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Forest T, Achaz G, Marbouty M, Bignaud A, Thierry A, Koszul R, Milhes M, Lledo J, Pons JM, Fuchs J. Chromosome-level genome assembly of the European green woodpecker Picus viridis. G3 (BETHESDA, MD.) 2024; 14:jkae042. [PMID: 38537260 PMCID: PMC11075563 DOI: 10.1093/g3journal/jkae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/15/2024] [Indexed: 05/08/2024]
Abstract
The European green woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here, we assembled a highly contiguous genome assembly for this species using a combination of short- and long-read sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37 Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a ∼30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the P. viridis genome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers. Five historical and seven contemporary samples have been resequenced and may give insights on the population history of this species.
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Affiliation(s)
- Thomas Forest
- Éco-anthropologie, Muséum national d’Histoire naturelle, CNRS UMR 7206, 75005 Paris, France
- CIRB, Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France
- Institut de Systématique Evolution Biodiversité, Muséum national d’Histoire naturelle CNRS SU EPHE UA, CP 51, 75005 Paris, France
| | - Guillaume Achaz
- CIRB, Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France
- Université Paris-Cité, 75006 Paris, France
| | - Martial Marbouty
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Marine Milhes
- PlaGe, INRAE, Genotoul, 31320 Castanet-Tolosan, France
| | - Joanna Lledo
- PlaGe, INRAE, Genotoul, 31320 Castanet-Tolosan, France
| | - Jean-Marc Pons
- Institut de Systématique Evolution Biodiversité, Muséum national d’Histoire naturelle CNRS SU EPHE UA, CP 51, 75005 Paris, France
| | - Jérôme Fuchs
- Institut de Systématique Evolution Biodiversité, Muséum national d’Histoire naturelle CNRS SU EPHE UA, CP 51, 75005 Paris, France
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2
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Yousefi M, Jouladeh‐Roudbar A, Kafash A. Mapping endemic freshwater fish richness to identify high-priority areas for conservation: An ecoregion approach. Ecol Evol 2024; 14:e10970. [PMID: 38371871 PMCID: PMC10870328 DOI: 10.1002/ece3.10970] [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: 07/27/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 02/20/2024] Open
Abstract
Freshwater ecosystems are experiencing accelerating global biodiversity loss. Thus, knowing where these unique ecosystems' species richness reaches a peak can facilitate their conservation planning. By hosting more than 290 freshwater fishes, Iran is a major freshwater fish hotspot in the Middle East. Considering the accelerating rate of biodiversity loss, there is an urgent need to identify species-rich areas and understand the mechanisms driving biodiversity distribution. In this study, we gathered distribution records of all endemic freshwater fishes of Iran (85 species) to develop their richness map and determine the most critical drivers of their richness patterns from an ecoregion approach. We performed a generalized linear model (GLM) with quasi-Poisson distribution to identify contemporary and historical determinants of endemic freshwater fish richness. We also quantified endemic fish similarity among the 15 freshwater ecoregions of Iran. Results showed that endemic freshwater fish richness is highest in the Zagros Mountains while a moderate level of richness was observed between Zagros and Alborz Mountains. High, moderate, and low richness of endemic freshwater fish match with Upper Tigris & Euphrates, Namak, and Kavir & Lut Deserts ecoregions respectively. Kura - South Caspian Drainages and Caspian Highlands were the most similar ecoregions and Orumiyeh was the most unique ecoregion according to endemic fish presence. Precipitation and precipitation change velocity since the Last Glacial Maximum were the most important predictors of endemic freshwater fish richness. Areas identified to have the highest species richness have high priority for the conservation of freshwater fish in Iran, therefore, should be considered in future protected areas development.
