1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Tang Q, Burri R, Liu Y, Suh A, Sundev G, Heckel G, Schweizer M. Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation. Mol Ecol 2021; 31:632-645. [PMID: 34674334 PMCID: PMC9298432 DOI: 10.1111/mec.16241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 02/03/2023]
Abstract
Morphological differentiation associated with evolutionary diversification is often explained with adaptive benefits but the processes and mechanisms maintaining cryptic diversity are still poorly understood. Using genome‐wide data, we show here that the pale sand martin Riparia diluta in Central and East Asia consists of three genetically deeply differentiated lineages which vary only gradually in morphology but broadly reflect traditional taxonomy. We detected no signs of gene flow along the eastern edge of the Qinghai‐Tibetan plateau between lowland south‐eastern Chinese R. d. fohkienensis and high‐altitude R. d. tibetana. Largely different breeding and migration timing between these low and high altitude populations as indicated by phenology data suggests that allochrony might act as prezygotic isolation mechanism in the area where their ranges abut. Mongolian populations of R. d. tibetana, however, displayed signs of limited mixed ancestries with Central Asian R. d. diluta. Their ranges meet in the area of a well‐known avian migratory divide, where western lineages take a western migration route around the Qinghai‐Tibetan plateau to winter quarters in South Asia, and eastern lineages take an eastern route to Southeast Asia. This might also be the case between western R. d. diluta and eastern R. d. tibetana as indicated by differing wintering grounds. We hypothesize that hybrids might have nonoptimal intermediate migration routes and selection against them might restrict gene flow. Although further potential isolation mechanisms might exist in the pale sand martin, our study points towards contrasting migration behaviour as an important factor in maintaining evolutionary diversity under morphological stasis.
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Affiliation(s)
- Qindong Tang
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Natural History Museum, Bern, Switzerland
| | - Reto Burri
- Schweizerische Vogelwarte, Sempach, Switzerland
| | - Yang Liu
- State Key Laboratory of Biocontrol, College of Ecology School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Alexander Suh
- School of Biological Sciences-Organisms and the Environment, University of East Anglia, Norwich, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society, Ulaanbaatar, Mongolia
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Manuel Schweizer
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Natural History Museum, Bern, Switzerland
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4
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Saxenhofer M, Labutin A, White TA, Heckel G. Host genetic factors associated with the range limit of a European hantavirus. Mol Ecol 2021; 31:252-265. [PMID: 34614264 PMCID: PMC9298007 DOI: 10.1111/mec.16211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 11/30/2022]
Abstract
The natural host ranges of many viruses are restricted to very specific taxa. Little is known about the molecular barriers between species that lead to the establishment of this restriction or generally prevent virus emergence in new hosts. Here, we identify genomic polymorphisms in a natural rodent host associated with a strong genetic barrier to the transmission of European Tula orthohantavirus (TULV). We analysed the very abrupt spatial transition between two major phylogenetic clades in TULV across the comparatively much wider natural hybrid zone between evolutionary lineages of their reservoir host, the common vole (Microtus arvalis). Genomic scans of 79,225 single nucleotide polymorphisms (SNPs) in 323 TULV‐infected host individuals detected 30 SNPs that were consistently associated with the TULV clades CEN.S or EST.S in two replicate sampling transects. Focusing the analysis on 199 voles with evidence of genomic admixture at the individual level (0.1–0.9) supported statistical significance for all 30 loci. Host genomic variation at these SNPs explained up to 37.6% of clade‐specific TULV infections. Genes in the vicinity of associated SNPs include SAHH, ITCH and two members of the Syngr gene family, which are involved in functions related to immune response or membrane transport. This study demonstrates the relevance of natural hybrid zones as systems not only for studying processes of evolutionary divergence and speciation, but also for the detection of evolving genetic barriers for specialized parasites.
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Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Génopode, Lausanne, Switzerland
| | - Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Thomas A White
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Génopode, Lausanne, Switzerland
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5
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Duarte MA, Fernandes CR, Heckel G, da Luz Mathias M, Bastos-Silveira C. Variation and Selection in the Putative Sperm-Binding Region of ZP3 in Muroid Rodents: A Comparison between Cricetids and Murines. Genes (Basel) 2021; 12:genes12091450. [PMID: 34573431 PMCID: PMC8469249 DOI: 10.3390/genes12091450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
In mammals, the zona pellucida glycoprotein 3 (ZP3) is considered a primary sperm receptor of the oocyte and is hypothesized to be involved in reproductive isolation. We investigated patterns of diversity and selection in the putative sperm-binding region (pSBR) of mouse ZP3 across Cricetidae and Murinae, two hyperdiverse taxonomic groups within muroid rodents. In murines, the pSBR is fairly conserved, in particular the serine-rich stretch containing the glycosylation sites proposed as essential for sperm binding. In contrast, cricetid amino acid sequences of the pSBR were much more variable and the serine-rich motif, typical of murines, was generally substantially modified. Overall, our results suggest a general lack of species specificity of the pSBR across the two muroid families. We document statistical evidence of positive selection acting on exons 6 and 7 of ZP3 and identified several amino acid sites that are likely targets of selection, with most positively selected sites falling within or adjacent to the pSBR.
