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Stanczak N, Harvey MS, Harms D, Hammel JU, Kotthoff U, Loria SF. A new pseudoscorpion genus (Garypinoidea: Garypinidae) from the Eocene supports extinction and range contraction in the European paleobiota. PeerJ 2023; 11:e15989. [PMID: 37953786 PMCID: PMC10637241 DOI: 10.7717/peerj.15989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/08/2023] [Indexed: 11/14/2023] Open
Abstract
During the Paleogene, the Holarctic experienced drastic climatic oscillations, including periods of extensive glaciation. These changes had a severe impact on both the flora and fauna causing widespread extinction and range shifts with some taxa retreating to refugia in the Mediterranean Basin. Here we provide evidence for this hypothesis using fossils from the pseudoscorpion family Garypinidae Daday, 1889 (Arachnida: Pseudoscorpiones). This family comprises 21 extant genera from all continents except Antarctica but is restricted to low mid-latitudes (<44°N) in the Northern Hemisphere. We provide the second record of garypinids from the European succinite ambers of the Eocene by describing the first extinct genus in Garypinidae, Baltamblyolpium gen. nov., which includes two species: Baltamblyolpium gizmotum sp. nov. from Baltic amber and Baltamblyolpium grabenhorsti sp. nov. from Bitterfeld amber. The new genus exhibits a morphology that closely resembles Neoamblyolpium Hoff, 1956 from western North America and the genus Amblyolpium Simon, 1898, which is widespread but includes taxa restricted to Mediterranean refugia in Europe. The discovery of a new fossil genus of Garypinidae from Europe confirms that the family was found at more northerly latitudes during the Eocene, however, extinction and range contraction resulted in their present-day relictual distribution in southern Europe like many other lineages that once thrived in the European "Baltic amber forest" of the Eocene.
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Affiliation(s)
- Nova Stanczak
- Department of Biology, University of Hamburg, Hamburg, Germany
- Section Arachnology, Centre for Taxonomy and Morphology, Museum of Nature Hamburg—Zoology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
| | - Mark S. Harvey
- Collections & Research, Western Australian Museum, Welshpool, Australia
- University of Western Australia, Crawley, Australia
| | - Danilo Harms
- Section Arachnology, Centre for Taxonomy and Morphology, Museum of Nature Hamburg—Zoology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
- Harry Butler Institute, Murdoch University, Murdoch, Australia
- Centre for Invasion Biology, University of Venda, Thohoyandou, South Africa
| | - Jörg U. Hammel
- Institute of Materials Physics, Helmholtz-Zentrum Hereon, Geesthacht, Germany
| | - Ulrich Kotthoff
- Centre for Biomonitoring and Conservation Science, Museum of Nature Hamburg—Geology-Paleontology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
| | - Stephanie F. Loria
- Section Arachnology, Centre for Taxonomy and Morphology, Museum of Nature Hamburg—Zoology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
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2
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Wang Y, Zhan H, Zhang Y, Long Z, Yang X. Mitochondrial genome analysis, phylogeny and divergence time evaluation of Strixaluco (Aves, Strigiformes, Strigidae). Biodivers Data J 2023; 11:e101942. [PMID: 38327340 PMCID: PMC10848841 DOI: 10.3897/bdj.11.e101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/11/2023] [Indexed: 02/09/2024] Open
Abstract
Background Prior research has shown that the European peninsulas were the main sources of Strixaluco colonisation of Northern Europe during the late glacial period. However, the phylogenetic relationship and the divergence time between S.aluco from Leigong Mountain Nature Reserve, Guizhou Province, China and the Strigiformes from overseas remains unclear. The mitochondrial genome structure of birds is a covalent double-chain loop structure that is highly conserved and, thus, suitable for phylogenetic analysis. This study examined the phylogenetic relationship and divergence time of Strix using the whole mitochondrial genome of S.aluco. New information In this study, the complete mitochondrial genome of Strixaluco, with a total length of 18,632 bp, is reported for the first time. A total of 37 genes were found, including 22 tRNAs, two rRNAs, 13 protein-coding genes and two non-coding control regions. Certain species of Tytoninae were used as out-group and PhyloSuite software was applied to build the ML-tree and BI-tree of Strigiformes. Finally, the divergence time tree was constructed using BEAST 2.6.7 software and the age of Miosurniadiurna fossil-bearing sediments (6.0-9.5 Ma) was set as internal correction point. The common ancestor of Strix was confirmed to have diverged during the Pleistocene (2.58-0.01 Ma). The combined action of the dramatic uplift of the Qinling Mountains in the Middle Pleistocene and the climate oscillation of the Pleistocene caused Strix divergence between the northern and southern parts of mainland China. The isolation of glacial-interglacial rotation and glacier refuge was the main reason for the divergence of Strixuralensis and S.aluco from their common ancestor during this period. This study provides a reference for the evolutionary history of S.aluco.
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Affiliation(s)
- Yeying Wang
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Haofeng Zhan
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Yu Zhang
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Zhengmin Long
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Xiaofei Yang
- Guizhou University, Guiyang, ChinaGuizhou UniversityGuiyangChina
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3
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Ratajc U, Lourenço R, Espín S, Virosta PS, Birrer S, Studler D, Wernham C, Vrezec A. The importance of population contextual data for large-scale biomonitoring using an apex predator: The Tawny Owl (Strix aluco). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160530. [PMID: 36574555 DOI: 10.1016/j.scitotenv.2022.160530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Top predators are often used as sentinel species in contaminant monitoring due to their exposure and vulnerability to persistent, bioaccumulative and, in some cases, biomagnificable contaminants. Some of their ecological traits can vary in space and time, and are known to influence the contamination levels and therefore information on ecological traits should be used as contextual data for correct interpretation of large-scale contaminant spatial patterns. These traits can explain spatiotemporal variation in contaminant exposure (traits such as diet and dispersal distances) or contaminant impacts (traits such as population trend and clutch size). The aim of our research was to review the spatial variation in selected contextual parameters in the Tawny Owl (Strix aluco), a species identified by the COST Action European Raptor Biomonitoring Facility as one of the most suitable candidates for pan-European biomonitoring. A considerable variation in availability of published and unpublished contextual data across Europe was found, with diet being the most extensively studied trait. We demonstrate that the Tawny Owl is a suitable biomonitor at local scale but also that taking spatial variation of other contextual data (e.g. diet) into account is necessary. We found spatial gaps in knowledge about the species ecology and biology in Southern Europe, along with gaps in certain population parameters (e.g. population trends) in several countries. Based on our findings, we proposed a minimal recommended scheme for monitoring of population contextual data as one of the first steps towards a pan-European monitoring scheme using the Tawny Owl.
