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Labutin A, Heckel G. Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage. Virus Evol 2024; 10:veae002. [PMID: 38361825 PMCID: PMC10868551 DOI: 10.1093/ve/veae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/08/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from forty-two locations in the contact region between clades for TULV infection by reverse transcription (RT)-PCR. Sequencing yielded twenty-three TULV Central North and twenty-one TULV Central South genomes, which differed by 14.9-18.5 per cent at the nucleotide and 2.2-3.7 per cent at the amino acid (AA) level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis, and genomic single nucleotide polymorphisms showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species, which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.
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Affiliation(s)
- Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
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Wang X, Peischl S, Heckel G. Demographic history and genomic consequences of 10,000 generations of isolation in a wild mammal. Curr Biol 2023; 33:2051-2062.e4. [PMID: 37178689 DOI: 10.1016/j.cub.2023.04.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/20/2022] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
Increased human activities caused the isolation of populations in many species-often associated with genetic depletion and negative fitness effects. The effects of isolation are predicted by theory, but long-term data from natural populations are scarce. We show, with full genome sequences, that common voles (Microtus arvalis) in the Orkney archipelago have remained genetically isolated from conspecifics in continental Europe since their introduction by humans over 5,000 years ago. Modern Orkney vole populations are genetically highly differentiated from continental conspecifics as a result of genetic drift processes. Colonization likely started on the biggest Orkney island and vole populations on smaller islands were gradually split off, without signs of secondary admixture. Despite having large modern population sizes, Orkney voles are genetically depauperate and successive introductions to smaller islands resulted in further reduction of genetic diversity. We detected high levels of fixation of predicted deleterious variation compared with continental populations, particularly on smaller islands, yet the fitness effects realized in nature are unknown. Simulations showed that predominantly mildly deleterious mutations were fixed in populations, while highly deleterious mutations were purged early in the history of the Orkney population. Relaxation of selection overall due to benign environmental conditions on the islands and the effects of soft selection may have contributed to the repeated, successful establishment of Orkney voles despite potential fitness loss. Furthermore, the specific life history of these small mammals, resulting in relatively large population sizes, has probably been important for their long-term persistence in full isolation.
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Affiliation(s)
- Xuejing Wang
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Stephan Peischl
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland.
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3
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Wu N, Wang S, Dujsebayeva TN, Chen D, Ali A, Guo X. Geography and past climate changes have shaped the evolution of a widespread lizard in arid Central Asia. Mol Phylogenet Evol 2023; 184:107781. [PMID: 37044189 DOI: 10.1016/j.ympev.2023.107781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
The complex orogenic history and structure of Central Asia, coupled with Pleistocene glacial cycles have generated its stepwise aridification. Such events would have significantly influenced the evolution of many mid-latitude species in arid Central Asia (ACA). In this study, we employed two mitochondrial genes (CO1 and ND2) and genome-wide SNPs, coupled with ecological niche modeling, to investigate the lineage diversification and historical demography within a widespread lizard Phrynocepahlus helioscopus, and their associations with geography and past climate change. We obtained themtDNA dataset for 300 individuals from 96 localities within the known range of the lizard, among which 51 individuals from 27 localities were selected for generating the SNP dataset via genotyping-by-sequencing approach. Phylogenetic analyses of the concatenated mtDNA dataset revealed eight geographically correlated lineages that diverged by 4.21-10.41% for the CO1 gene, which were estimated to have coalesced ∼4.47 million years ago. However, we observed mito-nuclear discordance pattern regarding the population of Clade V (P. helioscopus sergeevi) from Tajikistan. Ancestral area estimations suggested that P. helioscopus originated from the Fergana Valley and then dispersed into the adjacent areas in ACA along with a history of multiple allopatric divergence processes, suggesting that Fergana may have been the cradle of diversification of P. helioscopus. The intensification of aridification across Central Asia during the Late Pliocene may have facilitated the rapid radiation of this arid-adapted lizard throughout this vast territory. Subsequently, the geological events (e.g., uplift of the Hissar-Alay, transgressions of the Caspian Sea) and geographic barriers (e.g., Amu Darya River, Zerarshan River) during the Pleistocene triggered the progressive diversification of P. helioscopus. Interestingly, Clade VIII (P. helioscopus varius) experienced rapid population growth coupled with range expansion while Clade IV (P. helioscopus cameranoi) underwent drastic population expansion associated with range contraction during the Last Glacial Maximum. In Clade IV, but not in Clade VIII, environmental turnover contributes more to mitochondrial genetic distinctiveness than geographic distance. Overall, the SNP dataset demonstrates that geographic distance plays a greater role than environmental distance. Both the mtDNA dataset and the SNP dataset suggest local-scale genetic differentiation in Clade IV and Clade VIII, revealing potential geographic barriers in the Ili River Valley and the Junggar Basin, respectively. Twenty-seven outlier SNPs associated with environmental factors (precipitation and temperature) were identified, which supports the signature of local adaptation to the arid desert environment. Finally, our finding suggests taxonomic implications, such as support for full species status for P. saidalievi (Clade II) and P. meridionalis (Clade I). Future analyses based on further evidence and increased taxon and geographic sampling should be carried out to corroborate our findings.
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Affiliation(s)
- Na Wu
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wang
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China
| | - Tatjana N Dujsebayeva
- Laboratory of Ornithology and Herpetology, Institute of Zoology, Ministry of Sciences and High Education of Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Abid Ali
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianguang Guo
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China.
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4
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Cirkovic V, Dellicour S, Stamenkovic G, Siljic M, Gligic A, Stanojevic M. Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe. Virus Evol 2022; 8:veac112. [PMID: 37954511 PMCID: PMC10634634 DOI: 10.1093/ve/veac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/07/2022] [Accepted: 12/21/2022] [Indexed: 11/14/2023] Open
Abstract
Orthohantaviruses are zoonotic pathogens of humans, unique among the bunyaviruses in not being transmitted by an arthropod vector. Tula orthohantavirus (TULV) is an old-world hantavirus, of yet unclear human pathogenicity, with few reported cases of clinically relevant human infection. So far, phylogeographic studies exploring the global pathways of hantaviral migration are scarce and generally do not focus on a specific hantavirus species. The aim of the present study was to reconstruct the dispersal history of TULV lineages across Eurasia based on S segment sequences sampled from different geographic areas. Maximum-likelihood and Bayesian inference methods were used to perform the phylogenetic analysis and phylogeographic reconstructions. Sampling time and trapping localities were obtained for a total of 735 TULV S segment sequences available in public databases at the time of the study. The estimated substitution rate of the analyzed partial S segment alignment was 2.26 × 10-3 substitutions/site/year (95 per cent highest posterior density interval: 1.79 × 10-3 to 2.75 × 10-3). Continuous phylogeography of TULV S segment sequences placed the potential root and origin of TULV spread in the Black Sea region. In our study, we detect a single-lineage introduction of TULV to Europe, followed by local viral circulation further on.