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Affiliation(s)
- Masoud Yousefi
- Stiftung Neanderthal MuseumMettmannGermany
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum KoenigBonnGermany
| | | | - Anooshe Kafash
- School of Culture and SocietyAarhus UniversityAarhus CDenmark
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3
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Kafash A, Ashrafi S, Yousefi M. Modeling habitat suitability of bats to identify high priority areas for field monitoring and conservation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:25881-25891. [PMID: 34851481 DOI: 10.1007/s11356-021-17412-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Bats provide important ecosystem services but face severe threats due to land and climate changes. Although bats are an important component of mammal diversity in Iran, the ecology of many species remains virtually unstudied in the country. Here we applied the maximum entropy approach to model habitat suitability of bat species in Iran, identify the most important variables for their distribution, predict high priority areas for field monitoring and conservation, and estimate the coverage of the bat species' suitable habitats by the existing protected areas. We created a richness map for the twelve species to identify high priority areas for field monitoring and conservation. The results of species distribution modeling showed that Pipistrellus kuhlii (828,977.2 km2) and Miniopterus pallidus (646,581.9 km2) had the largest distribution ranges and Rhinopoma microphyllum (211,202.7 km2) and Rousettus aegyptiacus (218,278.6 km2) had the smallest distribution ranges in Iran. By averaging the importance of each ecological variable across the 12 species, we found that distance to forests (with a negative association) is the most important ecological driver of bat distribution in Iran. The Zagros Mountains were identified as a hotspot of bats based on the distribution of the 12 species. Our findings showed that small proportions of each species suitable habitats were covered by protected areas and protected suitable habitats varied from 3.2%for Pipistrellus kuhlii to15.9% for Tadarida teniotis. This study highlights the importance of forests for bat conservation showing that forest conservation is a high priority in the country. Areas which have the highest richness should be prioritized for field monitoring and conservation.
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Affiliation(s)
- Anooshe Kafash
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Tehran, Iran
| | - Sohrab Ashrafi
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Tehran, Iran.
| | - Masoud Yousefi
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Tehran, Iran
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4
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Pleistocene allopatric differentiation followed by recent range expansion explains the distribution and molecular diversity of two congeneric crustacean species in the Palaearctic. Sci Rep 2021; 11:22866. [PMID: 34819546 PMCID: PMC8613293 DOI: 10.1038/s41598-021-02164-8] [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: 07/20/2021] [Accepted: 11/03/2021] [Indexed: 11/09/2022] Open
Abstract
Pleistocene glaciations had a tremendous impact on the biota across the Palaearctic, resulting in strong phylogeographic signals of range contraction and rapid postglacial recolonization of the deglaciated areas. Here, we explore the diversity patterns and history of two sibling species of passively dispersing taxa typical of temporary ponds, fairy shrimps (Anostraca). We combine mitochondrial (COI) and nuclear (ITS2 and 18S) markers to conduct a range-wide phylogeographic study including 56 populations of Branchinecta ferox and Branchinecta orientalis in the Palaearctic. Specifically, we investigate whether their largely overlapping ranges in Europe resulted from allopatric differentiation in separate glacial refugia followed by a secondary contact and reconstruct their postglacial recolonization from the inhabited refugia. Our results suggest the existence of distinct refugia for the two species, with genetic divergence among intraspecific lineages consistent with late Pleistocene glacial cycles. While B. ferox lineages originated from Mediterranean refugia, the origin of B. orientalis lineages was possibly located on the Pannonian Plain. We showed that most dispersal events predominantly happened within 100 km, coupled with several recent long-distance events (> 1000 km). Hence the regional habitat density of suitable habitats in Central Europe is possibly a key to the co-existence of the two species. Overall, our study illustrates how isolation in combination with stochastic effects linked to glacial periods are important drivers of the allopatric differentiation of Palaearctic taxa.
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5
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Kafash A, Ashrafi S, Yousefi M. Biogeography of bats in Iran: Mapping and disentangling environmental and historical drivers of bat richness. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anooshe Kafash
- Department of Environmental Sciences Faculty of Natural Resources University of Tehran Tehran Iran
| | - Sohrab Ashrafi
- Department of Environmental Sciences Faculty of Natural Resources University of Tehran Tehran Iran
| | - Masoud Yousefi
- School of Biology College of Science University of Tehran Tehran Iran
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6
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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
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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7
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Kafash A, Ashrafi S, Yousefi M, Rastegar-Pouyani E, Rajabizadeh M, Ahmadzadeh F, Grünig M, Pellissier L. Reptile species richness associated to ecological and historical variables in Iran. Sci Rep 2020; 10:18167. [PMID: 33097758 PMCID: PMC7584626 DOI: 10.1038/s41598-020-74867-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/07/2020] [Indexed: 01/17/2023] Open
Abstract
Spatial gradients of species richness can be shaped by the interplay between historical and ecological factors. They might interact in particularly complex ways in heterogeneous mountainous landscapes with strong climatic and geological contrasts. We mapped the distribution of 171 lizard species to investigate species richness patterns for all species (171), diurnal species (101), and nocturnal species (70) separately. We related species richness with the historical (past climate change, mountain uplifting) and ecological variables (climate, topography and vegetation). We found that assemblages in the Western Zagros Mountains, north eastern and north western parts of Central Iranian Plateau have the highest number of lizard species. Among the investigated variables, annual mean temperature explained the largest variance for all species (10%) and nocturnal species (31%). For diurnal species, temperature change velocity shows strongest explained variance in observed richness pattern (26%). Together, our results reveal that areas with annual temperature of 15–20 °C, which receive 400–600 mm precipitation and experienced moderate level of climate change since the Last Glacial Maximum (LGM) have highest number of species. Documented patterns of our study provide a baseline for understanding the potential effect of ongoing climate change on lizard diversity in Iran.