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Affiliation(s)
- Margarida Alexandra Duarte
- Champalimaud Centre for the Uknown, Champalimaud Research, Champalimaud Foundation, Avenida Brasília, 1400-038 Lisboa, Portugal
- Museu Nacional de História Natural e da Ciência, Departamento de Zoologia e Antropologia, Universidade de Lisboa, Rua da Escola Politécnica, 58, Lisboa, 1250-102 Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal;
- Centro de Estudos de Ambiente e Mar, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Correspondence:
| | - Carlos Rodríguez Fernandes
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (C.R.F.); (C.B.-S.)
- Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland;
- SIB Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Amphipole, CH-1015 Lausanne, Switzerland
| | - Maria da Luz Mathias
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal;
- Centro de Estudos de Ambiente e Mar, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Cristiane Bastos-Silveira
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (C.R.F.); (C.B.-S.)
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6
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Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Mol Ecol 2021; 30:3797-3814. [PMID: 33638231 DOI: 10.1111/mec.15861] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/12/2021] [Indexed: 12/28/2022]
Abstract
Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder-rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.
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Affiliation(s)
- Anja M Westram
- IST Austria, Klosterneuburg, Austria.,Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Rui Faria
- Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
| | - Kerstin Johannesson
- Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Roger Butlin
- Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
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7
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Štohlová Putnová L, Štohl R, Ernst M, Svobodová K. A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic. Animals (Basel) 2021; 11:1701. [PMID: 34200330 DOI: 10.3390/ani11061701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/29/2022] Open
Abstract
Simple Summary The sika deer is a very flexible invasive species, capable of living dynamically in both large forests and mixed environment characterized by a prevalence of agricultural land. The Japanese sika deer was introduced to the Czech Republic at the end of the 19th century. The success of an introduced alien species may consist in their hybridizing with closely related taxa. Where few barriers to gene flow exist, rapid introgression of genetic traits from one species into another frequently occurs. The current Czech sika populations embody the most abundant and expanding group in continental Europe. In western Bohemia, we confirmed the interspecific hybridization with the native red deer. In this context, the red deer gene pool is endangered. The animals proliferate steadily in all directions and will most probably spread all over the Czech Republic if no major, timely changes in game management are adopted. Abstract Although inter-species hybrids between the red and sika deer can be phenotypically determined only exceptionally, there is the eventuality of identification via molecular genetic analysis. We used bi-parentally inherited microsatellite markers and a Bayesian statistical framework to re-examine the proportion of hybrids in the Czech red and sika deer populations. In total, 123 samples were collected, and the nuclear dataset consisted of 2668 allelic values. The number of alleles per locus ranged from 10 (BM1818) to 22 (BM888 and T193), yielding the mean of 16 alleles per locus across the deer. The mean allelic diversity of the red deer markedly exceeded that of the Japanese sika deer. Interspecific hybrids were detected, enabling us to confirm the genetic introgression of the sika deer into the red deer populations and vice versa in western Bohemia. The mean hybrid score equaled 10.6%, with 14.3% of the hybrids being among red deer–like individuals and 6.7% among sika-like ones. At two western Bohemian locations, namely, Doupovské hory and Slavkovský les, the total percentages of hybrid animals equaled 18.8 and 8.9, respectively. No red deer alleles were detected in the sika populations of the subregions of Kladská, Žlutice, and Lány. The NeighborNet network clearly separated the seven red and sika deer sampling populations according to the geography. The knowledge gained from the evaluated data is applicable in hunting management to reduce hybridization with the European deer.
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8
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Bímová BV, Macholán M, Ďureje Ľ, Bímová KB, Martincová I, Piálek J. Sperm quality, aggressiveness and generation turnover may facilitate unidirectional Y chromosome introgression across the European house mouse hybrid zone. Heredity (Edinb) 2020; 125:200-211. [PMID: 32528080 DOI: 10.1038/s41437-020-0330-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/29/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022] Open
Abstract
The widespread and locally massive introgression of Y chromosomes of the eastern house mouse (Mus musculus musculus) into the range of the western subspecies (M. m. domesticus) in Central Europe calls for an explanation of its underlying mechanisms. Given the paternal inheritance pattern, obvious candidates for traits mediating the introgression are characters associated with sperm quantity and quality. We can also expect traits such as size, aggression or the length of generation cycles to facilitate the spread. We have created two consomic strains carrying the non-recombining region of the Y chromosome of the opposite subspecies, allowing us to study introgression in both directions, something impossible in nature due to the unidirectionality of introgression. We analyzed several traits potentially related to male fitness. Transmission of the domesticus Y onto the musculus background had negative effects on all studied traits. Likewise, domesticus males possessing the musculus Y had, on average, smaller body and testes and lower sperm count than the parental strain. However, the same consomic males tended to produce less- dissociated sperm heads, to win more dyadic encounters, and to have shorter generation cycles than pure domesticus males. These data suggest that the domesticus Y is disadvantageous on the musculus background, while introgression in the opposite direction can confer a recognizable, though not always significant, selective advantage. Our results are thus congruent with the unidirectional musculus → domesticus Y chromosome introgression in Central Europe. In addition to some previous studies, they show this to be a multifaceted phenomenon demanding a multidisciplinary approach.