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Affiliation(s)
- Valentina Cirkovic
- Faculty of Medicine, University of
Belgrade, Dr Subotica 8, Belgrade 11000, Serbia
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université
Libre de Bruxelles, CP160/13, 50, av. FD Roosevelt, Bruxelles 1050,
Belgium
- Department of Microbiology, Immunology and
Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven 3000,
Belgium
| | - Gorana Stamenkovic
- University of Belgrade, Institute for Biological Research ‘Siniša
Stanković’, Bulevar despota Stefana 142, Belgrade 11108, Serbia
| | - Marina Siljic
- Faculty of Medicine, University of
Belgrade, Dr Subotica 8, Belgrade 11000, Serbia
| | - Ana Gligic
- Institute of Virology, Vaccines and Sera Torlak, Vojvode
Stepe 458, Belgrade 11000, Serbia
| | - Maja Stanojevic
- Faculty of Medicine, University of
Belgrade, Dr Subotica 8, Belgrade 11000, Serbia
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5
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Eccard JA, Herde A, Schuster AC, Liesenjohann T, Knopp T, Heckel G, Dammhahn M. Fitness, risk taking, and spatial behavior covary with boldness in experimental vole populations. Ecol Evol 2022; 12:e8521. [PMID: 35154645 PMCID: PMC8829380 DOI: 10.1002/ece3.8521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
Individuals of a population may vary along a pace-of-life syndrome from highly fecund, short-lived, bold, dispersive "fast" types at one end of the spectrum to less fecund, long-lived, shy, plastic "slow" types at the other end. Risk-taking behavior might mediate the underlying life history trade-off, but empirical evidence supporting this hypothesis is still ambiguous. Using experimentally created populations of common voles (Microtus arvalis)-a species with distinct seasonal life history trajectories-we aimed to test whether individual differences in boldness behavior covary with risk taking, space use, and fitness. We quantified risk taking, space use (via automated tracking), survival, and reproductive success (via genetic parentage analysis) in 8 to 14 experimental, mixed-sex populations of 113 common voles of known boldness type in large grassland enclosures over a significant part of their adult life span and two reproductive events. Populations were assorted to contain extreme boldness types (bold or shy) of both sexes. Bolder individuals took more risks than shyer ones, which did not affect survival. Bolder males but not females produced more offspring than shy conspecifics. Daily home range and core area sizes, based on 95% and 50% Kernel density estimates (20 ± 10 per individual, n = 54 individuals), were highly repeatable over time. Individual space use unfolded differently for sex-boldness type combinations over the course of the experiment. While day ranges decreased for shy females, they increased for bold females and all males. Space use trajectories may, hence, indicate differences in coping styles when confronted with a novel social and physical environment. Thus, interindividual differences in boldness predict risk taking under near-natural conditions and have consequences for fitness in males, which have a higher reproductive potential than females. Given extreme inter- and intra-annual fluctuations in population density in the study species and its short life span, density-dependent fluctuating selection operating differently on the sexes might maintain (co)variation in boldness, risk taking, and pace-of-life.
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Affiliation(s)
- Jana A Eccard
- Animal Ecology Institute of Biochemistry and Biology University of Potsdam Potsdam Germany
| | - Antje Herde
- Animal Ecology Institute of Biochemistry and Biology University of Potsdam Potsdam Germany
- Animal Behaviour Faculty of Biology University of Bielefeld Bielefeld Germany
| | - Andrea C Schuster
- Animal Ecology Institute of Biochemistry and Biology University of Potsdam Potsdam Germany
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Thilo Liesenjohann
- Animal Ecology Institute of Biochemistry and Biology University of Potsdam Potsdam Germany
- BioConsult SH GmbH & Co. KG Husum Germany
| | - Tatjana Knopp
- Animal Ecology Institute of Biochemistry and Biology University of Potsdam Potsdam Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Melanie Dammhahn
- Animal Ecology Institute of Biochemistry and Biology University of Potsdam Potsdam Germany
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Jansen van Rensburg A, Robin M, Phillips B, Van Buskirk J. European common frog ( Rana temporaria) recolonized Switzerland from multiple glacial refugia in northern Italy via trans- and circum-Alpine routes. Ecol Evol 2021; 11:15984-15994. [PMID: 34824805 PMCID: PMC8601898 DOI: 10.1002/ece3.8268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/20/2021] [Accepted: 10/05/2021] [Indexed: 11/12/2022] Open
Abstract
The high mountain ranges of Western Europe had a profound effect on the biotic recolonization of Europe from glacial refugia. The Alps present a particularly interesting case because they form an absolute barrier to dispersal for most taxa, obstructing recolonization from multiple refugia in northern Italy. Here, we investigate the effect of the European Alps on the phylogeographic history of the European common frog Rana temporaria. Based on partial cytochrome b and COXI sequences from Switzerland, we find two mitochondrial lineages roughly north and south of the Alpine ridge, with contact zones between them in eastern and western Switzerland. The northern haplogroup falls within the previously identified Western European haplogroup, while the southern haplogroup is unique to Switzerland. We find that the lineages diverged ~110 kya, at approximately the onset of the last glacial glaciation; this indicates that they are from different glacial refugia. Phylogenetic analyses suggest that the northern and southern haplogroups colonized Switzerland via trans- and circum-Alpine routes from at least two separate refugia in northern Italy. Our results illustrate how a complex recolonization history of the central European Alps can arise from the semi-permeable barrier created by high mountains.
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Affiliation(s)
- Alexandra Jansen van Rensburg
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Centre for Biodiversity and Environmental ResearchUniversity College LondonLondonUK
| | - Mathieu Robin
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Barret Phillips
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Josh Van Buskirk
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
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7
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Schneider J, Hoffmann B, Fevola C, Schmidt ML, Imholt C, Fischer S, Ecke F, Hörnfeldt B, Magnusson M, Olsson GE, Rizzoli A, Tagliapietra V, Chiari M, Reusken C, Bužan E, Kazimirova M, Stanko M, White TA, Reil D, Obiegala A, Meredith A, Drexler JF, Essbauer S, Henttonen H, Jacob J, Hauffe HC, Beer M, Heckel G, Ulrich RG. Geographical Distribution and Genetic Diversity of Bank Vole Hepaciviruses in Europe. Viruses 2021; 13:1258. [PMID: 34203238 PMCID: PMC8310187 DOI: 10.3390/v13071258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
The development of new diagnostic methods resulted in the discovery of novel hepaciviruses in wild populations of the bank vole (Myodes glareolus, syn. Clethrionomys glareolus). The naturally infected voles demonstrate signs of hepatitis similar to those induced by hepatitis C virus (HCV) in humans. The aim of the present research was to investigate the geographical distribution of bank vole-associated hepaciviruses (BvHVs) and their genetic diversity in Europe. Real-time reverse transcription polymerase chain reaction (RT-qPCR) screening revealed BvHV RNA in 442 out of 1838 (24.0%) bank voles from nine European countries and in one of seven northern red-backed voles (Myodes rutilus, syn. Clethrionomys rutilus). BvHV RNA was not found in any other small mammal species (n = 23) tested here. Phylogenetic and isolation-by-distance analyses confirmed the occurrence of both BvHV species (Hepacivirus F and Hepacivirus J) and their sympatric occurrence at several trapping sites in two countries. The broad geographical distribution of BvHVs across Europe was associated with their presence in bank voles of different evolutionary lineages. The extensive geographical distribution and high levels of genetic diversity of BvHVs, as well as the high population fluctuations of bank voles and occasional commensalism in some parts of Europe warrant future studies on the zoonotic potential of BvHVs.
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Affiliation(s)
- Julia Schneider
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (M.L.S.); (S.F.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (B.H.); (M.B.)
| | - Cristina Fevola
- Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (C.F.); (A.R.); (V.T.); (H.C.H.)
- Department of Virology, Faculty of Medicine, University of Helsinki, 00100 Helsinki, Finland
| | - Marie Luisa Schmidt
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (M.L.S.); (S.F.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Christian Imholt
- Vertebrate Research, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute (JKI), Toppheideweg 88, 48161 Münster, Germany; (C.I.); (D.R.); (J.J.)
| | - Stefan Fischer
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (M.L.S.); (S.F.)
| | - Frauke Ecke
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden; (F.E.); (B.H.); (M.M.); (G.E.O.)
| | - Birger Hörnfeldt
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden; (F.E.); (B.H.); (M.M.); (G.E.O.)
| | - Magnus Magnusson
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden; (F.E.); (B.H.); (M.M.); (G.E.O.)
| | - Gert E. Olsson
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden; (F.E.); (B.H.); (M.M.); (G.E.O.)
- Unit for Nature Conservation, County Administrative Board of Halland County, 30004 Halmstad, Sweden
| | - Annapaola Rizzoli
- Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (C.F.); (A.R.); (V.T.); (H.C.H.)
| | - Valentina Tagliapietra
- Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (C.F.); (A.R.); (V.T.); (H.C.H.)
| | - Mario Chiari
- Direzione Generale Welfare, U.O. Veterinaria, Piazza Città di Lombardia 1, 20124 Milan, Italy;
| | - Chantal Reusken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 Bilthoven, The Netherlands;
| | - Elena Bužan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia;
- Environmental Protection College, 3320 Velenje, Slovenia
| | - Maria Kazimirova
- Institute of Zoology, Slovak Academy of Sciences (SAS), 81438 Bratislava, Slovakia;
| | - Michal Stanko
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia;
| | - Thomas A. White
- Lancaster Environment Centre, Lancaster University, Lancaster LA2 0QZ, UK;
| | - Daniela Reil
- Vertebrate Research, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute (JKI), Toppheideweg 88, 48161 Münster, Germany; (C.I.); (D.R.); (J.J.)
| | - Anna Obiegala
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04109 Leipzig, Germany;
| | - Anna Meredith
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh EH8 9AB, UK;
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, 119991 Moscow, Russia
- German Centre for Infection Research (DZIF), Associated Partner Site Berlin, 10117 Berlin, Germany
| | - Sandra Essbauer
- Department Virology and Rickettsiology, Bundeswehr Institute of Microbiology, 80937 Munich, Germany;
| | - Heikki Henttonen
- Natural Resources Institute Finland (LUKE), 00791 Helsinki, Finland;
| | - Jens Jacob
- Vertebrate Research, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute (JKI), Toppheideweg 88, 48161 Münster, Germany; (C.I.); (D.R.); (J.J.)
| | - Heidi C. Hauffe
- Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (C.F.); (A.R.); (V.T.); (H.C.H.)