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Affiliation(s)
- Urška Ratajc
- Department of Organisms and Ecosystems Research, National Institute of Biology, SI-1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, SI-1000 Ljubljana, Slovenia.
| | - Rui Lourenço
- MED Mediterranean Institute for Agriculture, Environment and Development & CHANGE Global Change and Sustainability Institute LabOr Laboratory of Ornithology, IIFA, University of Évora, Pólo da Mitra, 7006-554 Évora, Portugal
| | - Silvia Espín
- Area of Toxicology, Faculty of Veterinary Medicine, University of Murcia, Campus Espinardo, 30100 Murcia, Spain
| | - Pablo Sánchez Virosta
- Area of Toxicology, Faculty of Veterinary Medicine, University of Murcia, Campus Espinardo, 30100 Murcia, Spain
| | - Simon Birrer
- Swiss Ornithological Institute, CH-6204 Sempach, Switzerland
| | | | - Chris Wernham
- British Trust for Ornithology (Scotland), Unit 15 Beta Centre, Stirling University Innovation Park, Stirling FK9 4NF, Scotland, UK
| | - Al Vrezec
- Department of Organisms and Ecosystems Research, National Institute of Biology, SI-1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, SI-1000 Ljubljana, Slovenia; Slovenian Museum of Natural History, SI-1000 Ljubljana, Slovenia
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Nasuelli M, Ilahiane L, Boano G, Cucco M, Galimberti A, Pavia M, Pioltelli E, Shafaeipour A, Voelker G, Pellegrino I. Phylogeography of Lanius senator in its breeding range: conflicts between alpha taxonomy, subspecies distribution and genetics. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2099989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Affiliation(s)
- M. Nasuelli
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, University of Piemonte Orientale, Vercelli, Italy
| | - L. Ilahiane
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, University of Piemonte Orientale, Vercelli, Italy
| | - G. Boano
- Museo Civico di Storia Naturale di Carmagnola, Torino, Italy
| | - M. Cucco
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, University of Piemonte Orientale, Vercelli, Italy
| | - A. Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - M. Pavia
- Museo di Geologia e Paleontologia, Dipartimento di Scienze della Terra, University of Torino, Torino, Italy
| | - E. Pioltelli
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - A. Shafaeipour
- Department of Biology, Faculty of Science, Yasouj University, Yasouj, Iran
| | - G. Voelker
- Department of Ecology and Conservation Biology, Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX, USA
| | - I. Pellegrino
- Dipartimento di Scienze ed Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
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Perktaş U. Range shift and loss of genetic diversity under climate change in the red-backed fairywren ( Malurus melanocephalus), an Australian endemic bird species. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Climatic variability is the most important force influencing the distribution dynamics of common and widespread species, with significant effects on their current biogeographical patterns. In this study, phylogeography was integrated with ecological niche modelling to understand the range dynamics of an Australian bird species, the red-backed fairywren (Malurus melanocephalus), under various climate change scenarios. Specifically, an ecological niche modelling approach with Bayesian-based phylogeographical analysis was used to develop robust inferences regarding the demographic history of the species. The predictions of the model were mostly consistent with the present distribution of the species. However, under the Last Interglacial bioclimatic conditions, the model predicted a significantly narrower distribution than today, indicating the existence of allopatric refugia. Predictions for the Last Glacial Maximum indicated that the species had a wider distribution, extending northwards. Additionally, predictions for the future (2050 and 2070) indicated that the species will probably have a narrower distribution than at present, which will be shifted eastwards. The extended Bayesian skyline plot analysis, which provides a robust analysis of fluctuations in the effective population size throughout the evolutionary history of a species, produced results highly consistent with the ecological niche modelling predictions for the red-backed fairywren. This is the first study to investigate the Late Quaternary history of an endemic avian taxon from Australia using ecological niche modelling and Bayesian-based demographic analysis.
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Affiliation(s)
- Utku Perktaş
- Department of Biology (Biogeography Research Laboratory), Faculty of Science, Hacettepe University , 06800 Beytepe, Ankara , Turkey
- Department of Ornithology, American Museum of Natural History , Central Park West at 79th Street, New York, NY 10024 , USA
- Biodiversity Institute, University of Kansas , Lawrence, KS 66045 , USA
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Novaković BB, Raković MB, Čiampor Jr F, Teofilova TM, Živić IM. Genetic variability of the riffle beetle Elmis maugetii Latreille, 1802 (Coleoptera: Elmidae) in Europe and North Africa. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01206-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Body Condition in the Tawny Owl Strix aluco near the Northern Limit of Its Range: Effects of Individual Characteristics and Environmental Conditions. Animals (Basel) 2022; 12:ani12202843. [PMID: 36290228 PMCID: PMC9597763 DOI: 10.3390/ani12202843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/06/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The present study examines how the variations in food supply and winter weather are reflected in the body condition of female and male Tawny Owls Strix aluco of different colour morphs in a population near the southern coast of Finland. Winter weather conditions before breeding seemed to have effects on the food availability of Tawny Owls: the depth of the snow cover showed a positive relationship, and the frequency of temperature fluctuations around the freezing point had a negative relationship. In females, intrinsic factors such as colour morph and age, as well as the body condition of the mate and the stage of the season, governed body condition. In males, only age and the stage of the season suggested associations with body condition. Probably due to the efficient use of alternative prey, the effects of fluctuations of vole populations on the body condition of Tawny Owls are only moderate. Abstract The body condition of boreal species of vole-eaters seems to vary largely according to fluctuations in vole populations and weather conditions of the preceding winter. I studied females and males of the Tawny Owl Strix aluco of temperate origin near the northern limit of the species’ range in southern Finland to reveal if they show similar patterns to the boreal species. Winter weather conditions before breeding seemed to have pronounced effects on the food availability of Tawny Owls. In females, intrinsic factors such as colour morph and age, as well as the body condition of the mate and the stage of the season (Julian date), governed body condition. In males, only age and Julian date showed pronounced relationships with body condition. The results suggest that deep snow cover protects vole populations through winter until spring better than a minor amount of snow and that frequent temperature fluctuations around the freezing point in early spring make voles more available for owls that are preparing for breeding. This was also reflected positively in the body condition of female owls. Probably due to the efficient use of alternative prey, the effects of fluctuating vole populations on the body condition of Tawny Owls are, in general, only moderate.
