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Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
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Wolfgramm H, Martens J, Töpfer T, Vamberger M, Pathak A, Stuckas H, Päckert M. Asymmetric allelic introgression across a hybrid zone of the coal tit ( Periparus ater) in the central Himalayas. Ecol Evol 2021; 11:17332-17351. [PMID: 34938512 PMCID: PMC8668783 DOI: 10.1002/ece3.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/07/2022] Open
Abstract
In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (Periparus ater) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western "spot-winged tit" (P. a. melanolophus) and Eastern Himalayan coal tits (P. a. aemodius) occur across a narrow range of <100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern P. a. aemodius into far western populations of phenotypic P. a. melanolophus but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.
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Affiliation(s)
- Hannes Wolfgramm
- Senckenberg Natural History Collections DresdenDresdenGermany
- Present address:
Department of Functional GenomicsInterfaculty Institute of Genetics and Functional GenomicsUniversity Medicine GreifswaldGreifswaldGermany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE)Johannes Gutenberg UniversityMainzGermany
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity ChangeZoological Research Museum Alexander KoenigBonnGermany
| | | | - Abhinaya Pathak
- Department of National Parks and Wildlife ConservationKathmanduNepal
| | - Heiko Stuckas
- Senckenberg Natural History Collections DresdenDresdenGermany
| | - Martin Päckert
- Senckenberg Natural History Collections DresdenDresdenGermany
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Javaheri Tehrani S, Kvist L, Mirshamsi O, Ghasempouri SM, Aliabadian M. Genetic divergence, admixture and subspecific boundaries in a peripheral population of the great tit, Parus major (Aves: Paridae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Secondary contact zones have been formed between several pairs of avian species and subspecies in northern and north-eastern Iran during the post-Pleistocene and Holocene periods. Three subspecies groups out of the four in the great tit (Parus major), major, bokharensis and cinereus, are believed to have come into local or regional secondary contact in north-eastern Iran. Parus major intermedius is also known from this region and has long been suggested to have a hybrid origin from hybridization between the yellow western (major) subspecies group and the grey-coloured eastern (bokharensis or cinereus) subspecies group based on its intermediate plumage coloration. Here, we investigated the evidence of intergradation between subspecies groups and the evolutionary origin of P. m. intermedius using mitochondrial DNA sequences and microsatellites, and approximate Bayesian computation to test competing scenarios for the demographic history of the populations. Our analyses indicate a divergence origin for intermedius that resulted from expansion of the major subspecies group. Low mitochondrial diversity and high genetic differentiation in comparison with central populations suggest that intermedius is a peripheral population. Microsatellite data show no signs of nuclear admixture between the bokharensis and major subspecies groups. However, one phenotypically intermedius specimen had bokharensis mtDNA and major nuclear DNA in the assumed hybrid zone (Lotf Abad), supporting past introgression.
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Affiliation(s)
- Sahar Javaheri Tehrani
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran
| | - Laura Kvist
- Ecology and Genetics Research Unit, University of Oulu, POB 3000, 90014 Oulu, Finland
| | - Omid Mirshamsi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran
- Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran
| | - Seyed Mahmoud Ghasempouri
- Department of Environmental Science, Natural Resources and Marine Sciences Faculty, Tarbiat Modares University, Noor POB 46414-356, Iran
| | - Mansour Aliabadian
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran
- Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran
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Pârâu LG, Wink M. Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review. JOURNAL OF ORNITHOLOGY 2021; 162:937-959. [PMID: 34007780 PMCID: PMC8118378 DOI: 10.1007/s10336-021-01893-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10336-021-01893-x.
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Affiliation(s)
- Liviu G. Pârâu
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
- Present Address: SARS-CoV-2 Data Evaluation Office, Eurofins Genomics Europe Applied Genomics GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
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Albrecht F, Hering J, Fuchs E, Illera JC, Ihlow F, Shannon TJ, Collinson JM, Wink M, Martens J, Päckert M. Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns of Ibero-Maghrebian and Cyrenaican populations. PLoS One 2020; 15:e0230151. [PMID: 32191719 PMCID: PMC7082076 DOI: 10.1371/journal.pone.0230151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/22/2020] [Indexed: 11/19/2022] Open
Abstract
The Mediterranean Basin represents a Global Biodiversity Hotspot where many organisms show high inter- and intraspecific differentiation. Extant phylogeographic patterns of terrestrial circum-Mediterranean faunas were mainly shaped through Pleistocene range shifts and range fragmentations due to retreat into different glacial refugia. Thus, several extant Mediterranean bird species have diversified by surviving glaciations in different hospitable refugia and subsequently expanded their distribution ranges during the Holocene. Such a scenario was also suggested for the Eurasian Wren (Nannus troglodytes) despite the lack of genetic data for most Mediterranean subspecies. Our phylogenetic multi-locus analysis comprised 18 out of 28 currently accepted subspecies of N. troglodytes, including all but one subspecies which are present in the Mediterranean Basin. The resulting phylogenetic reconstruction dated the onset of the entire Holarctic radiation of three Nannus species to the early Pleistocene. In the Eurasian Wren, two North African subspecies represented separate basal lineages from the Maghreb (N. t. kabylorum) and from the Libyan Cyrenaica (N. t. juniperi), being only distantly related to other Mediterranean populations. Although N. troglodytes appeared to be paraphyletic with respect to the Nearctic Winter Wren (N. hiemalis), respective nodes did not receive strong statistical support. In contrast, paraphyly of the Ibero-Maghrebian taxon N. t. kabylorum was strongly supported. Southern Iberian populations of N. t. kabylorum did not clade with Maghrebian populations of the same subspecies but formed a sister clade to a highly diverse European clade (including nominate N. t. troglodytes and eight further taxa). In accordance with a pattern also found in other birds, Eurasian populations were split into a western clade (Europe, Caucasus) and an eastern clade (Central Asia, Sino-Himalayas, East Asia). This complex phylogeographic pattern revealed cryptic diversification in N. troglodytes, especially in the Iberio-Maghrebian region.