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (B.H.); (M.B.)
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (M.L.S.); (S.F.)
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8
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Schmidt S, Reil D, Jeske K, Drewes S, Rosenfeld UM, Fischer S, Spierling NG, Labutin A, Heckel G, Jacob J, Ulrich RG, Imholt C. Spatial and Temporal Dynamics and Molecular Evolution of Tula orthohantavirus in German Vole Populations. Viruses 2021; 13:1132. [PMID: 34208398 PMCID: PMC8231151 DOI: 10.3390/v13061132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/21/2021] [Accepted: 06/03/2021] [Indexed: 12/21/2022] Open
Abstract
Tula orthohantavirus (TULV) is a rodent-borne hantavirus with broad geographical distribution in Europe. Its major reservoir is the common vole (Microtus arvalis), but TULV has also been detected in closely related vole species. Given the large distributional range and high amplitude population dynamics of common voles, this host-pathogen complex presents an ideal system to study the complex mechanisms of pathogen transmission in a wild rodent reservoir. We investigated the dynamics of TULV prevalence and the subsequent potential effects on the molecular evolution of TULV in common voles of the Central evolutionary lineage. Rodents were trapped for three years in four regions of Germany and samples were analyzed for the presence of TULV-reactive antibodies and TULV RNA with subsequent sequence determination. The results show that individual (sex) and population-level factors (abundance) of hosts were significant predictors of local TULV dynamics. At the large geographic scale, different phylogenetic TULV clades and an overall isolation-by-distance pattern in virus sequences were detected, while at the small scale (<4 km) this depended on the study area. In combination with an overall delayed density dependence, our results highlight that frequent, localized bottleneck events for the common vole and TULV do occur and can be offset by local recolonization dynamics.
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Affiliation(s)
- Sabrina Schmidt
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (S.S.); (K.J.); (S.D.); (U.M.R.); (S.F.); (N.G.S.); (R.G.U.)
| | - Daniela Reil
- Animal Ecology, Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany;
| | - Kathrin Jeske
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (S.S.); (K.J.); (S.D.); (U.M.R.); (S.F.); (N.G.S.); (R.G.U.)
| | - Stephan Drewes
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (S.S.); (K.J.); (S.D.); (U.M.R.); (S.F.); (N.G.S.); (R.G.U.)
| | - Ulrike M. Rosenfeld
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (S.S.); (K.J.); (S.D.); (U.M.R.); (S.F.); (N.G.S.); (R.G.U.)
| | - Stefan Fischer
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (S.S.); (K.J.); (S.D.); (U.M.R.); (S.F.); (N.G.S.); (R.G.U.)
| | - Nastasja G. Spierling
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (S.S.); (K.J.); (S.D.); (U.M.R.); (S.F.); (N.G.S.); (R.G.U.)
| | - Anton Labutin
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; (A.L.); (G.H.)
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; (A.L.); (G.H.)
| | - Jens Jacob
- Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute (JKI), 48161 Münster, Germany;
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (S.S.); (K.J.); (S.D.); (U.M.R.); (S.F.); (N.G.S.); (R.G.U.)
| | - Christian Imholt
- Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute (JKI), 48161 Münster, Germany;
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9
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García JT, Domínguez‐Villaseñor J, Alda F, Calero‐Riestra M, Pérez Olea P, Fargallo JA, Martínez‐Padilla J, Herranz J, Oñate JJ, Santamaría A, Motro Y, Attie C, Bretagnolle V, Delibes J, Viñuela J. A complex scenario of glacial survival in Mediterranean and continental refugia of a temperate continental vole species (
Microtus arvalis
) in Europe. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jesús T. García
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
| | | | - Fernando Alda
- Museum of Natural Science, Department of Biological Sciences Louisiana State University Baton Rouge Louisiana USA
| | - María Calero‐Riestra
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
| | - Pedro Pérez Olea
- Terrestrial Ecology Group (TEG), Departamento de Ecología Universidad Autónoma de Madrid Madrid Spain
| | - Juan Antonio Fargallo
- Department of Evolutionary Ecology Museo Nacional de Ciencias Naturales MNCN‐CSIC Madrid Spain
| | | | - Jesús Herranz
- Terrestrial Ecology Group (TEG), Departamento de Ecología Universidad Autónoma de Madrid Madrid Spain
| | - Juan José Oñate
- Terrestrial Ecology Group (TEG), Departamento de Ecología Universidad Autónoma de Madrid Madrid Spain
| | - Ana Santamaría
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
| | - Yoav Motro
- Plant Protection and Inspection Services Ministry of Agriculture and Rural Development Bet Dagan Israel
| | | | - Vincent Bretagnolle
- Centre d’Etudes Biologiques de Chizé, UMR 7372 CNRS and Université de la Rochelle La Rochelle France
- LTSER Zone Atelier Plaine and Val de Sèvre CNRS Villiers‐en‐Bois France
| | | | - Javier Viñuela
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
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10
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Stojak J, Tarnowska E. Polish suture zone as the goblet of truth in post-glacial history of mammals in Europe. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00433-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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11
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Saxenhofer M, Schmidt S, Ulrich RG, Heckel G. Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus. PLoS Biol 2019; 17:e3000142. [PMID: 30785873 PMCID: PMC6382107 DOI: 10.1371/journal.pbio.3000142] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Here, we demonstrate that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus. We found a very strong association between the distributions of two major phylogenetic clades in Tula orthohantavirus (TULV) and the rodent host lineages in a natural hybrid zone of the European common vole (Microtus arvalis). The spatial transition between the virus clades in replicated geographic clines is at least eight times narrower than between the hybridizing host lineages. This suggests a strong barrier for effective virus transmission despite frequent dispersal and gene flow among local host populations, and translates to a complete turnover of the adaptive background of TULV within a few hundred meters in the open, unobstructed landscape. Genetic differences between TULV clades are homogenously distributed in the genomes and mostly synonymous (93.1%), except for a cluster of nonsynonymous changes in the 5′ region of the viral envelope glycoprotein gene, potentially involved in host-driven isolation. Evolutionary relationships between TULV clades indicate an emergence of these viruses through rapid differential adaptation to the previously diverged host lineages that resulted in levels of ecological isolation exceeding the progress of speciation in their vertebrate hosts. Like host, like virus; analysis of a natural hybrid zone in the European common vole reveals speciation processes in Tula hantaviruses triggered by evolutionary divergence in the rodent host lineages. Natural biodiversity is driven by stochastic processes and evolutionary adaptation to ecological niches. In viruses, adaptation to specific hosts may cause diversification and eventually lead to the emergence of novel viruses. Here, we studied diversity in Tula orthohantavirus (TULV) in relation to evolutionary divergence in its natural rodent host, the European common vole (Microtus arvalis). In a geographical region in which two distinct evolutionary lineages in the common vole interact and interbreed (a hybrid zone), we found two substantially different TULV clades. Phylogenetic analyses revealed that the divergence among virus clades was likely triggered by a shift of an ancestral virus between the previously diverged host lineages in the hybrid zone. The strong association between virus clades and host lineages at a fine geographical scale results in effective separation of TULVs, despite incomplete reproductive isolation and frequent gene flow among local host populations. Virus genome sequences pointed to the amino-terminal part of the envelope protein as an important region for functional differentiation among these virus clades.