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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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Pons J, Campión D, Chiozzi G, Ettwein A, Grangé J, Kajtoch Ł, Mazgajski TD, Rakovic M, Winkler H, Fuchs J. Phylogeography of a widespread Palaearctic forest bird species: The White‐backed Woodpecker (Aves, Picidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jean‐Marc Pons
- Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE Sorbonne Universités Muséum National d’Histoire Naturelle, UMR 7205 Paris Cedex France
| | - David Campión
- Área de Biodiversidad, Biodibertsitate Arloa, Padre Adoain Pamplona‐Iruñea Spain
| | | | | | | | - Łukasz Kajtoch
- Institute of Systematics and Evolution of Animals Polish Academy of Sciences Kraków Poland
| | | | | | - Hans Winkler
- Department of Integrative Biology and Evolution Konrad Lorenz‐Institute of Ethology Vienna Austria
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE Sorbonne Universités Muséum National d’Histoire Naturelle, UMR 7205 Paris Cedex France
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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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11
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Zaccara S, Quadroni S, Vanetti I, Carosi A, La Porta G, Crosa G, Britton R, Lorenzoni M. Morphologic and genetic variability in the Barbus fishes (Teleostei, Cyprinidae) of Central Italy. ZOOL SCR 2019. [DOI: 10.1111/zsc.12341] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Serena Zaccara
- Department of Theoretical and Applied Sciences University of Insubria Varese VA Italy
| | - Silvia Quadroni
- Department of Theoretical and Applied Sciences University of Insubria Varese VA Italy
| | - Isabella Vanetti
- Department of Theoretical and Applied Sciences University of Insubria Varese VA Italy
| | - Antonella Carosi
- Department of Chemistry, Biology and Biotechnology University of Perugia Perugia PG Italy
| | - Gianandrea La Porta
- Department of Chemistry, Biology and Biotechnology University of Perugia Perugia PG Italy
| | - Giuseppe Crosa
- Department of Theoretical and Applied Sciences University of Insubria Varese VA Italy
| | - Robert Britton
- Centre for Conservation Ecology and Environmental Change Bournemouth University Poole Dorset UK
| | - Massimo Lorenzoni
- Department of Chemistry, Biology and Biotechnology University of Perugia Perugia PG Italy
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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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13
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Drovetski SV, Fadeev IV, Raković M, Lopes RJ, Boano G, Pavia M, Koblik EA, Lohman YV, Red'kin YA, Aghayan SA, Reis S, Drovetskaya SS, Voelker G. A test of the European Pleistocene refugial paradigm, using a Western Palaearctic endemic bird species. Proc Biol Sci 2018; 285:rspb.2018.1606. [PMID: 30355709 DOI: 10.1098/rspb.2018.1606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/01/2018] [Indexed: 11/12/2022] Open
Abstract
Hewitt's paradigm for effects of Pleistocene glaciations on European populations assumes their isolation in peninsular refugia during glacial maxima, followed by re-colonization of broader Europe during interstadials. This paradigm is well supported by studies of poorly dispersing taxa, but highly dispersive birds have not been included. To test this paradigm, we use the dunnock (Prunella modularis), a Western Palaearctic endemic whose range includes all major European refugia. MtDNA gene tree, multilocus species tree and species delimitation analyses indicate the presence of three distinct lineages: one in the Iberian refugium, one in the Caucasus refugium, and one comprising the Italian and Balkan refugia and broader Europe. Our gene flow analysis suggests isolation of both the Iberian and Caucasus lineages but extensive exchange between Italy, the Balkans and broader Europe. Demographic stability could not be rejected for any refugial population, except the very recent expansion in the Caucasus. By contrast, northern European populations may have experienced two expansion periods. Iberia and Caucasus had much smaller historical populations than other populations. Although our results support the paradigm, in general, they also suggest that in highly dispersive taxa, isolation of neighbouring refugia was incomplete, resulting in large super-refugial populations.
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Affiliation(s)
- Sergei V Drovetski
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20004, USA
| | - Igor V Fadeev
- Department of Collections, State Darwin Museum, Vavilova St. 57, 117292 Moscow, Russia
| | - Marko Raković
- Natural History Museum Belgrade, Njegoševa 51, 11000 Belgrade, Serbia
| | - Ricardo J Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Giovanni Boano
- Natural History Museum of Carmagnola, San Francesco di Sales 188, 10022 Carmagnola, Italy
| | - Marco Pavia
- Department of Earth Sciences, University of Turin, Valperga Caluso 35, 10125 Turin, Italy
| | - Evgeniy A Koblik
- Department of Ornithology, Zoological Museum of Moscow State University, Bol'shaya Nikitskaya Street 6, 103009 Moscow, Russia
| | | | - Yaroslav A Red'kin
- Department of Ornithology, Zoological Museum of Moscow State University, Bol'shaya Nikitskaya Street 6, 103009 Moscow, Russia
| | - Sargis A Aghayan
- Laboratory of Zoology, Research Institute of Biology, Yerevan State University, Alex Manoogian 1, Yerevan, Armenia
| | - Sandra Reis
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | | | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, 77843 TX, USA
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Evolutionary progression of mitochondrial gene rearrangements and phylogenetic relationships in Strigidae (Strigiformes). Gene 2018; 674:8-14. [PMID: 29940272 DOI: 10.1016/j.gene.2018.06.066] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 01/09/2023]
Abstract
The bird mitogenome is generally considered to have a conservative genome size, consistent gene content, and similar gene order. As more mitogenomes are sequenced, mitochondrial (mt) gene rearrangements have been frequently identified among diverse birds. Within two genera (Bubo and Strix) of typical owls (Strigidae, Strigiformes), the rearrangement of the mt gene has been a subject of debate. In the current study, we first sequenced the whole mitogenomes of S. uralensis and B. scandiaca and resequenced the entire mitogenome of B. bubo. By combining our data with previously sequenced mitogenomes in Strigidae, we examined the mt gene rearrangements in the family and attempted to reconstruct the evolutionary progression of these rearrangements. The mitogenomes were then used to review the phylogenies of Strigidae. Most mitogenomes exhibited the ancestral gene order (A) in Strigidae. The ancestral gene order in the previously published mitogenome of B. bubo was found to be incorrect. We determined the mt gene order (the duplicate tRNAThr-CR, B) and discovered two additional mt gene orders (the duplicate tRNAGlu-L-CR and CR, C and D) in the Bubo and Strix genera. Gene order B was likely derived from A by a tandem duplication of the region spanning from tRNAThr to CR. The other two modified gene orders, C and D, were likely derived from B by further degenerations or deletions of one copy of specific duplicated genes. We also preliminarily reconstructed the evolutionary progression of mt gene rearrangements and discussed maintenance of the duplicated CR in the genera. Additionally, the phylogenetic trees based on the mitogenomes supported the division of Strigidae into three subfamilies: Ninoxinae + (Surniinae + Striginae). Within the Striginae clade, the four genera formed a phylogenetic relationship: Otus + (Asio + (Bubo + Strix)). This suggests that Otus firstly diverges in their evolutionary history, and Bubo and Strix show a close relationship. B. bubo, B. blakistoni and B. scandiaca form a clade should be considered members of the same genus. The well-supported topology obtained in our Bayesian inference (BI) and maximum likelihood (ML) analyses of Strigid mitogenomes suggests that these genomes are informative for constructing phylogenetic relationships.
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15
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Kindler C, Graciá E, Fritz U. Extra-Mediterranean glacial refuges in barred and common grass snakes (Natrix helvetica, N. natrix). Sci Rep 2018; 8:1821. [PMID: 29379101 PMCID: PMC5788984 DOI: 10.1038/s41598-018-20218-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/16/2018] [Indexed: 11/30/2022] Open
Abstract
Extra-Mediterranean glacial refugia of thermophilic biota, in particular in northern latitudes, are controversial. In the present study we provide genetic evidence for extra-Mediterranean refugia in two species of grass snake. The refuge of a widely distributed western European lineage of the barred grass snake (Natrix helvetica) was most likely located in southern France, outside the classical refuges in the southern European peninsulas. One genetic lineage of the common grass snake (N. natrix), distributed in Scandinavia, Central Europe and the Balkan Peninsula, had two distinct glacial refuges. We show that one was located in the southern Balkan Peninsula. However, Central Europe and Scandinavia were not colonized from there, but from a second refuge in Central Europe. This refuge was located in between the northern ice sheet and the Alpine glaciers of the last glaciation and most likely in a permafrost region. Another co-distributed genetic lineage of N. natrix, now massively hybridizing with the aforementioned lineage, survived the last glaciation in a structured refuge in the southern Balkan Peninsula, according to the idea of 'refugia-within-refugia'. It reached Central Europe only very recently. This study reports for the first time the glacial survival of a thermophilic egg-laying reptile species in Central Europe.