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Affiliation(s)
- Anooshe Kafash
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran.,Institute of Terrestrial Ecosystems, ETH Zurich, Zurich, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Sohrab Ashrafi
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran. .,Ecology and Conservation Research Group (ECRG), Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran.
| | - Masoud Yousefi
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran.,Ecology and Conservation Research Group (ECRG), Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | | | - Mahdi Rajabizadeh
- Department of Computer Science, Tarbiat Modares University, Tehran, Iran
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Marc Grünig
- Institute of Terrestrial Ecosystems, ETH Zurich, Zurich, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Loïc Pellissier
- Institute of Terrestrial Ecosystems, ETH Zurich, Zurich, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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8
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Tellería JL, Carbonell R, Fandos G, Tena E, Onrubia A, Qninba A, Aguirre JI, Hernández-Téllez I, Martín CA, Ramírez Á. Distribution of the European turtle dove (Streptopelia turtur) at the edge of the South-Western Palaearctic: transboundary differences and conservation prospects. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-01414-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Firneno TJ, O'Neill JR, Portik DM, Emery AH, Townsend JH, Fujita MK. Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads. Mol Ecol 2020; 29:3543-3559. [PMID: 32500624 DOI: 10.1111/mec.15496] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/18/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear discordance in this complex, we used spatially explicit genetic data to test species limits and relationships, characterize demographic history, and quantify gene flow. We found extensive mitonuclear discordance among the three recognized species within this group, especially in populations within the Chortís Highlands of Honduras. Our data reveal nuclear introgression within the Chortís Highlands populations that was most probably driven by cyclical range expansions due to climatic fluctuations. Though we determined introgression occurred within the nuclear genome, our data suggest that it is not the key factor in driving mitonuclear discordance in the entire species complex. Rather, due to a lack of discernible geographic pattern between mitochondrial and nuclear DNA, as well as a relatively recent divergence time of this complex, we concluded that mitonuclear discordance has been caused by incomplete lineage sorting. Our study provides a framework to test sources of mitonuclear discordance and highlights the importance of using multiple marker types to test species boundaries in cryptic species.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Justin R O'Neill
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | | | - Alyson H Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Josiah H Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA.,Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Escuela Agrícola Panamericana Zamorano, Municipalidad de San Antonio de Oriente, Francisco Morazán, Honduras
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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Perktaş U, Groth JG, Barrowclough GF. Phylogeography, Species Limits, Phylogeny, and Classification of the Turacos (Aves: Musophagidae) Based on Mitochondrial and Nuclear DNA Sequences. AMERICAN MUSEUM NOVITATES 2020. [DOI: 10.1206/3949.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Utku Perktaş
- Division of Vertebrate Zoology (Ornithology), American Museum of Natural History
| | - Jeff G. Groth
- Division of Vertebrate Zoology (Ornithology), American Museum of Natural History
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11
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Florentin J, Dutoit T, Verlinden O. Detection and identification of European woodpeckers with deep convolutional neural networks. ECOL INFORM 2020. [DOI: 10.1016/j.ecoinf.2019.101023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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İbİş O, Özcan S, Kırmanoğlu C, Keten A, Tez C. Genetic Analysis of Turkish lynx (Lynx lynx) Based on Mitochondrial DNA Sequences. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419110061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Kamp L, Pasinelli G, Milanesi P, Drovetski SV, Kosiński Z, Kossenko S, Robles H, Schweizer M. Significant Asia‐Europe divergence in the middle spotted woodpecker (Aves, Picidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12320] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Laura Kamp
- Naturhistorisches Museum der Burgergemeinde Bern Bern Switzerland
- Institute of Ecology and Evolution Universität Bern Bern Switzerland
- Swiss Ornithological Station Sempach Switzerland
| | | | | | - Sergei V. Drovetski
- Laboratories of Analytical Biology, National Museum of Natural History Smithsonian Institution Washington DC
| | - Ziemowit Kosiński
- Department of Avian Biology and Ecology, Institute of Environmental Biology, Faculty of Biology Adam Mickiewicz University Poznań Poland
| | - Serguei Kossenko
- State Nature Biosphere Reserve "Bryansky Les," Nerussa Station Bryansk Region Russia
| | - Hugo Robles
- Evolutionary Ecology Group (EVECO) University of Antwerp Wilrijk Belgium