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Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
| | - Sabrina Schmidt
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Insel Riems, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
- * E-mail:
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12
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Golenishchev F, Malikov V, Petrova T, Bodrov S, Abramson N. Toward assembling a taxonomic puzzle: Case study of Iranian gray voles of the subgenus Microtus (Rodentia, Cricetidae). Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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13
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Climatic influences on the genetic structure and distribution of the common vole and field vole in Europe. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0395-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Bize P, Lowe I, Lehto Hürlimann M, Heckel G. Effects of the Mitochondrial and Nuclear Genomes on Nonshivering Thermogenesis in a Wild Derived Rodent. Integr Comp Biol 2018; 58:532-543. [DOI: 10.1093/icb/icy072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Pierre Bize
- School of Biological Sciences, University of Aberdeen, Zoology Building, AB24 2TZ Aberdeen, UK
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Imogen Lowe
- School of Biological Sciences, University of Aberdeen, Zoology Building, AB24 2TZ Aberdeen, UK
| | - Mikko Lehto Hürlimann
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Gerald Heckel
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Hochschulstrasse 6, CH-3012 Bern, Switzerland
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15
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Schmid S, Neuenschwander S, Pitteloud C, Heckel G, Pajkovic M, Arlettaz R, Alvarez N. Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics. Ecol Evol 2018; 8:1480-1495. [PMID: 29435226 PMCID: PMC5792620 DOI: 10.1002/ece3.3699] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/06/2017] [Accepted: 11/10/2017] [Indexed: 12/14/2022] Open
Abstract
Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next-generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus, a steppic Southwestern-Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of O. decorus following human-mediated land-use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.
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Affiliation(s)
- Sarah Schmid
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | | | - Camille Pitteloud
- Department of Environmental Systems ScienceEidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Gerald Heckel
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Mila Pajkovic
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Raphaël Arlettaz
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Nadir Alvarez
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Natural History Museum of GenevaGenevaSwitzerland
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16
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Stojak J, McDevitt AD, Herman JS, Kryštufek B, Uhlíková J, Purger JJ, Lavrenchenko LA, Searle JB, Wójcik JM. Between the Balkans and the Baltic: Phylogeography of a Common Vole Mitochondrial DNA Lineage Limited to Central Europe. PLoS One 2016; 11:e0168621. [PMID: 27992546 PMCID: PMC5161492 DOI: 10.1371/journal.pone.0168621] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022] Open
Abstract
The common vole (Microtus arvalis) has been a model species of small mammal for studying end-glacial colonization history. In the present study we expanded the sampling from central and eastern Europe, analyzing contemporary genetic structure to identify the role of a potential 'northern glacial refugium', i.e. a refugium at a higher latitude than the traditional Mediterranean refugia. Altogether we analyzed 786 cytochrome b (cytb) sequences (representing mitochondrial DNA; mtDNA) from the whole of Europe, adding 177 new sequences from central and eastern Europe, and we conducted analyses on eight microsatellite loci for 499 individuals (representing nuclear DNA) from central and eastern Europe, adding data on 311 new specimens. Our new data fill gaps in the vicinity of the Carpathian Mountains, the potential northern refugium, such that there is now dense sampling from the Balkans to the Baltic Sea. Here we present evidence that the Eastern mtDNA lineage of the common vole was present in the vicinity of this Carpathian refugium during the Last Glacial Maximum and the Younger Dryas. The Eastern lineage expanded from this refugium to the Baltic and shows low cytb nucleotide diversity in those most northerly parts of the distribution. Analyses of microsatellites revealed a similar pattern but also showed little differentiation between all of the populations sampled in central and eastern Europe.
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Affiliation(s)
- Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Jeremy S. Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
| | - Boris Kryštufek
- Vertebrate Department, Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - Jitka Uhlíková
- Nature Conservation Agency of the Czech Republic, Prague, Czech Republic
| | - Jenő J. Purger
- Department of Ecology, Institute of Biology, University in Pécs, Pécs, Hungary
| | - Leonid A. Lavrenchenko
- Department of Mammalian Microevolution, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Jan M. Wójcik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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17
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Schmidt S, Saxenhofer M, Drewes S, Schlegel M, Wanka KM, Frank R, Klimpel S, von Blanckenhagen F, Maaz D, Herden C, Freise J, Wolf R, Stubbe M, Borkenhagen P, Ansorge H, Eccard JA, Lang J, Jourdain E, Jacob J, Marianneau P, Heckel G, Ulrich RG. High genetic structuring of Tula hantavirus. Arch Virol 2016; 161:1135-49. [PMID: 26831932 DOI: 10.1007/s00705-016-2762-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/14/2016] [Indexed: 10/22/2022]
Abstract
Tula virus (TULV) is a vole-associated hantavirus with low or no pathogenicity to humans. In the present study, 686 common voles (Microtus arvalis), 249 field voles (Microtus agrestis) and 30 water voles (Arvicola spec.) were collected at 79 sites in Germany, Luxembourg and France and screened by RT-PCR and TULV-IgG ELISA. TULV-specific RNA and/or antibodies were detected at 43 of the sites, demonstrating a geographically widespread distribution of the virus in the studied area. The TULV prevalence in common voles (16.7 %) was higher than that in field voles (9.2 %) and water voles (10.0 %). Time series data at ten trapping sites showed evidence of a lasting presence of TULV RNA within common vole populations for up to 34 months, although usually at low prevalence. Phylogenetic analysis demonstrated a strong genetic structuring of TULV sequences according to geography and independent of the rodent species, confirming the common vole as the preferential host, with spillover infections to co-occurring field and water voles. TULV phylogenetic clades showed a general association with evolutionary lineages in the common vole as assessed by mitochondrial DNA sequences on a large geographical scale, but with local-scale discrepancies in the contact areas.
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Affiliation(s)
- Sabrina Schmidt
- Federal Research Institute for Animal Health, OIE Collaborating Centre for Zoonoses in Europe, Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Moritz Saxenhofer
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Genopode, 1015, Lausanne, Switzerland
| | - Stephan Drewes
- Federal Research Institute for Animal Health, OIE Collaborating Centre for Zoonoses in Europe, Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Mathias Schlegel
- Federal Research Institute for Animal Health, OIE Collaborating Centre for Zoonoses in Europe, Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17493, Greifswald, Insel Riems, Germany.,Seramun Diagnostica GmbH, 15754, Heidesee, Germany
| | - Konrad M Wanka
- Federal Research Institute for Animal Health, OIE Collaborating Centre for Zoonoses in Europe, Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Raphael Frank
- Goethe-University, Institute of Ecology, Evolution and Diversity, Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, 60438, Frankfurt am Main, Germany
| | - Sven Klimpel
- Goethe-University, Institute of Ecology, Evolution and Diversity, Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, 60438, Frankfurt am Main, Germany
| | | | - Denny Maaz
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Christiane Herden
- Institute for Veterinary Pathology, Justus-Liebig-Universität Gießen, 35392, Gießen, Germany
| | - Jona Freise
- Task-Force Veterinärwesen, Fachbereich Schädlingsbekämpfung, Niedersächsisches Landesamt für Verbraucherschutz und Lebensmittelsicherheit, 26133, Oldenburg, Germany
| | - Ronny Wolf
- Institute for Biology, University of Leipzig, 04103, Leipzig, Germany
| | - Michael Stubbe
- Institute of Zoology, Martin-Luther-University Halle, 06099, Halle, Germany
| | - Peter Borkenhagen
- Säugetierkundliche Arbeitsgemeinschaft Schleswig-Holstein, 24253, Probsteierhagen, Germany
| | - Hermann Ansorge
- Senckenberg Museum of Natural History, 02826, Görlitz, Germany
| | - Jana A Eccard
- Institute for Biochemistry and Biology, Animal Ecology, University of Potsdam, 14469, Potsdam, Germany
| | - Johannes Lang
- Institut für Tierökologie und Naturbildung, Hauptstraße 30, 35321, Gonterskirchen, Germany
| | - Elsa Jourdain
- INRA, French National Institute for Agricultural Research, UR0346 Animal Epidemiology Unit, Saint-Genès Champanelle, France
| | - Jens Jacob
- Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forestry, Vertebrate Research, Julius Kühn-Institute, 48161, Münster, Germany
| | - Philippe Marianneau
- Virology Unit, Laboratory of Lyon, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 69364, Lyon, France
| | - Gerald Heckel
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Genopode, 1015, Lausanne, Switzerland
| | - Rainer G Ulrich
- Federal Research Institute for Animal Health, OIE Collaborating Centre for Zoonoses in Europe, Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17493, Greifswald, Insel Riems, Germany.