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Affiliation(s)
- Carolin Kindler
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Eva Graciá
- Ecology Area, Department of Applied Biology, Miguel Hernández University, Av. de la Universidad, Torreblanca, 03202, Elche, Spain
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany.
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16
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Ülker ED, Tavşanoğlu Ç, Perktaş U. Ecological niche modelling of pedunculate oak (Quercus robur) supports the ‘expansion–contraction’ model of Pleistocene biogeography. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Hanna ZR, Henderson JB, Sellas AB, Fuchs J, Bowie RCK, Dumbacher JP. Complete mitochondrial genome sequences of the northern spotted owl ( Strix occidentalis caurina) and the barred owl ( Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PeerJ 2017; 5:e3901. [PMID: 29038757 PMCID: PMC5639871 DOI: 10.7717/peerj.3901] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/18/2017] [Indexed: 11/20/2022] Open
Abstract
We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226–19,522 nt in length and included copies of all mitochondrial genes except tRNAPro, ND6, and tRNAGlu. Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes.
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Affiliation(s)
- Zachary R Hanna
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America.,Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
| | - James B Henderson
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
| | - Anna B Sellas
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America.,Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Jérôme Fuchs
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,UMR 7205 Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - John P Dumbacher
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
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Ait Belkacem A, Gast O, Stuckas H, Canal D, LoValvo M, Giacalone G, Päckert M. North African hybrid sparrows (Passer domesticus, P. hispaniolensis) back from oblivion - ecological segregation and asymmetric mitochondrial introgression between parental species. Ecol Evol 2016; 6:5190-206. [PMID: 27551376 PMCID: PMC4984497 DOI: 10.1002/ece3.2274] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 01/23/2023] Open
Abstract
A stabilized hybrid form of the house sparrow (Passer domesticus) and the Spanish sparrow (P. hispaniolensis) is known as Passer italiae from the Italian Peninsula and a few Mediterranean islands. The growing attention for the Italian hybrid sparrow and increasing knowledge on its biology and genetic constitution greatly contrast the complete lack of knowledge of the long‐known phenotypical hybrid sparrow populations from North Africa. Our study provides new data on the breeding biology and variation of mitochondrial DNA in three Algerian populations of house sparrows, Spanish sparrows, and phenotypical hybrids. In two field seasons, the two species occupied different breeding habitats: Spanish sparrows were only found in rural areas outside the cities and bred in open‐cup nests built in large jujube bushes. In contrast, house sparrows bred only in the town centers and occupied nesting holes in walls of buildings. Phenotypical hybrids were always associated with house sparrow populations. House sparrows and phenotypical hybrids started breeding mid of March, and most pairs had three successive clutches, whereas Spanish sparrows started breeding almost one month later and had only two successive clutches. Mitochondrial introgression is strongly asymmetric because about 75% of the rural Spanish sparrow population carried house sparrow haplotypes. In contrast, populations of the Italian hybrid form, P. italiae, were genetically least diverse among all study populations and showed a near‐fixation of house sparrow haplotypes that elsewhere were extremely rare or that were even unique for the Italian Peninsula. Such differences between mitochondrial gene pools of Italian and North African hybrid sparrow populations provide first evidence that different demographic histories have shaped the extant genetic diversity observed on both continents.
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Affiliation(s)
- Abdelkrim Ait Belkacem
- Faculty of Sciences of nature and lifes Department of Agropastoralism University of Djelfa BP. 3117 17000 Djelfa Algeria
| | - Oliver Gast
- Senckenberg Naturhistorische Sammlungen Königsbrücker Landstraße 159D-01109 Dresden Germany; Institute of Vertebrate Biology Czech Academy of Sciences External Research Facility Studenec Studenec 122675 02 Koněšín Czech Republic
| | - Heiko Stuckas
- Senckenberg Naturhistorische Sammlungen Königsbrücker Landstraße 159 D-01109 Dresden Germany
| | - David Canal
- Department of Evolutionary Ecology Estación Biológica de Doñana - CSIC Avda. Américo Vespucio s/n 41092 Seville Spain
| | - Mario LoValvo
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche Via Archirafi 18 I-90123 Palermo Italy
| | | | - Martin Päckert
- Senckenberg Naturhistorische Sammlungen Königsbrücker Landstraße 159 D-01109 Dresden Germany
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Li J, Zhao M, Wei S, Luo Z, Wu H. Geologic events coupled with Pleistocene climatic oscillations drove genetic variation of Omei treefrog (Rhacophorus omeimontis) in southern China. BMC Evol Biol 2015; 15:289. [PMID: 26690899 PMCID: PMC4687352 DOI: 10.1186/s12862-015-0572-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pleistocene climatic oscillations and historical geological events may both influence current patterns of genetic variation, and the species in southern China that faced unique climatic and topographical events have complex evolutionary histories. However, the relative contributions of climatic oscillations and geographical events to the genetic variation of these species remain undetermined. To investigate patterns of genetic variation and to test the hypotheses about the factors that shaped the distribution of this genetic variation in species of southern China, mitochondrial genes (cytochrome b and NADH dehydrogenase subunit 2) and nine microsatellite loci of the Omei tree frog (Rhacophorus omeimontis) were amplified in this study. RESULTS The genetic diversity in the populations of R. omeimontis was high. The phylogenetic trees reconstructed from the mitochondrial DNA (mtDNA) haplotypes and the Bayesian genetic clustering analysis based on microsatellite data both revealed that all populations were divided into three lineages (SC, HG and YN). The two most recent splitting events among the lineages coincided with recent geological events (including the intense uplift of the Qinghai-Tibet Plateau, QTP and the subsequent movements of the Yun-Gui Plateau, YGP) and the Pleistocene glaciations. Significant expansion signals were not detected in mismatch analyses or neutrality tests. And the effective population size of each lineage was stable during the Pleistocene. CONCLUSIONS Based on the results of this study, complex geological events (the recent dramatic uplift of the QTP and the subsequent movements of the YGP) and the Pleistocene glaciations were apparent drivers of the rapid divergence of the R. omeimontis lineages. Each diverged lineages survived in situ with limited gene exchanges, and the stable demographics of lineages indicate that the Pleistocene climatic oscillations were inconsequential for this species. The analysis of genetic variation in populations of R. omeimontis contributes to the understanding of the effects of changes in climate and of geographical events on the dynamic development of contemporary patterns of genetic variation in the species of southern China.
