: Journal of Biogeography, Wiley, Vol. 42, No. 1 ( 2015-01), p. 179-192
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    URL: Article
    DOI: 10.1111/jbi.2014.42.issue-1
    DOI: 10.1111/jbi.12407
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 2020428-0
    detail.hit.zdb_id: 188963-1
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  • 5
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    The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai–Tibet Plateau
    Proceedings of the National Academy of Sciences ; 2021
    In:  Proceedings of the National Academy of Sciences Vol. 118, No. 13 ( 2021-03-30)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 13 ( 2021-03-30)
    Abstract: Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai–Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL , we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2012398118
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 6
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    Long‐term isolation and stability explain high genetic diversity in the Eastern Himalaya
    Wiley ; 2014
    In:  Molecular Ecology Vol. 23, No. 3 ( 2014-02), p. 705-720
    Details
    In: Molecular Ecology, Wiley, Vol. 23, No. 3 ( 2014-02), p. 705-720
    Abstract: 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 ( A lcippe morrisonia , S tachyridopsis ruficeps , P arus monticolus and A egithalos 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.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.2014.23.issue-3
    DOI: 10.1111/mec.12619
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
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  • 7
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    Alpine burrow-sharing mammals and birds show similar population-level climate change risks
    Springer Science and Business Media LLC ; 2023
    In:  Nature Climate Change Vol. 13, No. 9 ( 2023-09), p. 990-996
    Details
    In: Nature Climate Change, Springer Science and Business Media LLC, Vol. 13, No. 9 ( 2023-09), p. 990-996
    Type of Medium: Online Resource
    ISSN: 1758-678X , 1758-6798
    URL: Article
    DOI: 10.1038/s41558-023-01772-8
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2603450-5
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  • 8
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    Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows
    Oxford University Press (OUP) ; 2020
    In:  National Science Review Vol. 7, No. 1 ( 2020-01-01), p. 113-127
    Details
    In: National Science Review, Oxford University Press (OUP), Vol. 7, No. 1 ( 2020-01-01), p. 113-127
    Abstract: Known as the ‘third polar region’, the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. Previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial phase of highland adaptation remain poorly understood. We studied a human commensal, the Eurasian Tree Sparrow, which has followed human agriculture to the Qinghai-Tibet Plateau. Despite strong phenotypic differentiation at multiple levels, in particular in muscle-related phenotypes, highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years. In a one-month acclimation experiment investigating phenotypic plasticity, we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes. Through population genetic analyses, we identified a signature of polygenic adaptation, whereby shifts in allele frequencies are spread across multiple loci, many of which are associated with muscle-related processes. Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution, shedding light on early stages of adaptive evolution to a novel environment.
    Type of Medium: Online Resource
    ISSN: 2095-5138 , 2053-714X
    URL: Article
    DOI: 10.1093/nsr/nwz138
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2745465-4
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  • 9
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    Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas
    Springer Science and Business Media LLC ; 2015
    In:  Scientific Reports Vol. 5, No. 1 ( 2015-09-25)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 5, No. 1 ( 2015-09-25)
    Abstract: Species that undertake altitudinal migrations are exposed to a considerable seasonal variation in oxygen levels and temperature. How they cope with this was studied in a population of great tit ( Parus major ) that breeds at high elevations and winters at lower elevations in the eastern Himalayas. Comparison of population genomics of high altitudinal great tits and those living in lowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (amino sugar, 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 and MAPK pathways modulate the hypoxia-inducible factors, HIF-1α and VEGF protein expression thus indirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategies observed in high altitudinal great tits differ from those described in a closely related species on the Tibetan Plateau, the sedentary ground tit ( Parus humilis ). This species has enhanced selection in lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparative population genomics also revealed selection for larger body size in high altitudinal great tits.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/srep14256
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2615211-3
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  • 10
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    Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau
    Springer Science and Business Media LLC ; 2013
    In:  Nature Communications Vol. 4, No. 1 ( 2013-07-01)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 4, No. 1 ( 2013-07-01)
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/ncomms3071
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2013
    detail.hit.zdb_id: 2553671-0
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