| | - Manuel Schweizer
- Naturhistorisches Museum der Burgergemeinde Bern Bern Switzerland
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14
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İbiş O, Koepfli KP, Özcan S, Tez C. Genetic analysis of Turkish martens: Do two species of the genusMartesoccur in Anatolia? ZOOL SCR 2018. [DOI: 10.1111/zsc.12289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Osman İbiş
- Department of Agricultural Biotechnology; Faculty of Agriculture; Erciyes University; Kayseri Turkey
- Genome and Stem Cell Center (GENKOK); Erciyes University; Kayseri Turkey
| | - Klaus-Peter Koepfli
- National Zoological Park; Smithsonian Conservation Biology Institute; Washington District of Columbia
- Theodosius Dobzhansky Center for Genome Bioinformatics; Saint Petersburg State University; Saint Petersburg Russia
| | - Servet Özcan
- Genome and Stem Cell Center (GENKOK); Erciyes University; Kayseri Turkey
- Department of Biology; Faculty of Sciences; Erciyes University; Kayseri Turkey
| | - Coşkun Tez
- Department of Biology; Faculty of Sciences; Erciyes University; Kayseri Turkey
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15
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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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16
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İbiş O, Kılıç M, Özcan S, Tez C. Genetic characterization of the Turkish gray hamster (Cricetulus migratorius) based on mitochondrial cytochrome b and 12S rRNA sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:819-830. [PMID: 28840764 DOI: 10.1080/24701394.2017.1365849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Although genetic diversity and phylogenetic status of the gray hamster (Cricetulus migratorius) have been investigated from different regions in previous studies, genetic data on this species from Turkey are still lacking, since previous data have been based on a limited number of gray hamsters sampled across the Anatolian part of Turkey. The aim of this study was to determine the genetic diversity of the Anatolian population and to reveal the phylogenetic relationships among the Anatolian population and conspecific populations of the gray hamster. The complete and partial fragments of mitochondrial Cyt b and 12S rRNA from the 20 Turkish samples were amplified and sequenced. Ten 12S rRNA (901 bp) and 15 Cyt b (1140 bp) haplotypes found in this work were not previously reported. Based on Bayesian, Maximum Likelihood, Neighbour-Joining and Median-Joining network analyses by using mitochondrial data under the name Cricetulus, the results of phylogenetic and network analyses indicated that there was a deep separation among the distinct lineages within the genus Cricetulus. When considering the position of the Turkish haplotypes in median joining network, the Anatolian part of Turkey may have hosted a source population of the gray hamster for expansion to adjacent regions in the past period. Additionally, the Anatolian population of gray hamster had relatively high haplotype diversity and the present study propounded the importance of data obtained from the Anatolian population of gray hamster to reveal the phylogenetic relationships among conspecific populations of the gray hamster.
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Affiliation(s)
- Osman İbiş
- a Department of Agricultural Biotechnology, Faculty of Agriculture , Erciyes University , Kayseri , Turkey.,b Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey
| | - Metin Kılıç
- c Graduate School of Natural and Applied Sciences , Erciyes University , Kayseri , Turkey
| | - Servet Özcan
- b Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey.,d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
| | - Coşkun Tez
- b Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey.,d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
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17
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Phuong MA, Bi K, Moritz C. Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex. Mol Ecol 2017; 26:4743-4755. [PMID: 28734067 DOI: 10.1111/mec.14238] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 06/15/2017] [Indexed: 01/06/2023]
Abstract
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture data set and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes. Here, we showed that these mtDNA lineages likely formed in allopatry during the Pleistocene, but responded differentially to climatic changes that occurred since the last interglacial (~120,000 years ago). We find that the Northern lineage maintained a stable range throughout this period, correlating with genetic distinctiveness among all genetic markers and low migration rates with the other lineages. In contrast, our results suggested that the Southern lineage expanded from Baja California Sur during the Late Pleistocene to overlap and potentially swamp a contracting Central lineage. High rates of intraspecific gene flow between Southern lineage individuals among expansion origin and expansion edge populations largely eroded Central ancestry from autosomal markers. However, male-biased dispersal in this system preserved signals of this past hybridization and introgression event in matrilineal-biased X-chromosome and mtDNA markers. Our results highlight the importance of range stability in maintaining the persistence of phylogeographic lineages, whereas unstable range dynamics can increase the tendency for lineages to merge upon secondary contact.