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Affiliation(s)
- Jun Li
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
| | - Mian Zhao
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
| | - Shichao Wei
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
| | - Zhenhua Luo
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
| | - Hua Wu
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
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20
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Perktaş U, Gür H, Ada E. Historical demography of the Eurasian green woodpecker: integrating phylogeography and ecological niche modelling to test glacial refugia hypothesis. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a9.2015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Utku Perktaş
- Department of Biology (Zoology Section), Faculty of Science, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, 10024 New York, NY, U.S.A
| | - Hakan Gür
- Department of Biology, Faculty of Arts and Sciences, Ahi Evran University, Bağbaşı, 40100 Kırşehir, Turkey
| | - Eren Ada
- Department of Biology (Zoology Section), Faculty of Science, Hacettepe University, 06800 Beytepe, Ankara, Turkey
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21
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Doña J, Ruiz-Ruano FJ, Jovani R. DNA barcoding of Iberian Peninsula and North Africa Tawny Owls Strix aluco suggests the Strait of Gibraltar as an important barrier for phylogeography. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4475-4478. [PMID: 26465068 DOI: 10.3109/19401736.2015.1089573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Eight subspecies have been proposed within the Tawny Owl (Strix aluco) species. However, recent molecular data have challenged this view, encouraging further work in this species complex. Here we reevaluated the taxonomic status between the North-Western African Tawny Owl, S. a. mauritanica, and its closest Iberian Tawny Owl population (from the S. a. sylvatica to S. a. aluco clade) separated by the Strait of Gibraltar. The Tawny Owl is a non-migratory and territorial species, and juvenile dispersal is restricted to a few kilometers around the natal site. This limited dispersal and the barrier imposed by the Strait of Gibraltar predicted a strong differentiation between the two populations. We tested this using DNA barcoding, Bayesian phylogenetic and species delimitation analysis. We found that an 81.1% of variation is due to the intergroups variation. In addition, the inter-intraspecific distances distribution revealed a barcoding gap among the two subspecies. Also, posterior probabilities and the PAB value allowed to reject the hypothesis that observed degree of distinctiveness is due to random coalescence processes. These findings clearly support the Strait of Gibraltar as an isolating barrier for this species. The subspecific status is confirmed and species status is even suggested for S. a. mauritanica.
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Affiliation(s)
- Jorge Doña
- a Department of Evolutionary Ecology , Estación Biológica de Doñana (CSIC) , Avda. Americo Vespucio S/N , Sevilla , Spain and
| | | | - Roger Jovani
- a Department of Evolutionary Ecology , Estación Biológica de Doñana (CSIC) , Avda. Americo Vespucio S/N , Sevilla , Spain and
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22
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Pons JM, Thibault JC, Fournier J, Olioso G, Rakovic M, Tellini Florenzano G, Fuchs J. Genetic variation among Corsican and continental populations of the Eurasian treecreeper (Aves:Certhia familiaris) reveals the existence of a palaeoendemic mitochondrial lineage. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12485] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jean-Marc Pons
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS MNHN UPMC EPHE; Département Systématique et Evolution; Muséum national d'Histoire naturelle; Case Postale 51 55 rue Buffon F-75005 Paris France
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI); Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
| | - Jean-Claude Thibault
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS MNHN UPMC EPHE; Département Systématique et Evolution; Muséum national d'Histoire naturelle; Case Postale 51 55 rue Buffon F-75005 Paris France
| | - Jérôme Fournier
- Centre de Recherche sur la Biologie des Populations d'Oiseaux; Département Ecologie et Gestion de la Biodiversité; Muséum National d'Histoire Naturelle; Case Postale 51 55 rue Buffon F-75005 Paris France
| | | | - Marko Rakovic
- Natural History Museum of Belgrade; Njegoseva 51 Serbia
| | | | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS MNHN UPMC EPHE; Département Systématique et Evolution; Muséum national d'Histoire naturelle; Case Postale 51 55 rue Buffon F-75005 Paris France
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI); Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
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Dool SE, Puechmaille SJ, Dietz C, Juste J, Ibáñez C, Hulva P, Roué SG, Petit EJ, Jones G, Russo D, Toffoli R, Viglino A, Martinoli A, Rossiter SJ, Teeling EC. Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers. Mol Ecol 2014; 22:4055-70. [PMID: 23889545 DOI: 10.1111/mec.12373] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 01/03/2023]
Abstract
The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was reconstructed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multimarker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA (cytb-tRNA-control region; 1630 bp) and eight variable microsatellite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species' demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero-Maghreb region and an eastern location (Anatolia/Middle East)-that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species' movements since the Last Glacial Maximum and suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.
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Affiliation(s)
- Serena E Dool
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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Sağlam İK, Küçükyıldırım S, Çağlar SS. Diversification of montane species via elevation shifts: the case of the Kaçkar cricket Phonochorion
(Orthoptera). J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- İsmail K. Sağlam
- Department of Biology; Faculty of Science; Hacettepe University; Beytepe, Ankara Turkey
| | - Sibel Küçükyıldırım
- Department of Biology; Faculty of Science; Hacettepe University; Beytepe, Ankara Turkey
| | - Selim S. Çağlar
- Department of Biology; Faculty of Science; Hacettepe University; Beytepe, Ankara Turkey
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Hong YJ, Kim YJ, Murata K, Lee H, Min MS. Determining the Specific Status of Korean Collared Scops Owls. ANIMAL SYSTEMATICS, EVOLUTION AND DIVERSITY 2013. [DOI: 10.5635/ased.2013.29.2.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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26
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Forcina G, Panayides P, Guerrini M, Nardi F, Gupta B, Mori E, Al-Sheikhly O, Mansoori J, Khaliq I, Rank D, Parasharya B, Khan A, Hadjigerou P, Barbanera F. Molecular evolution of the Asian francolins (Francolinus, Galliformes): A modern reappraisal of a classic study in speciation. Mol Phylogenet Evol 2012; 65:523-34. [DOI: 10.1016/j.ympev.2012.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 11/27/2022]
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27
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Perktaş U, Quintero E. A wide geographical survey of mitochondrial DNA variation in the great spotted woodpecker complex,Dendrocopos major(Aves: Picidae). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.02003.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Utku Perktaş
- Department of Ornithology; American Museum of Natural History; Central Park West at 79th Street; New York; NY; 10024; USA
| | - Esther Quintero
- Department of Ornithology; American Museum of Natural History; Central Park West at 79th Street; New York; NY; 10024; USA
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PERKTAS UTKU, BARROWCLOUGH GEORGEF, GROTH JEFFG. Phylogeography and species limits in the green woodpecker complex (Aves: Picidae): multiple Pleistocene refugia and range expansion across Europe and the Near East. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01750.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Bajc M, Čas M, Ballian D, Kunovac S, Zubić G, Grubešić M, Zhelev P, Paule L, Grebenc T, Kraigher H. Genetic differentiation of the Western Capercaillie highlights the importance of South-eastern Europe for understanding the species phylogeography. PLoS One 2011; 6:e23602. [PMID: 21897847 PMCID: PMC3163590 DOI: 10.1371/journal.pone.0023602] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 07/20/2011] [Indexed: 11/19/2022] Open
Abstract
The Western Capercaillie (Tetrao urogallus L.) is a grouse species of open boreal or high altitude forests of Eurasia. It is endangered throughout most mountain range habitat areas in Europe. Two major genetically identifiable lineages of Western Capercaillie have been described to date: the southern lineage at the species' southernmost range of distribution in Europe, and the boreal lineage. We address the question of genetic differentiation of capercaillie populations from the Rhodope and Rila Mountains in Bulgaria, across the Dinaric Mountains to the Slovenian Alps. The two lineages' contact zone and resulting conservation strategies in this so-far understudied area of distribution have not been previously determined. The results of analysis of mitochondrial DNA control region sequences of 319 samples from the studied populations show that Alpine populations were composed exclusively of boreal lineage; Dinaric populations of both, but predominantly (96%) of boreal lineage; and Rhodope-Rila populations predominantly (>90%) of southern lineage individuals. The Bulgarian mountains were identified as the core area of the southern lineage, and the Dinaric Mountains as the western contact zone between both lineages in the Balkans. Bulgarian populations appeared genetically distinct from Alpine and Dinaric populations and exhibited characteristics of a long-term stationary population, suggesting that they should be considered as a glacial relict and probably a distinct subspecies. Although all of the studied populations suffered a decline in the past, the significantly lower level of genetic diversity when compared with the neighbouring Alpine and Bulgarian populations suggests that the isolated Dinaric capercaillie is particularly vulnerable to continuing population decline. The results are discussed in the context of conservation of the species in the Balkans, its principal threats and legal protection status. Potential conservation strategies should consider the existence of the two lineages and their vulnerable Dinaric contact zone and support the specificities of the populations.