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Affiliation(s)
- Barbora Vošlajerová Bímová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic.,Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Veveří 97, 602 00, Brno, Czech Republic
| | - Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Veveří 97, 602 00, Brno, Czech Republic. .,Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Ľudovít Ďureje
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
| | - Kateřina Berchová Bímová
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences in Prague, Kamýcká 1176, 165 00, Prague, Czech Republic
| | - Iva Martincová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
| | - Jaroslav Piálek
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
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9
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McEntee JP, Burleigh JG, Singhal S. Dispersal Predicts Hybrid Zone Widths across Animal Diversity: Implications for Species Borders under Incomplete Reproductive Isolation. Am Nat 2020; 196:9-28. [PMID: 32552108 DOI: 10.1086/709109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hybrid zones occur as range boundaries for many animal taxa. One model for how hybrid zones form and stabilize is the tension zone model, a version of which predicts that hybrid zone widths are determined by a balance between random dispersal into hybrid zones and selection against hybrids. Here, we examine whether random dispersal and proxies for selection against hybrids (genetic distances between hybridizing pairs) can explain variation in hybrid zone widths across 131 hybridizing pairs of animals. We show that these factors alone can explain ∼40% of the variation in zone width among animal hybrid zones, with dispersal explaining far more of the variation than genetic distances. Patterns within clades were idiosyncratic. Genetic distances predicted hybrid zone widths particularly well for reptiles, while this relationship was opposite tension zone predictions in birds. Last, the data suggest that dispersal and molecular divergence set lower bounds on hybrid zone widths in animals, indicating that there are geographic restrictions on hybrid zone formation. Overall, our analyses reinforce the fundamental importance of dispersal in hybrid zone formation and more generally in the ecology of range boundaries.
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10
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Dufresnes C, Berroneau M, Dubey S, Litvinchuk SN, Perrin N. The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs. Sci Rep 2020; 10:5502. [PMID: 32218506 DOI: 10.1038/s41598-020-62382-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/11/2020] [Indexed: 01/13/2023] Open
Abstract
Because it is indicative of reproductive isolation, the amount of genetic introgression across secondary contact zones is increasingly considered in species delimitation. However, patterns of admixture at range margins can be skewed by the regional dynamics of hybrid zones. In this context, we posit an important role for phylogeographic history: hybrid zones located within glacial refugia (putatively formed during the Late-Pleistocene) should be better defined than those located in post-glacial or introduced ranges (putatively formed during the Holocene and the Anthropocene). We test this hypothesis in a speciation continuum of tree frogs from the Western Palearctic (Hyla), featuring ten identified contacts between species spanning Plio-Pleistocene to Miocene divergences. We review the rich phylogeographic literature of this group and examine the overlooked transition between H. arborea and H. molleri in Western France using a multilocus dataset. Our comparative analysis supports a trend that contacts zones resulting from post-glacial expansions and human translocations feature more extensive introgression than those established within refugial areas. Integrating the biogeographic history of incipient species, i.e. their age since first contact together with their genetic divergence, thus appears timely to draw sound evolutionary and taxonomic inferences from patterns of introgression across hybrid zones.