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Affiliation(s)
- Mark A Phuong
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Ke Bi
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Craig Moritz
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Acton, ACT, Australia
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Fiera C, Habel JC, Kunz M, Ulrich W. Large-scale phylogenetic structure of European springtails (Collembola) depends on species range size and postglacial colonization history. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Cristina Fiera
- Institute of Biology; Romanian Academy; 296 Splaiul Independenţei PO Box 56-53 RO-060031 Bucharest Romania
| | - Jan Christian Habel
- Terrestrial Ecology Research Group; Department of Ecology and Ecosystem Management; Technische Universität München; D-85354 Freising-Weihenstephan Germany
| | - Mieczysław Kunz
- Department of Geomatics and Cartography; Nicolaus Copernicus University in Torun; Lwowska 1 PL-87-100 Toruń Poland
| | - Werner Ulrich
- Chair of Ecology and Biogeography; Nicolaus Copernicus University in Torun; Lwowska 1 PL-87-100 Toruń Poland
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CIORPAC M, DRUICĂ RC, GHIORGHIȚĂ G, COJOCARU D, GORGAN DL. CHD genes: a reliable marker for bird populations and phylogenetic analysis?Case study of the superfamily Sylvioidea (Aves: Passeriformes). TURK J ZOOL 2016. [DOI: 10.3906/zoo-1510-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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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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Hadas L, Hermon D, Boldo A, Arieli G, Gafny R, King R, Bar-Gal GK. Wild gazelles of the southern Levant: genetic profiling defines new conservation priorities. PLoS One 2015; 10:e0116401. [PMID: 25760948 PMCID: PMC4356595 DOI: 10.1371/journal.pone.0116401] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 12/09/2014] [Indexed: 12/05/2022] Open
Abstract
The mountain gazelle (Gazella gazelle), Dorcas gazelle (Gazella Dorcas) and acacia gazelle (Gazella arabica acacia) were historically abundant in the southern Levant, and more specifically in Israel. Anthropogenic and natural changes have caused a rapid decline in gazelle populations, raising concerns about their conservation status and future survival. The genetic profile of 111 wild gazelles from Israel was determined based on three regions of mitochondrial DNA (control region, Cytochrome b and 12S ribosomal RNA) and nine nuclear microsatellite markers. Genetic analysis of the mountain gazelle population, the largest known population of this rare species, revealed adequate diversity levels and gene flow between subpopulations. Nevertheless, ongoing habitat degradation and other human effects, such as poaching, suggest the need for drastic measures to prevent species extinction. Dorcas gazelles in Israel displayed inbreeding within subpopulations while still maintaining considerable genetic diversity overall. This stable population, represented by a distinctive genetic profile, is fragmented and isolated from its relatives in neighboring localities. Based on the genetic profile of a newly sampled subpopulation in Israel, we provide an alternative hypothesis for the historic dispersal of Dorcas gazelle, from the Southern Levant to northern Africa. The small acacia gazelle population was closest to gazelles from the Farasan Islands of Saudi Arabia, based on mitochondrial markers. The two populations did not share haplotypes, suggesting that these two populations may be the last remnant wild gazelles of this species worldwide. Only a dozen acacia gazelles survive in Israel, and urgent steps are needed to ensure the survival of this genetically distinctive lineage. The genetic assessments of our study recognize new conservation priorities for each gazelle species in the Southern Levant.
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Affiliation(s)
- Lia Hadas
- The Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dalia Hermon
- DNA and Forensic Biology Laboratory, Division of Identification and Forensic Science, Israel Police, National Headquarters, Jerusalem, Israel
| | - Amizor Boldo
- Supervision and Enforcement Division, Israel Nature and Parks Authority, Jerusalem, Israel
| | - Gal Arieli
- Supervision and Enforcement Division, Israel Nature and Parks Authority, Jerusalem, Israel
| | - Ron Gafny
- DNA and Forensic Biology Laboratory, Division of Identification and Forensic Science, Israel Police, National Headquarters, Jerusalem, Israel
| | - Roni King
- Science and Conservation Division, Israel Nature and Parks Authority, Jerusalem, Israel
| | - Gila Kahila Bar-Gal
- The Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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22
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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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