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Affiliation(s)
- Marko Bajc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Miran Čas
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | | | - Saša Kunovac
- Faculty of Forestry, Sarajevo, Bosnia and Herzegovina
| | - Goran Zubić
- Municipality Kupres, Republic of Srpska, Bosnia and Herzegovina
| | | | | | - Ladislav Paule
- Faculty of Forestry, Technical University, Zvolen, Slovakia
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Hojka Kraigher
- Slovenian Forestry Institute, Ljubljana, Slovenia
- * E-mail:
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Burbrink FT, Pyron RA. THE IMPACT OF GENE-TREE/SPECIES-TREE DISCORDANCE ON DIVERSIFICATION-RATE ESTIMATION. Evolution 2011; 65:1851-61. [PMID: 21729043 DOI: 10.1111/j.1558-5646.2011.01260.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frank T Burbrink
- Department of Biology, The College of Staten Island, The City University of New York, Staten Island, New York 10314, USA
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31
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HU ZM, LI W, LI JJ, DUAN DL. Post-Pleistocene demographic history of the North Atlantic endemic Irish moss Chondrus crispus: glacial survival, spatial expansion and gene flow. J Evol Biol 2010; 24:505-17. [DOI: 10.1111/j.1420-9101.2010.02186.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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LO BRUTTO SABRINA, SARÀ MAURIZIO, ARCULEO MARCO. Italian Peninsula preserves an evolutionary lineage of the fat dormouse Glis glis L. (Rodentia: Gliridae). Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01573.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ruiz EA, Rinehart JE, Hayes JL, Zuñiga G. Historical demography and phylogeography of a specialist bark beetle, Dendroctonus pseudotsugae Hopkins (Curculionidae: Scolytinae). ENVIRONMENTAL ENTOMOLOGY 2010; 39:1685-1697. [PMID: 22546468 DOI: 10.1603/en09339] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Contemporary distribution of North American species has been shaped by past glaciation events during the Quaternary period. However, their effects were not as severe in the southern Rocky Mountains and Northern Mexico as elsewhere in North America. In this context, we test hypotheses about the historical demography of Dendroctonus pseudotsugae, based on 136 haplotypes of mitochondrial cytochrome oxidase I. The phylogenetic analysis yielded four haplogroups corresponding to northwestern United States and southwestern Canada (NUS), southwestern United States (Arizona, SUS), northwestern Mexico (Sierra Madre Occidental, SMOC), and northeastern Mexico (Sierra Madre Oriental, SMOR). Predictions of demographic expansion were examined through neutrality tests against population growth and mismatch distribution. Results showed that the NUS and SMOC haplogroups have experienced demographic expansion events, whereas the SUS and SMOR haplogroups have not. Divergence times between pairs of haplogroups were estimated from early to middle Pleistocene. The longer divergence time between NUS and all other haplogroups could be the result of refugia within the Pacific Northwest and northern Rocky Mountains and long-term isolation from southernmost populations in Mexico. The results obtained in this study are in agreement with the evolutionary history of the host Douglas-fir, as the warmer climates of interglacial periods pushed conifers northward of Colorado, New Mexico, and Arizona, whereas environmental changes reduced the population size of Douglas-fir and forced fragmentation of distribution range southward into northern Mexico.
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Affiliation(s)
- Enrico A Ruiz
- Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, col. Santo Tomás, C.P. 11340, México, D.F., México.
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Solonen T. Factors Affecting Reproduction in the Tawny OwlStrix alucoin Southern Finland. ANN ZOOL FENN 2009. [DOI: 10.5735/086.046.0407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Barbanera F, Zuffi M, Guerrini M, Gentilli A, Tofanelli S, Fasola M, Dini F. Molecular phylogeography of the asp viper Vipera aspis (Linnaeus, 1758) in Italy: Evidence for introgressive hybridization and mitochondrial DNA capture. Mol Phylogenet Evol 2009; 52:103-14. [PMID: 19236928 DOI: 10.1016/j.ympev.2009.02.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 02/04/2009] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
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Hourlay F, Libois R, D'Amico F, Sarà M, O'Halloran J, Michaux JR. Evidence of a highly complex phylogeographic structure on a specialist river bird species, the dipper (Cinclus cinclus). Mol Phylogenet Evol 2008; 49:435-44. [PMID: 18762260 DOI: 10.1016/j.ympev.2008.07.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 06/05/2008] [Accepted: 07/30/2008] [Indexed: 10/21/2022]
Abstract
This study details the phylogeographic pattern of the white-throated dipper (Cinclus cinclus), a Palearctic, temperate, passerine bird that is exclusively associated with flowing water. Our results reveal a complex phylogeographic structure with at least five distinct lineages for the Western Palearctic region. As for many species of the Western Palearctic fauna and flora, this genetic structure is probably linked to the isolation of populations in different southern refuges during glacial periods. Furthermore, the isolation of populations in Scandinavia and/or Eastern regions, but also in Morocco and probably in Corsica, was accentuated by ecological and biogeographic barriers during Quaternary interglacial periods. During glacial periods, Italy, Sicily and the Balkano-Carpathian region acted as major refuge zones for the dipper. At the end of the last ice age, Western Europe was repopulated by dippers from an Italian refuge, while Eastern Europe was recolonised by Balkano-Carpathian birds. A large contact zone between these two lineages was evidenced and extends from Luxembourg to Hungary. Finally, our results indicate the need to clarify the taxonomic status of the dipper, especially concerning the European subspecies whose validity appears uncertain.