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18
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Stojak J, Wójcik JM, Ruczyńska I, Searle JB, McDevitt AD. Contrasting and congruent patterns of genetic structuring in two Microtus vole species using museum specimens. MAMMAL RES 2016. [DOI: 10.1007/s13364-015-0260-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Fang F, Ji Y, Zhao Q, Wang Y, Gao W, Chu K, Sun H. Phylogeography of the Chinese endemic freshwater crabSinopotamon acutum(Brachyura, Potamidae). ZOOL SCR 2015. [DOI: 10.1111/zsc.12131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fang Fang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yongkun Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Qiang Zhao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yujuan Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Wei Gao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Kelin Chu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hongying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
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20
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Beysard M, Krebs-Wheaton R, Heckel G. Tracing reinforcement through asymmetrical partner preference in the European common vole Microtus arvalis. BMC Evol Biol 2015; 15:170. [PMID: 26303785 PMCID: PMC4548911 DOI: 10.1186/s12862-015-0455-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/13/2015] [Indexed: 12/04/2022] Open
Abstract
Background The mechanistic basis of speciation and in particular the contribution of behaviour to the completion of the speciation process is often contentious. Contact zones between related taxa provide a situation where selection against hybridization might reinforce separation by behavioural mechanisms, which could ultimately fully isolate the taxa. One of the most abundant European mammals, the common vole Microtus arvalis, forms multiple natural hybrid zones where rapidly diverging evolutionary lineages meet in secondary contact. Very narrow zones of hybridization spanning only a few kilometres and sex-specific gene flow patterns indicate reduced fitness of natural hybrids and incipient speciation between some of the evolutionary lineages. In this study, we examined the contribution of behavioural mechanisms to the speciation process in these rodents by fine-mapping allopatric and parapatric populations in the hybrid zone between the Western and Central lineages and experimental testing of the partner preferences of wild, pure-bred and hybrid female common voles. Results Genetic analysis based on microsatellite markers revealed the presence of multiple parapatric and largely non-admixed populations at distances of about 10 km at the edge of the area of natural hybridization between the Western and Central lineages. Wild females from Western parapatric populations and lab-born F1 hybrids preferred males from the Western lineage whereas wild females of Central parapatric origin showed no measurable preference. Furthermore, wild and lab-born females from allopatric populations of the Western or Central lineages showed no detectable preference for males from either lineage. Conclusions The detected partner preferences are consistent with asymmetrical reinforcement of pre-mating reproductive isolation mechanisms in the European common vole and with earlier results suggesting that hybridization is more detrimental to the Western lineage. As a consequence, these differences in behaviour might contribute to a further geographical stabilization of this moving hybrid zone. Such behavioural processes could also provide a mechanistic perspective for frequently-detected asymmetrical introgression patterns in the largely allopatrically diversifying Microtus genus and other rapidly speciating rodents.
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Affiliation(s)
- Mathias Beysard
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH 3012, Bern, Switzerland. .,Swiss Institute of Bioinformatics, Genopode, CH 1015, Lausanne, Switzerland.
| | - Rebecca Krebs-Wheaton
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH 3012, Bern, Switzerland. .,Present Address: Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306, Ploen, Germany.
| | - Gerald Heckel
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH 3012, Bern, Switzerland. .,Swiss Institute of Bioinformatics, Genopode, CH 1015, Lausanne, Switzerland.
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21
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Stojak J, McDevitt AD, Herman JS, Searle JB, Wójcik JM. Post-glacial colonization of eastern Europe from the Carpathian refugium: evidence from mitochondrial DNA of the common voleMicrotus arvalis. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12535] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Joanna Stojak
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
| | - Allan D. McDevitt
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; 3000 Leuven Belgium
| | - Jeremy S. Herman
- Department of Natural Sciences; National Museums Scotland; Edinburgh EH1 1JF UK
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14853-2701 USA
| | - Jan M. Wójcik
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
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22
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Continental-scale footprint of balancing and positive selection in a small rodent (Microtus arvalis). PLoS One 2014; 9:e112332. [PMID: 25383542 PMCID: PMC4226552 DOI: 10.1371/journal.pone.0112332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/06/2014] [Indexed: 01/01/2023] Open
Abstract
Genetic adaptation to different environmental conditions is expected to lead to large differences between populations at selected loci, thus providing a signature of positive selection. Whereas balancing selection can maintain polymorphisms over long evolutionary periods and even geographic scale, thus leads to low levels of divergence between populations at selected loci. However, little is known about the relative importance of these two selective forces in shaping genomic diversity, partly due to difficulties in recognizing balancing selection in species showing low levels of differentiation. Here we address this problem by studying genomic diversity in the European common vole (Microtus arvalis) presenting high levels of differentiation between populations (average FST = 0.31). We studied 3,839 Amplified Fragment Length Polymorphism (AFLP) markers genotyped in 444 individuals from 21 populations distributed across the European continent and hence over different environmental conditions. Our statistical approach to detect markers under selection is based on a Bayesian method specifically developed for AFLP markers, which treats AFLPs as a nearly codominant marker system, and therefore has increased power to detect selection. The high number of screened populations allowed us to detect the signature of balancing selection across a large geographic area. We detected 33 markers potentially under balancing selection, hence strong evidence of stabilizing selection in 21 populations across Europe. However, our analyses identified four-times more markers (138) being under positive selection, and geographical patterns suggest that some of these markers are probably associated with alpine regions, which seem to have environmental conditions that favour adaptation. We conclude that despite favourable conditions in this study for the detection of balancing selection, this evolutionary force seems to play a relatively minor role in shaping the genomic diversity of the common vole, which is more influenced by positive selection and neutral processes like drift and demographic history.
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Cucchi T, Barnett R, Martínková N, Renaud S, Renvoisé E, Evin A, Sheridan A, Mainland I, Wickham-Jones C, Tougard C, Quéré JP, Pascal M, Pascal M, Heckel G, O'Higgins P, Searle JB, Dobney KM. The changing pace of insular life: 5000 years of microevolution in the Orkney vole (Microtus arvalis orcadensis). Evolution 2014; 68:2804-20. [PMID: 24957579 PMCID: PMC5366975 DOI: 10.1111/evo.12476] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 06/09/2014] [Indexed: 12/21/2022]
Abstract
Island evolution may be expected to involve fast initial morphological divergence followed by stasis. We tested this model using the dental phenotype of modern and ancient common voles (Microtus arvalis), introduced onto the Orkney archipelago (Scotland) from continental Europe some 5000 years ago. First, we investigated phenotypic divergence of Orkney and continental European populations and assessed climatic influences. Second, phenotypic differentiation among Orkney populations was tested against geography, time, and neutral genetic patterns. Finally, we examined evolutionary change along a time series for the Orkney Mainland. Molar gigantism and anterior-lobe hypertrophy evolved rapidly in Orkney voles following introduction, without any transitional forms detected. Founder events and adaptation appear to explain this initial rapid evolution. Idiosyncrasy in dental features among different island populations of Orkney voles is also likely the result of local founder events following Neolithic translocation around the archipelago. However, against our initial expectations, a second marked phenotypic shift occurred between the 4th and 12th centuries AD, associated with increased pastoral farming and introduction of competitors (mice and rats) and terrestrial predators (foxes and cats). These results indicate that human agency can generate a more complex pattern of morphological evolution than might be expected in island rodents.
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Affiliation(s)
- Thomas Cucchi
- CNRS-Muséum National d'Histoire Naturelle, UMR 7209, Archéoozoologie, histoire des sociétés humaines et de peuplements animaux, 55 rue Buffon, 75005, Paris, France; Department of Archaeology, University of Aberdeen, St. Mary's, Elphinstone Road, Aberdeen, United Kingdom.