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Affiliation(s)
- Frederik Albrecht
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System Research, Dresden, Saxony, Germany
- * E-mail:
| | - Jens Hering
- Verein Sächsischer Ornithologen e.V., Limbach-Oberfrohna, Saxony, Germany
| | - Elmar Fuchs
- Verein Sächsischer Ornithologen e.V., Weimar, Thuringia, Germany
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Asturias, Spain
| | - Flora Ihlow
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System Research, Dresden, Saxony, Germany
| | - Thomas J. Shannon
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - J. Martin Collinson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Rhineland-Palatinate, Germany
| | - Martin Päckert
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System Research, Dresden, Saxony, Germany
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Zuccon D, Pons JM, Boano G, Chiozzi G, Gamauf A, Mengoni C, Nespoli D, Olioso G, Pavia M, Pellegrino I, Raković M, Randi E, Rguibi Idrissi H, Touihri M, Unsöld M, Vitulano S, Brambilla M. Type specimens matter: new insights on the systematics, taxonomy and nomenclature of the subalpine warbler (Sylvia cantillans) complex. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractWe revise the taxonomy of the Sylvia cantillans complex, a group of phenotypically distinct warblers with mainly parapatric distributions around a large part of the Mediterranean basin. We redefine the species limits using a combination of mitochondrial and nuclear markers and we objectively link available names to the genetically defined lineages by genotyping the surviving type specimens. In addition, the study of archival documents clarifies the exact composition of type series and provides further evidence for the identification of lost types. These results support the recognition of three species-level taxa: Moltoni’s warbler, Sylvia subalpina (north-central Italy, Corsica, Sardinia and the Balearics); the western subalpine warbler, S. iberiae (North Africa, Iberia, southern France and extreme north-west Italy); and the eastern subalpine warbler, S. cantillans, with subspecies S. cantillans cantillans (southern Italy, Sicily) and S. cantillans albistriata (Balkans, Greece, western Turkey).
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Affiliation(s)
- Dario Zuccon
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR7205 CNRS MNHN UPMC EPHE Sorbonne Université, Muséum National d’Histoire Naturelle, Paris, France
| | - Jean-Marc Pons
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR7205 CNRS MNHN UPMC EPHE Sorbonne Université, Muséum National d’Histoire Naturelle, Paris, France
| | | | | | - Anita Gamauf
- Natural History Museum Vienna, Bird Collection, Vienna, Austria
| | - Chiara Mengoni
- Area per la Genetica della Conservazione, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO), Italy
| | - Davide Nespoli
- Area per la Genetica della Conservazione, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO), Italy
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | | | - Marco Pavia
- Museo di Geologia e Paleontologia, Dipartimento di Scienze della Terra, Università degli Studi di Torino, Torino, Italy
| | - Irene Pellegrino
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Marko Raković
- Natural History Museum of Belgrade, Belgrade, Serbia
| | - Ettore Randi
- Dipartimento Scienze Biologiche, Geologiche ed Ambientali, Università di Bologna, Bologna, Italy
- Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Hamid Rguibi Idrissi
- École Supérieure de Technologie, Université Ibn Zohr, Laâyoune, Morocco
- Laboratoire ‘Biodiversité, Écologie et Génome’, Faculté des Sciences de Rabat, Rabat, Morocco
| | - Moez Touihri
- Laboratoire de Recherche de Diversité, Gestion et Conservation des Systèmes, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Markus Unsöld
- Bavarian State Collection of Zoology, Section Ornithology, Munich, Germany
| | | | - Mattia Brambilla
- Fondazione Lombardia per l’Ambiente, Settore biodiversità e aree protette, Seveso (MB), Italy
- Museo delle Scienze, Sezione Zoologia dei Vertebrati, Corso del Lavoro e della Scienza 3, Trento, Italy
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Esquer-Garrigos Y, Streiff R, Party V, Nidelet S, Navascués M, Greenfield MD. Pleistocene origins of chorusing diversity in Mediterranean bush-cricket populations ( Ephippiger diurnus). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Yareli Esquer-Garrigos
- CBGP, INRA, CIRAD, IRD, Université de Montpellier, Montpellier, France
- DGIMI, INRA, Université de Montpellier, Montpellier, France
- Université de Tours, Tours, France
| | - Réjane Streiff
- CBGP, INRA, CIRAD, IRD, Université de Montpellier, Montpellier, France
- DGIMI, INRA, Université de Montpellier, Montpellier, France
| | | | - Sabine Nidelet
- CBGP, INRA, CIRAD, IRD, Université de Montpellier, Montpellier, France
| | | | - Michael D Greenfield
- Université de Tours, Tours, France
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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Pons JM, Cibois A, Fournier J, Fuchs J, Olioso G, Thibault JC. Gene flow and genetic divergence among mainland and insular populations across the south-western range of the Eurasian treecreeper ( Certhia familiaris, Aves). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jean-Marc Pons
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Alice Cibois
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Geneva, Switzerland
| | - Jérôme Fournier
- Centre de Recherche sur la Biologie des Populations d’Oiseaux, Centre d’Ecologie et des Sciences de la Conservation (CESCO), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, Paris, France
| | - Jérôme Fuchs
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | | | - Jean-Claude Thibault
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
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