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Affiliation(s)
- F Hourlay
- Zoogeography Researchs Unit, Institut de Botanique, Université de Liège, 4000 Liège, Belgium.
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Lopes IF, Miño CI, Del Lama SN. Genetic diversity and evidence of recent demographic expansion in waterbird populations from the Brazilian Pantanal. BRAZ J BIOL 2008; 67:849-57. [PMID: 18278351 DOI: 10.1590/s1519-69842007000500007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Accepted: 08/28/2007] [Indexed: 11/22/2022] Open
Abstract
The present study determined nuclear and mitochondrial (mtDNA) levels of genetic variability and phylogeographic patterns in breeding populations of Roseate Spoonbill (N=57), Wood Stork (N=89), and Jabiru Stork (N=30), sampled in the Brazilian Pantanal. These species were selected since they are bioindicators of wetlands health and are threatened in other parts of their distribution. As they are in close association with this ecosystem, they are appropriate for studying the effects of Pleistocene climatic changes on their demographic patterns. Levels of nuclear genetic diversity in Pantanal populations were not significantly different from those of other populations throughout the American continent, where they are considered threatened or of special concern. Reduced levels of mtDNA genetic diversity were observed in the Central American population of Jabiru Stork in comparison to the Pantanal population. Recent demographic expansion in the Pantanal was markedly evidenced by unimodal patterns of mismatch distribution and Fus Fs neutrality test in these three species. We hypothesize that the average time of population expansion (between 30,843 and 14,233 years before present) is associated to responses of these birds populations to paleoclimatic changes in these wetlands during the last glaciation period. We recommend special conservation efforts with the Jabiru Stork populations, a genetic monitoring program based on mtDNA, and an ecological characterization of these waterbirds species throughout their distribution range.
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Affiliation(s)
- I F Lopes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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40
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Fickel J, Hauffe HC, Pecchioli E, Soriguer R, Vapa L, Pitra C. Cladogenesis of the European brown hare (Lepus europaeus Pallas, 1778). EUR J WILDLIFE RES 2008. [DOI: 10.1007/s10344-008-0175-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ruedi M, Walter S, Fischer MC, Scaravelli D, Excoffier L, Heckel G. Italy as a major Ice Age refuge area for the bat Myotis myotis (Chiroptera: Vespertilionidae) in Europe. Mol Ecol 2008; 17:1801-14. [PMID: 18331245 DOI: 10.1111/j.1365-294x.2008.03702.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The distribution of biota from the temperate regions changed considerably during the climatic fluctuations of the Quaternary. This is especially true for many bat species that depend on warm roosts to install their nursery colonies. Surveys of genetic variation among European bats have shown that the southern peninsulas (Iberia and the Balkans) harbour endemic diversity, but to date, no such surveys have been conducted in the third potential glacial refuge area, the Apennine peninsula. We report here the phylogeographical analysis of 115 greater mouse-eared bats (Myotis myotis) sampled throughout Italy, and show that 15 of the 18 different haplotypes found in the mitochondrial control region of these bats were unique to the Apennine peninsula. Colonies within this region also showed substantial genetic structure at both mitochondrial (Phi(ST) = 0.47, P < 0.001) and nuclear markers (F(ST) = 0.039, P < 0.001). Based on a comprehensive survey of 575 bats from Europe, these genetic markers further indicate that central Italian populations of M. myotis are more closely related to Greek samples from across the Adriatic Sea, than to other Italian bats. Mouse-eared bat populations from the Apennine peninsula thus represent a complex mixture of several endemic lineages, which evolved in situ, with others that colonized this region more recently along an Adriatic route. Our broad survey also confirms that the Alps represent a relatively impermeable barrier to gene flow for Apennine lineages, even for vagile animals such as bats. These results underline the conservation value of bats from this region and the need to include the Apennine peninsula in phylogeographical surveys in order to provide a more accurate view of the evolution of bats in Europe.
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Affiliation(s)
- Manuel Ruedi
- Natural History Museum of Geneva, PO Box, 1211 Genève 6, Switzerland.
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Gong W, Zeng Z, Chen YY, Chen C, Qiu YX, Fu CX. Glacial refugia of Ginkgo biloba and human impact on its genetic diversity: evidence from chloroplast DNA. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2008; 50:368-374. [PMID: 18713370 DOI: 10.1111/j.1744-7909.2007.00375.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Variations in the trnK region of chloroplast DNA were investigated in the present study using polymerase chain reaction-restriction fragment length polymorphism to detect the genetic structure and to infer the possible glacial refugia of Ginkgo biloba L. in China. In total, 220 individuals from 12 populations in China and three populations outside China were analyzed, representing the largest number of populations studied by molecular markers to date. Nineteen haplotypes were produced and haplotype A was found in all populations. Populations in south-western China, including WC, JF, PX, and SP, contained 14 of the 19 haplotypes and their genetic diversity ranged from 0.771 4 to 0.867 6. The TM population from China also showed a high genetic diversity (H = 0.848 5). Most of the genetic variation existed within populations and the differentiation among populations was low (G(ST) = 0.2). According to haplotype distribution and the historical record, we suggest that populations of G. biloba have been subjected to extensive human impact, which has compounded our attempt to infer glacial refugia for Ginkgo. Nevertheless, the present results suggest that the center of genetic diversity of Ginkgo is mainly in south-western China and in situ conservation is needed to protect and preserve the genetic resources.
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Affiliation(s)
- Wei Gong
- Laboratory of Systematic Evolutionary Botany and Biodiversity, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Elmer KR, Dávila JA, Lougheed SC. Cryptic diversity and deep divergence in an upper Amazonian leaflitter frog, Eleutherodactylus ockendeni. BMC Evol Biol 2007; 7:247. [PMID: 18154647 PMCID: PMC2254618 DOI: 10.1186/1471-2148-7-247] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2006] [Accepted: 09/13/2007] [Indexed: 11/25/2022] Open
Abstract
Background The forests of the upper Amazon basin harbour some of the world's highest anuran species richness, but to date we have only the sparsest understanding of the distribution of genetic diversity within and among species in this region. To quantify region-wide genealogical patterns and to test for the presence of deep intraspecific divergences that have been documented in some other neotropical anurans, we developed a molecular phylogeny of the wide-spread terrestrial leaflitter frog Eleutherodactylus ockendeni (Leptodactylidae) from 13 localities throughout its range in Ecuador using data from two mitochondrial genes (16S and cyt b; 1246 base pairs). We examined the relation between divergence of mtDNA and the nuclear genome, as sampled by five species-specific microsatellite loci, to evaluate indirectly whether lineages are reproductively isolated where they co-occur. Our extensive phylogeographic survey thus assesses the spatial distribution of E. ockendeni genetic diversity across eastern Ecuador. Results We identified three distinct and well-supported clades within the Ecuadorean range of E. ockendeni: an uplands clade spanning north to south, a northeastern and central lowlands clade, and a central and southeastern clade, which is basal. Clades are separated by 12% to 15% net corrected p-distance for cytochrome b, with comparatively low sequence divergence within clades. Clades marginally overlap in some geographic areas (e.g., Napo River basin) but are reproductively isolated, evidenced by diagnostic differences in microsatellite PCR amplification profiles or DNA repeat number and coalescent analyses (in MDIV) best modelled without migration. Using Bayesian (BEAST) and net phylogenetic estimates, the Southeastern Clade diverged from the Upland/Lowland clades in the mid-Miocene or late Oligocene. Lowland and Upland clades speciated more recently, in the early or late Miocene. Conclusion Our findings uncover previously unsuspected cryptic species diversity within the common leaflitter frog E. ockendeni, with at least three different species in Ecuador. While these clades are clearly geographically circumscribed, they do not coincide with any existing landscape barriers. Divergences are ancient, from the Miocene, before the most dramatic mountain building in the Ecuadorean Andes. Therefore, this diversity is not a product of Pleistocene refuges. Our research coupled with other studies suggests that species richness in the upper Amazon is drastically underestimated by current inventories based on morphospecies.