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Guerra D, Hegglin D, Bacciarini L, Schnyder M, Deplazes P. Stability of the southern European border of Echinococcus multilocularis in the Alps: evidence that Microtus arvalis is a limiting factor. Parasitology 2014; 141:1-10. [PMID: 24932666 DOI: 10.1017/s0031182014000730] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
SUMMARY The known range of the zoonotic fox tapeworm Echinococcus multilocularis has expanded since the 1990s, and today this parasite is recorded in higher abundances throughout large parts of Europe. This phenomenon is mostly attributed to the increasing European fox populations and their invasion of urban habitats. However, these factors alone are insufficient to explain the heterogeneous distribution of the parasite in Europe. Here, we analysed the spatial interrelationship of E. multilocularis with the known distribution of seven vole species in Ticino, southern Switzerland. Among 404 necropsied foxes (1990-2006) and 79 fox faecal samples (2010-2012), E. multilocularis was consistently found in the north of the investigated area. No expansion of this endemic focus was recorded during the 22 years of the study period. This stable endemic focus is coincident with the known distribution of the vole species Microtus arvalis but not, or only partly, with the distribution of the other autochthonous vole species. Our results give evidence that this vole species plays a crucial role in the maintenance of the parasite's life cycle and that its absence could be a limiting factor for the spread of E. multilocularis in this region.
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Affiliation(s)
- Diogo Guerra
- Institute of Parasitology, University of Zurich,Winterthurerstrasse 266a, CH-8057 Zurich,Switzerland
| | - Daniel Hegglin
- Institute of Parasitology, University of Zurich,Winterthurerstrasse 266a, CH-8057 Zurich,Switzerland
| | - Luca Bacciarini
- Cantonal Veterinary Office,Via Dogana 16, CH-6500 Bellinzona,Switzerland
| | - Manuela Schnyder
- Institute of Parasitology, University of Zurich,Winterthurerstrasse 266a, CH-8057 Zurich,Switzerland
| | - Peter Deplazes
- Institute of Parasitology, University of Zurich,Winterthurerstrasse 266a, CH-8057 Zurich,Switzerland
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25
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First molecular evidence for Puumala hantavirus in Poland. Viruses 2014; 6:340-53. [PMID: 24452006 PMCID: PMC3917447 DOI: 10.3390/v6010340] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/10/2014] [Accepted: 01/14/2014] [Indexed: 11/16/2022] Open
Abstract
Puumala virus (PUUV) causes mild to moderate cases of haemorrhagic fever with renal syndrome (HFRS), and is responsible for the majority of hantavirus infections of humans in Fennoscandia, Central and Western Europe. Although there are relatively many PUUV sequences available from different European countries, little is known about the presence of this virus in Poland. During population studies in 2009 a total of 45 bank voles were trapped at three sites in north-eastern Poland, namely islands on Dejguny and Dobskie Lakes and in a forest near Mikołajki. S and M segment-specific RT-PCR assays detected PUUV RNA in three animals from the Mikołajki site. The obtained partial S and M segment sequences demonstrated the highest similarity to the corresponding segments of a PUUV strain from Latvia. Analysis of chest cavity fluid samples by IgG ELISA using a yeast-expressed PUUV nucleocapsid protein resulted in the detection of two seropositive samples, both being also RT-PCR positive. Interestingly, at the trapping site in Mikołajki PUUV-positive bank voles belong to the Carpathian and Eastern genetic lineages within this species. In conclusion, we herein present the first molecular evidence for PUUV in the rodent reservoir from Poland.
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Beysard M, Heckel G. Structure and dynamics of hybrid zones at different stages of speciation in the common vole (Microtus arvalis). Mol Ecol 2014; 23:673-87. [DOI: 10.1111/mec.12613] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Mathias Beysard
- Computational and Molecular Population Genetics; Institute of Ecology and Evolution; University of Bern; CH 3012 Bern Switzerland
- Swiss Institute of Bioinformatics; Genopode CH 1015 Lausanne Switzerland
| | - Gerald Heckel
- Computational and Molecular Population Genetics; Institute of Ecology and Evolution; University of Bern; CH 3012 Bern Switzerland
- Swiss Institute of Bioinformatics; Genopode CH 1015 Lausanne Switzerland
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27
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Lischer HE, Excoffier L, Heckel G. Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles. Mol Biol Evol 2013; 31:817-31. [DOI: 10.1093/molbev/mst271] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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28
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Dong L, Heckel G, Liang W, Zhang Y. Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers. Mol Ecol 2013; 22:3376-90. [PMID: 23692215 DOI: 10.1111/mec.12315] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 11/27/2022]
Abstract
The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest species, we analysed morphological characters, mitochondrial DNA sequences and nuclear microsatellite loci in the Silver Pheasant (Lophura nycthemera). In a pattern generally consistent with phenotypic clusters, but not nominal subspecies, deeply divergent mitochondrial lineages restricted to different geographic regions were detected. Coalescent simulations indicated that the time of main divergence events corresponded to major glacial periods in the Pleistocene and gene flow was only partially lowered by drainage barriers between some populations. Intraspecific cytonuclear discordance was revealed in mitochondrial lineages from Hainan Island and the Sichuan Basin with evidence of nuclear gene flow from neighbouring populations into the latter. Unexpectedly, hybridization was revealed in Yingjiang between the Silver Pheasant and Kalij Pheasant (Lophura leucomelanos) with wide genetic introgression at both the mtDNA and nuclear levels. Our results highlight a novel phylogeographic pattern in a subtropical area generated from the combined effects of climate oscillation, partial drainage barriers and interspecific hybridization. Cytonuclear discordance combined with morphological differentiation implies that complex historical factors shaped the divergence process in this biodiversity hot spot area of southern China.
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Affiliation(s)
- Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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29
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Sauer J, Oldeland J, Hausdorf B. Continuing fragmentation of a widespread species by geographical barriers as initial step in a land snail radiation on crete. PLoS One 2013; 8:e62569. [PMID: 23658748 PMCID: PMC3641037 DOI: 10.1371/journal.pone.0062569] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/23/2013] [Indexed: 11/18/2022] Open
Abstract
The phylogeographic structure of the land snail Xerocrassa mesostena on Crete inferred from AFLP markers and mitochondrial cox1 sequences can be explained by three mechanisms: gene flow restriction, population expansion and leptokurtic dispersal. Gene flow restriction by geographic barriers caused subdivision of the gene pool into distinct clusters. Population expansion was probably facilitated by deforestation of Crete in the postglacial. Newly available areas were colonized by leptokurtic dispersal, i.e. slow active expansion resulting in isolation by distance within the clusters and occasional long distance dispersal events that resulted in departures from the isolation by distance model. Less than one percent of the AFLP markers show correlations with environmental variables. Random phylogeographic breaks in the distribution of the mitochondrial haplotype groups indicate that single locus markers, especially mitochondrial DNA, might result in a misleading picture of the phylogeographic structure of a species. Restriction of gene flow between metapopulations caused by geographical barriers can interact with sexual selection resulting in the differentiation of these metapopulations into separate species without noticeable ecological differentiation. Evidence for gene flow between parapatrically distributed evolutionary units representing different stages of the speciation process suggests that the ongoing process of fragmentation of the X. mesostena complex might be an example for parapatric speciation. The lack of ecological differentiation between these units confirms theoretical predictions that divergent selection for local adaptation is not required for rapid speciation.
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Affiliation(s)
- Jan Sauer
- Department of Chemical Ecology, University of Bielefeld, Bielefeld, Germany
- Zoological Museum, University of Hamburg, Hamburg, Germany
| | - Jens Oldeland
- Biodiversity, Evolution and Ecology of Plants, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany
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30
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Sex-specific clines support incipient speciation in a common European mammal. Heredity (Edinb) 2013; 110:398-404. [PMID: 23340600 DOI: 10.1038/hdy.2012.124] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Hybrid zones provide excellent opportunities to study processes and mechanisms underlying reproductive isolation and speciation. Here we investigated sex-specific clines of molecular markers in hybrid zones of morphologically cryptic yet genetically highly-diverged evolutionary lineages of the European common vole (Microtus arvalis). We analyzed the position and width of four secondary contact zones along three independent transects in the region of the Alps using maternally (mitochondrial DNA) and paternally (Y-chromosome) inherited genetic markers. Given male-biased dispersal in the common vole, a selectively neutral secondary contact would show broader paternal marker clines than maternal ones. In a selective case, for example, involving a form of Haldane's rule, Y-chromosomal clines would not be expected to be broader than maternal markers because they are transmitted by the heterogametic sex and thus gene flow would be restricted. Consistent with the selective case, paternal clines were significantly narrower or at most equal in width to maternal clines in all contact zones. In addition, analyses using maximum likelihood cline-fitting detected a shift of paternal relative to maternal clines in three of four contact zones. These patterns suggest that processes at the contact zones in the common vole are not selectively neutral, and that partial reproductive isolation is already established between these evolutionary lineages. We conclude that hybrid zone movement, sexual selection and/or genetic incompatibilities are likely associated with an unusual unidirectional manifestation of Haldane's rule in this common European mammal.
