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  • 1
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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
    SSG: 12
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  • 2
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    Dramatic niche shifts and morphological change in two insular bird species
    The Royal Society ; 2015
    In:  Royal Society Open Science Vol. 2, No. 3 ( 2015-03), p. 140364-
    Details
    In: Royal Society Open Science, The Royal Society, Vol. 2, No. 3 ( 2015-03), p. 140364-
    Abstract: Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis , from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii , from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla 's niche change has led to divergence in both structure and plumage.
    Type of Medium: Online Resource
    ISSN: 2054-5703
    URL: Article
    DOI: 10.1098/rsos.140364
    Language: English
    Publisher: The Royal Society
    Publication Date: 2015
    detail.hit.zdb_id: 2787755-3
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  • 3
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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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  • 4
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    Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex
    Springer Science and Business Media LLC ; 2019
    In:  BMC Evolutionary Biology Vol. 19, No. 1 ( 2019-12)
    Details
    In: BMC Evolutionary Biology, Springer Science and Business Media LLC, Vol. 19, No. 1 ( 2019-12)
    Type of Medium: Online Resource
    ISSN: 1471-2148
    URL: Article
    DOI: 10.1186/s12862-019-1481-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2041493-6
    detail.hit.zdb_id: 3053924-9
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  • 5
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    Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
    Oxford University Press (OUP) ; 2019
    In:  GigaScience Vol. 8, No. 5 ( 2019-05-01)
    Details
    In: GigaScience, Oxford University Press (OUP), Vol. 8, No. 5 ( 2019-05-01)
    Type of Medium: Online Resource
    ISSN: 2047-217X
    URL: Article
    DOI: 10.1093/gigascience/giz003
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2708999-X
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  • 6
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    A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture
    Springer Science and Business Media LLC ; 2022
    In:  Communications Biology Vol. 5, No. 1 ( 2022-08-23)
    Details
    In: Communications Biology, Springer Science and Business Media LLC, Vol. 5, No. 1 ( 2022-08-23)
    Abstract: The New World Vulture [ Coragyps ] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [ Coragyps ] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus , but genomic data shows occidentalis to be deeply nested within the South American clade of atratus . Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution.
    Type of Medium: Online Resource
    ISSN: 2399-3642
    URL: Article
    DOI: 10.1038/s42003-022-03811-0
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2919698-X
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  • 7
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    Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern
    Springer Science and Business Media LLC ; 2022
    In:  Heredity Vol. 128, No. 3 ( 2022-03), p. 159-168
    Details
    In: Heredity, Springer Science and Business Media LLC, Vol. 128, No. 3 ( 2022-03), p. 159-168
    Abstract: A taxonomic classification that accurately captures evolutionary history is essential for conservation. Genomics provides powerful tools for delimiting species and understanding their evolutionary relationships. This allows for a more accurate and detailed view on conservation status compared with other, traditionally used, methods. However, from a practical and ethical perspective, gathering sufficient samples for endangered taxa may be difficult. Here, we use museum specimens to trace the evolutionary history and species boundaries in an Asian oriole clade. The endangered silver oriole has long been recognized as a distinct species based on its unique coloration, but a recent study suggested that it might be nested within the maroon oriole-species complex. To evaluate species designation, population connectivity, and the corresponding conservation implications, we assembled a de novo genome and used whole-genome resequencing of historical specimens. Our results show that the silver orioles form a monophyletic lineage within the maroon oriole complex and that maroon and silver forms continued to interbreed after initial divergence, but do not show signs of recent gene flow. Using a genome scan, we identified genes that may form the basis for color divergence and act as reproductive barriers. Taken together, our results confirm the species status of the silver oriole and highlight that taxonomic revision of the maroon forms is urgently needed. Our study demonstrates how genomics and Natural History Collections (NHC) can be utilized to shed light on the taxonomy and evolutionary history of natural populations and how such insights can directly benefit conservation practitioners when assessing wild populations.
    Type of Medium: Online Resource
    ISSN: 0018-067X , 1365-2540
    URL: Article
    DOI: 10.1038/s41437-022-00499-0
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2006446-9
    detail.hit.zdb_id: 2423-5
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  • 8
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    Fine‐scale barriers to connectivity across a fragmented South‐East Asian landscape in six songbird species
    Wiley ; 2020
    In:  Evolutionary Applications Vol. 13, No. 5 ( 2020-05), p. 1026-1036
    Details
    In: Evolutionary Applications, Wiley, Vol. 13, No. 5 ( 2020-05), p. 1026-1036
    Abstract: Habitat fragmentation is a major extinction driver. Despite dramatically increasing fragmentation across the globe, its specific impacts on population connectivity across species with differing life histories remain difficult to characterize, let alone quantify. Here, we investigate patterns of population connectivity in six songbird species from Singapore, a highly fragmented tropical rainforest island. Using massive panels of genome‐wide single nucleotide polymorphisms across dozens of samples per species, we examined population genetic diversity, inbreeding, gene flow and connectivity among species along a spectrum of ecological specificities. We found a higher resilience to habitat fragmentation in edge‐tolerant and forest‐canopy species as compared to forest‐dependent understorey insectivores. The latter exhibited levels of genetic diversity up to three times lower in Singapore than in populations from contiguous forest elsewhere. Using dense genomic and geographic sampling, we identified individual barriers such as reservoirs that effectively minimize gene flow in sensitive understorey birds, revealing that terrestrial forest species may exhibit levels of sensitivity to fragmentation far greater than previously expected. This study provides a blueprint for conservation genomics at small scales with a view to identifying preferred locations for habitat corridors, flagging candidate populations for restocking with translocated individuals and improving the design of future reserves.
    Type of Medium: Online Resource
    ISSN: 1752-4571 , 1752-4571
    URL: Issue
    URL: Article
    DOI: 10.1111/eva.v13.5
    DOI: 10.1111/eva.12918
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2405496-3
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  • 9
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    A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins
    Wiley ; 2022
    In:  Molecular Ecology Resources Vol. 22, No. 7 ( 2022-10), p. 2672-2684
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 22, No. 7 ( 2022-10), p. 2672-2684
    Abstract: Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present‐day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high‐throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v22.7
    DOI: 10.1111/1755-0998.13660
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 10
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    No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus)
    MDPI AG ; 2019
    In:  Diversity Vol. 11, No. 4 ( 2019-04-15), p. 58-
    Details
    In: Diversity, MDPI AG, Vol. 11, No. 4 ( 2019-04-15), p. 58-
    Abstract: The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions.
    Type of Medium: Online Resource
    ISSN: 1424-2818
    URL: Article
    DOI: 10.3390/d11040058
    Language: English
    Publisher: MDPI AG
    Publication Date: 2019
    detail.hit.zdb_id: 2518137-3
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