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Affiliation(s)
- Kathryn R Elmer
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada.
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44
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Origin of, and conservation units in, the Irish red squirrel (Sciurus vulgaris) population. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9419-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Johnson JA, Dunn PO, Bouzat JL. Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickens. Mol Ecol 2007; 16:2203-22. [PMID: 17561885 DOI: 10.1111/j.1365-294x.2007.03285.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Current methods of DNA sequence analysis attempt to reconstruct historical patterns of population structure and growth from contemporary samples. However, these techniques may be influenced by recent population bottlenecks, which have the potential to eliminate lineages that reveal past changes in demography. One way to examine the performance of these demographic methods is to compare samples from populations before and after recent bottlenecks. We compared estimates of demographic history from populations of greater prairie-chickens (Tympanuchus cupido) before and after recent bottlenecks using four common methods (nested clade analysis [NCA], Tajima's D, mismatch distribution, and MDIV). We found that NCA did not perform well in the presence of bottleneck events, although it did recover some genetic signals associated with increased isolation and the extinction of intermediate populations. The majority of estimates for Tajima's D, including those from bottlenecked populations, were not significantly different from zero, suggesting our data conformed to neutral expectations. In contrast, mismatch distributions including the raggedness index were more likely to identify recently bottlenecked populations with this data set. Estimates of population mutation rate (theta), population divergence time (t), and time to the most recent common ancestor (TMRCA) from MDIV were similar before and after bottlenecks; however, estimates of gene flow (M) were significantly lower in a few cases following a bottleneck. These results suggest that caution should be used when assessing demographic history from contemporary data sets, as recently fragmented and bottlenecked populations may have lost lineages that affect inferences of their demographic history.
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Affiliation(s)
- Jeff A Johnson
- Department of Biological Sciences, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201, USA.
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Brito PH. Contrasting patterns of mitochondrial and microsatellite genetic structure among Western European populations of tawny owls (Strix aluco). Mol Ecol 2007; 16:3423-37. [PMID: 17688543 DOI: 10.1111/j.1365-294x.2007.03401.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A recent study of mitochondrial phylogeography of tawny owls (Strix aluco) in western Europe suggested that this species survived the Pleistocene glaciations in three allopatric refugia located in Iberia, Italy, and the Balkans, and the latter was likely the predominant source of postglacial colonization of northern Europe. New data from seven microsatellite loci from 184 individual owls distributed among 14 populations were used to assess the genetic congruence between nuclear and mitochondrial DNA (mtDNA) markers. Microsatellites corroborated the major phylogeographical conclusions reached on the basis of the mtDNA sequences, but also showed important differences leading to novel inferences. Microsatellites corroborated the three major refugia and supported the Balkan origin of northern populations. When corrected for differences in effective population size, microsatellites and mtDNA yielded generally congruent overall estimates of population structure (N*ST=0.12 vs. RST=0.16); however, there was substantial heterogeneity in the RST among the seven nuclear loci that was not correlated with heterozygosity. Populations representing the Balkans postglacial expansion interact with populations from the other two refugia forming two clines near the Alps and the Pyrenees. In both cases, the apparent position of the contact zones differed substantially between markers due to the genetic composition of populations sampled in northern Italy and Madrid. Microsatellite data did not corroborate the lower genetic diversity of northern, recently populated regions as was found with mtDNA; this discrepancy was taken as evidence for a recent bottleneck recovery. Finally, this study suggests that congruence among genetic markers should be more likely in cases of range expansion into new areas than when populations interact across contact zones.
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Affiliation(s)
- Patrícia H Brito
- American Museum of Natural History, Ornithology Department, Central Park West at 79th Street, New York, NY 10024, USA.
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High genetic diversity in the blue-listed British Columbia population of the purple martin maintained by multiple sources of immigrants. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9358-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ficetola GF, Garner TWJ, De Bernardi F. Genetic diversity, but not hatching success, is jointly affected by postglacial colonization and isolation in the threatened frog, Rana latastei. Mol Ecol 2007; 16:1787-97. [PMID: 17444892 DOI: 10.1111/j.1365-294x.2006.03198.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Both postglacial colonization and habitat fragmentation can reduce the genetic diversity of populations, which in turn can affect fitness. However, since these processes occur at different spatial and temporal scales, the consequences of either process may differ. To disentangle the relative role of isolation and postglacial colonization in determining genetic diversity and fitness, we studied microsatellite diversity of 295 individuals from 10 populations and measured the hatch rate of 218 clutches from eight populations of a threatened frog, R. latastei. The populations that were affected by fragmentation to a greater extent suffered higher embryo mortality and reduced hatch rate, while no effects of distance from glacial refugium on hatch rate were detected. Altogether, distance from glacial refugium and isolation explained > 90% of variation in genetic diversity. We found that the genetic diversity was lowest in populations both isolated and far from the glacial refugium, and that distance from refugium seems to have the primary role in determining genetic diversity. The relationship between genetic diversity and hatch rate was not significant. However, the proportion of genetic diversity lost through recent isolation had a significant, negative effect on fitness. It is possible that selection at least partially purged the negative effects of the ancestral loss of genetic diversity.
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Y chromosome genetic variation in the Italian peninsula is clinal and supports an admixture model for the Mesolithic-Neolithic encounter. Mol Phylogenet Evol 2006; 44:228-39. [PMID: 17275346 DOI: 10.1016/j.ympev.2006.11.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 10/30/2006] [Accepted: 11/21/2006] [Indexed: 11/24/2022]
Abstract
The Italian peninsula, given its geographical location in the middle of the Mediterranean basin, was involved in the process of the peopling of Europe since the very beginning, with first settlements dating to the Upper Paleolithic. Later on, the Neolithic revolution left clear evidence in the archeological record, with findings going back to 7000 B.C. We have investigated the demographic consequences of the agriculture revolution in this area by genotyping Y chromosome markers for almost 700 individuals from 12 different regions. Data analysis showed a non-random distribution of the observed genetic variation, with more than 70% of the Y chromosome diversity distributed along a North-South axis. While the Greek colonisation during classical time appears to have left no significant contribution, the results support a male demic diffusion model, even if population replacement was not complete and the degree of Neolithic admixture with Mesolithic inhabitants was different in different areas of Italy.
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