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31
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Bastos-Silveira C, Santos SM, Monarca R, Mathias MDL, Heckel G. Deep mitochondrial introgression and hybridization among ecologically divergent vole species. Mol Ecol 2012; 21:5309-23. [DOI: 10.1111/mec.12018] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 12/23/2022]
Affiliation(s)
| | - Sara M. Santos
- Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; Campo Grande; 1749-016; Lisbon; Portugal
| | - Rita Monarca
- Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; Campo Grande; 1749-016; Lisbon; Portugal
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32
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Kindler E, Arlettaz R, Heckel G. Deep phylogeographic divergence and cytonuclear discordance in the grasshopper Oedaleus decorus. Mol Phylogenet Evol 2012; 65:695-704. [PMID: 22884526 DOI: 10.1016/j.ympev.2012.07.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 07/06/2012] [Accepted: 07/23/2012] [Indexed: 11/16/2022]
Abstract
The grasshopper Oedaleus decorus is a thermophilic insect with a large, mostly south-Palaearctic distribution range, stretching from the Mediterranean regions in Europe to Central-Asia and China. In this study, we analyzed the extent of phylogenetic divergence and the recent evolutionary history of the species based on 274 specimens from 26 localities across the distribution range in Europe. Phylogenetic relationships were determined using sequences of two mitochondrial loci (ctr, ND2) with neighbour-joining and Bayesian methods. Additionally, genetic differentiation was analyzed based on mitochondrial DNA and 11 microsatellite markers using F-statistics, model-free multivariate and model-based Bayesian clustering approaches. Phylogenetic analyses detected consistently two highly divergent, allopatrically distributed lineages within O. decorus. The divergence among these Western and Eastern lineages meeting in the region of the Alps was similar to the divergence of each lineage to the sister species O. asiaticus. Genetic differentiation for ctr was extremely high between Western and Eastern grasshopper populations (F(ct)=0.95). Microsatellite markers detected much lower but nevertheless very significant genetic structure among population samples. The nuclear data also demonstrated a case of cytonuclear discordance because the affiliation with mitochondrial lineages was incongruent in Northern Italy. Taken together these results provide evidence of an ancient separation within Oedaleus and either historical introgression of mtDNA among lineages and/or ongoing sex-specific gene flow in this grasshopper. Our study stresses the importance of multilocus approaches for unravelling the history and status of taxa of uncertain evolutionary divergence.
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Affiliation(s)
- Eveline Kindler
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
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33
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Affiliation(s)
- David P L Toews
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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34
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Arteaga MC, Piñero D, Eguiarte LE, Gasca J, Medellín RA. Genetic structure and diversity of the nine-banded armadillo in Mexico. J Mammal 2012. [DOI: 10.1644/11-mamm-a-211.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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35
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Laurence S, Coltman DW, Gorrell JC, Schulte-Hostedde AI. Genetic structure of muskrat (Ondatra zibethicus) and its concordance with taxonomy in North America. J Hered 2011; 102:688-96. [PMID: 21810770 DOI: 10.1093/jhered/esr071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extrinsic factors such as physical barriers play an important role in shaping population genetic structure. A reduction in gene flow leading to population structuring may ultimately lead to population divergence. These divergent populations are often considered subspecies. Because genetic differentiation may represent differences between subspecies, patterns of genetic structure should reflect subspecies groupings. In this study, we examine the contemporary population genetic structure of muskrat (n = 331) and assess the relevance of 4 geographically distinct subspecies designations across northern North America using 9 microsatellite loci. We predicted that patterns of gene flow and genetic structure would reflect the described subspecies. We found evidence of genetic differentiation between western and eastern regions, and muskrats from Newfoundland (NF) showed significantly lower genetic diversity than central regions. A strong isolation by distance pattern was also detected within the eastern cluster. Our results did not differentiate Ondatra zibethicus spatulus (northwest) from O. z. albus (central), but they suggest a distinction between O. z. obscurus (NF) and O. z. zibethicus (east). This study highlights the need for more phylogenetic studies in order to better understand intraspecific divergence and the genetic characterization of subspecies.
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Affiliation(s)
- Sophie Laurence
- Department of Biology, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario, Canada.
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36
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WANG IANJ. Choosing appropriate genetic markers and analytical methods for testing landscape genetic hypotheses. Mol Ecol 2011. [DOI: 10.1111/j.1365-294x.2011.05123.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Mertens M, Kindler E, Emmerich P, Esser J, Wagner-Wiening C, Wölfel R, Petraityte-Burneikiene R, Schmidt-Chanasit J, Zvirbliene A, Groschup MH, Dobler G, Pfeffer M, Heckel G, Ulrich RG, Essbauer SS. Phylogenetic analysis of Puumala virus subtype Bavaria, characterization and diagnostic use of its recombinant nucleocapsid protein. Virus Genes 2011; 43:177-91. [PMID: 21598005 DOI: 10.1007/s11262-011-0620-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022]
Abstract
Puumala virus (PUUV) is the predominant hantavirus species in Germany causing large numbers of mild to moderate cases of haemorrhagic fever with renal syndrome (HFRS). During an outbreak in South-East Germany in 2004 a novel PUUV subtype designated Bavaria was identified as the causative agent of HFRS in humans [1]. Here we present a molecular characterization of this PUUV strain by investigating novel partial and almost entire nucleocapsid (N) protein-encoding small (S-) segment sequences and partial medium (M-) segment sequences from bank voles (Myodes glareolus) trapped in Lower Bavaria during 2004 and 2005. Phylogenetic analyses confirmed their classification as subtype Bavaria, which is further subdivided into four geographical clusters. The entire N protein, harbouring an amino-terminal hexahistidine tag, of the Bavarian strain was produced in yeast Saccharomyces cerevisiae and showed a slightly different reactivity with N-specific monoclonal antibodies, compared to the yeast-expressed N protein of the PUUV strain Vranica/Hällnäs. Endpoint titration of human sera from different parts of Germany and from Finland revealed only very slight differences in the diagnostic value of the different recombinant proteins. Based on the novel N antigen indirect and monoclonal antibody capture IgG-ELISAs were established. By using serum panels from Germany and Finland their validation demonstrated a high sensitivity and specificity. In summary, our investigations demonstrated the Bavarian PUUV strain to be genetically divergent from other PUUV strains and the potential of its N protein for diagnostic applications.
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Affiliation(s)
- Marc Mertens
- Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
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38
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Fischer MC, Foll M, Excoffier L, Heckel G. Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis). Mol Ecol 2011; 20:1450-62. [PMID: 21352386 DOI: 10.1111/j.1365-294x.2011.05015.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adaptation to adverse environmental conditions such as high altitude requires physiological and/or morphological changes. Genome scans provide a means to identify the genetic basis of such adaptations without previous knowledge about the particular genetic variants or traits under selection. In this study, we scanned 3027 amplified fragment length polymorphisms (AFLP) in four populations of the common vole Microtus arvalis for loci associated with local adaptation and high altitude. We investigated voles from two populations at high elevation (~2000 m a.s.l.) representing the upper limit of the altitudinal distribution of the species and two geographically close low-altitude populations (<600 m a.s.l.). Statistical analysis incorporated a new Bayesian F(ST) outlier approach specifically developed for AFLP markers, which considers the intensity of AFLP bands instead of mere presence/absence and allows to derive population-based estimates of allele frequencies and F(IS) values. Computer simulations showed that this approach increases the statistical power of the detection of AFLP markers under selection almost to the power of single nucleotide polymorphism (SNP) data without compromising specificity. Our enhanced genome scan resulted in 20 prime candidate markers for positive selection, which show mostly extremely high allele frequency differences between the low- and high-altitude populations. The comparison of global- and pairwise-enhanced genome scans demonstrated further that very strong selective signatures may also be associated with single populations suggesting the importance of local adaptation in alpine populations of common voles.
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Affiliation(s)
- Martin C Fischer
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern, Switzerland
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39
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40
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Johne R, Heckel G, Plenge-Bönig A, Kindler E, Maresch C, Reetz J, Schielke A, Ulrich RG. Novel hepatitis E virus genotype in Norway rats, Germany. Emerg Infect Dis 2010; 16:1452-5. [PMID: 20735931 PMCID: PMC3294985 DOI: 10.3201/eid1609.100444] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human hepatitis E virus infections may be caused by zoonotic transmission of virus genotypes 3 and 4. To determine whether rodents are a reservoir, we analyzed the complete nucleotide sequence of a hepatitis E–like virus from 2 Norway rats in Germany. The sequence suggests a separate genotype for this hepatotropic virus.
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Affiliation(s)
- Reimar Johne
- Federal Institute for Risk Assessment, Berlin, Germany
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41
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FOLL MATTHIEU, FISCHER MARTINC, HECKEL GERALD, EXCOFFIER LAURENT. Estimating population structure from AFLP amplification intensity. Mol Ecol 2010; 19:4638-47. [PMID: 20874760 DOI: 10.1111/j.1365-294x.2010.04820.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- MATTHIEU FOLL
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH‐3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Genopole, 1015 Lausanne, Switzerland
| | - MARTIN C. FISCHER
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH‐3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Genopole, 1015 Lausanne, Switzerland
| | - GERALD HECKEL
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH‐3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Genopole, 1015 Lausanne, Switzerland
| | - LAURENT EXCOFFIER
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH‐3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Genopole, 1015 Lausanne, Switzerland
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42
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Hahne J, Jenkins T, Halle S, Heckel G. Establishment success and resulting fitness consequences for vole dispersers. OIKOS 2010. [DOI: 10.1111/j.1600-0706.2010.18589.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Fink S, Fischer MC, Excoffier L, Heckel G. Genomic scans support repetitive continental colonization events during the rapid radiation of voles (Rodentia: Microtus): the utility of AFLPs versus mitochondrial and nuclear sequence markers. Syst Biol 2010; 59:548-72. [PMID: 20834011 DOI: 10.1093/sysbio/syq042] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single locus studies might not resolve phylogenetic relationships and the evolutionary history of taxa. The analysis of multiple markers promises higher resolution, and congruence among loci may indicate that the phylogenies represent the underlying species history. Here, we examine the utility of a genome-wide approach based on amplified fragment length polymorphisms (AFLP) and several DNA sequence markers in resolving phylogenetic signals in the rapidly radiating rodent genus Microtus which produced about 70 vole species within the last 1.2-2 myr. The current Holarctic distribution of Microtus is assumed to have resulted from three independent colonization events out of Asia to North America, Europe, and northern Asia without subsequent colonization, which would have led to deep splits between species from different continents. We investigated this hypothesis of three single colonization events by reconstructing the phylogenetic relationships among species from all three continents based on data from the first exon of the nuclear arginine vasopressin receptor 1a gene (EXON1), an adjacent noncoding region and the mitochondrial cytochrome b gene. The phylogenetic patterns obtained from these sequence markers are contrasted to genome-wide data on more than 1800 amplified fragment length polymorphisms (AFLP) analyzed for the same samples. Our results show that the single sequence markers partially resolve the phylogenetic relationships within Microtus, but with some incongruence mostly between EXON1 and the other loci. However, deeper nodes of the radiation are only weakly supported and neither the combination of the markers nor additional nuclear sequences improved the resolution significantly. AFLPs provided much stronger support for major continent-specific clades, and show also that reciprocal monophyly of American and European voles is incomplete. Our results demonstrate that Microtus voles colonized the American and European continents each repeatedly in several independent events on similar colonization routes during their radiation. More generally, this study supports the suitability of AFLPs as an alternative to sequence markers to resolve the evolutionary history of rapidly radiating taxa.
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Affiliation(s)
- Sabine Fink
- Department of Biology, Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
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Rodríguez F, Pérez T, Hammer SE, Albornoz J, Domínguez A. Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra). BMC Evol Biol 2010; 10:222. [PMID: 20649956 PMCID: PMC2923631 DOI: 10.1186/1471-2148-10-222] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2009] [Accepted: 07/22/2010] [Indexed: 01/24/2023] Open
Abstract
Background The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region) and microsatellites (20 loci) to include all subspecies and cover its entire distribution range. Results We found discordant microsatellite (μsat) and mitochondrial (mt) DNA phylogenies. Mitochondrial phylogenies form three clades, West, Central and East (mtW, mtC and mtE), at variance with taxonomic classification. Our divergence age estimates indicate an initial separation into branches mtW-mtC and mtE 1.7 million years ago (mya), in the late Pliocene-early Pleistocene, quickly followed by the split of clades mtW and mtC. Clade mtW contains haplotypes from the Iberian peninsula and the western Alps, Clade mtC includes haplotypes from the Apennines and the Massif of Chartreuse and Clade mtE comprises populations to the east of the Alps. Divergence among populations within these three major clades is recent (< 0.5 mya). New microsatellite multilocus genotypes added to previously published data revealed differences between every pair of subspecies, forming three well defined groups (μsatW, μsatC and μsatE) also with a strong geographic signature. Grouping does not correspond with the mitochondrial lineages but is closer to morphology and taxonomic classification. Recent drastic reductions in population size can be noted for the subspecies ornata as an extremely low diversity. Conclusions The phylogeographic patterns for mtDNA and microsatellites suggest an evolutionary history with limited range contractions and expansions during the Quaternary period and reflect a major effect of the Alpine barrier on west-east differentiation. The contrasting phylogenies for mtDNA and microsatellites indicate events of hybridization among highly divergent lineages in the central area of distribution. Our study points to the importance of reticulate evolution, with periods of isolation and reduction of population size followed by expansions and hybridizations, in the diversification at the level of close species or subspecies.
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Affiliation(s)
- Fernando Rodríguez
- Departamento de Biología Funcional, Universidad de Oviedo, Genética, Julián Clavería 6, 33071 Oviedo, Spain
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BUŽAN ELENAV, FÖRSTER DANIELW, SEARLE JEREMYB, KRYŠTUFEK BORIS. A new cytochrome b phylogroup of the common vole (Microtus arvalis) endemic to the Balkans and its implications for the evolutionary history of the species. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01451.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
The steadily advancing fields of landscape genetics and phylogeography share many goals. However, there are some very distinct differences between these two disciplines, including the kinds of data and analyses commonly used, the timescale over which these data are informative, and the hypotheses the data are used to examine. Recently, a number of studies appear to have confused or synonymized phylogeography and landscape genetics. The difference is not merely semantic; understanding the distinctions between these fields is important for ensuring that researchers are aware of the temporal scale over which their data are informative.
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Affiliation(s)
- Ian J Wang
- Department of Evolution and Ecology, Center for Population Biology, University of California, 1 Shields Ave, Davis, CA 95616, USA.
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Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L. ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics 2010; 11:116. [PMID: 20202215 PMCID: PMC2848233 DOI: 10.1186/1471-2105-11-116] [Citation(s) in RCA: 284] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 03/04/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. RESULTS Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. CONCLUSION ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.
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Affiliation(s)
- Daniel Wegmann
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
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Abstract
To examine the host association of Tula virus (TULV), a hantavirus present in large parts of Europe, we investigated a total of 791 rodents representing 469 Microtus arvalis and 322 Microtus agrestis animals from northeast, northwest, and southeast Germany, including geographical regions with sympatric occurrence of both vole species, for the presence of TULV infections. Based on serological investigation, reverse transcriptase PCR, and subsequent sequence analysis of partial small (S) and medium (M) segments, we herein show that TULV is carried not only by its commonly known host M. arvalis but also frequently by M. agrestis in different regions of Germany for a prolonged time period. At one trapping site, TULV was exclusively detected in M. agrestis, suggesting an isolated transmission cycle in this rodent reservoir separate from spillover infections of TULV-carrying M. arvalis. Phylogenetic analysis of the S and M segment sequences demonstrated geographical clustering of the TULV sequences irrespective of the host, M. arvalis or M. agrestis. The novel TULV lineages from northeast, northwest, and southeast Germany described here are clearly separated from each other and from other German, European, or Asian lineages, suggesting their stable geographical localization and fast sequence evolution. In conclusion, these results demonstrate that TULV represents a promiscuous hantavirus with a large panel of susceptible hosts. In addition, this may suggest an alternative evolution mode, other than a strict coevolution, for this virus in its Microtus hosts, which should be proven in further large-scale investigations on sympatric Microtus hosts.
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