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Ryll R, Heckel G, Corman VM, Drexler JF, Ulrich RG. Genomic and spatial variability of a European common vole hepevirus. Arch Virol 2019; 164:2671-2682. [PMID: 31399875 DOI: 10.1007/s00705-019-04347-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/13/2019] [Indexed: 02/07/2023]
Abstract
Rodents host different orthohepeviruses, namely orthohepevirus C genotype HEV-C1 (rat hepatitis E virus, HEV) and the additional putative genotypes HEV-C3 and HEV-C4. Here, we screened 2,961 rodents from Central Europe by reverse transcription polymerase chain reaction (RT-PCR) and identified HEV RNA in 13 common voles (Microtus arvalis) and one bank vole (Myodes glareolus) with detection rates of 2% (95% confidence interval [CI]: 1-3.4) and 0.08% (95% CI: 0.002-0.46), respectively. Sequencing of a 279-nucleotide RT-PCR amplicon corresponding to a region within open reading frame (ORF) 1 showed a high degree of similarity to recently described common vole-associated HEV (cvHEV) sequences from Hungary. Five novel complete cvHEV genome sequences from Central Europe showed the typical HEV genome organization with ORF1, ORF2 and ORF3 and RNA secondary structure. Uncommon features included a noncanonical start codon in ORF3, multiple insertions and deletions within ORF1 and ORF2/ORF3, and the absence of a putative ORF4. Phylogenetic analysis showed all of the novel cvHEV sequences to be monophyletic, clustering most closely with an unassigned bird-derived sequence and other sequences of the species Orthohepevirus C. The nucleotide and amino acid sequence divergence of the common vole-derived sequences was significantly correlated with the spatial distance between the trapping sites, indicating mostly local evolutionary processes. Detection of closely related HEV sequences in common voles in multiple localities over a distance of 800 kilometers suggested that common voles are infected by cvHEV across broad geographic distances. The common vole-associated HEV strain is clearly divergent from HEV sequences recently found in narrow-headed voles (Microtus gregalis) and other cricetid rodents.
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Affiliation(s)
- René Ryll
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Gerald Heckel
- University of Bern, Institute of Ecology and Evolution, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne, Switzerland
| | - Victor M Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Campus Charité Mitte, Charitéplatz 1, 10098, Berlin, Germany.,German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Campus Charité Mitte, Charitéplatz 1, 10098, Berlin, Germany. .,German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany.
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, 17493, Greifswald-Insel Riems, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany.
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13
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Dufresnes C, Strachinis I, Suriadna N, Mykytynets G, Cogălniceanu D, Székely P, Vukov T, Arntzen JW, Wielstra B, Lymberakis P, Geffen E, Gafny S, Kumlutaş Y, Ilgaz Ç, Candan K, Mizsei E, Szabolcs M, Kolenda K, Smirnov N, Géniez P, Lukanov S, Crochet PA, Dubey S, Perrin N, Litvinchuk SN, Denoël M. Phylogeography of a cryptic speciation continuum in Eurasian spadefoot toads (Pelobates). Mol Ecol 2019; 28:3257-3270. [PMID: 31254307 DOI: 10.1111/mec.15133] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/30/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
Cryptic phylogeographic diversifications provide unique models to examine the role of phylogenetic divergence on the evolution of reproductive isolation, without extrinsic factors such as ecological and behavioural differentiation. Yet, to date very few comparative studies have been attempted within such radiations. Here, we characterize a new speciation continuum in a group of widespread Eurasian amphibians, the Pelobates spadefoot toads, by conducting multilocus (restriction site associated DNA sequencing and mitochondrial DNA) phylogenetic, phylogeographic and hybrid zone analyses. Within the P. syriacus complex, we discovered species-level cryptic divergences (>5 million years ago [My]) between populations distributed in the Near-East (hereafter P. syriacus sensu stricto [s.s.]) and southeastern Europe (hereafter P. balcanicus), each featuring deep intraspecific lineages. Altogether, we could scale hybridizability to divergence time along six different stages, spanning from sympatry without gene flow (P. fuscus and P. balcanicus, >10 My), parapatry with highly restricted hybridization (P. balcanicus and P. syriacus s.s., >5 My), narrow hybrid zones (~15 km) consistent with partial reproductive isolation (P. fuscus and P. vespertinus, ~3 My), to extensive admixture between Pleistocene and refugial lineages (≤2 My). This full spectrum empirically supports a gradual build up of reproductive barriers through time, reversible up until a threshold that we estimate at ~3 My. Hence, cryptic phylogeographic lineages may fade away or become reproductively isolated species simply depending on the time they persist in allopatry, and without definite ecomorphological divergence.
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Affiliation(s)
- Christophe Dufresnes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Hintermann & Weber SA, Montreux, Switzerland.,Laboratory for Conservation Biology, University of Lausanne, Lausanne, Switzerland
| | - Ilias Strachinis
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nataliia Suriadna
- Melitopol Insitute of Ecology and Social Technologies of University "Ukraine", Melitopol, Zaporizhia, Ukraine
| | | | - Dan Cogălniceanu
- Faculty of Natural Sciences and Agricultural Sciences, University Ovidius Constanţa, Constanţa, Romania
| | - Paul Székely
- Departamento de Ciencias Biológicas, EcoSs Lab, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Tanja Vukov
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Crete, Greece
| | - Eli Geffen
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Sarig Gafny
- School of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Kamil Candan
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Edvárd Mizsei
- Department of Tisza River Research, Danube Research Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Márton Szabolcs
- Department of Tisza River Research, Danube Research Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Krzysztof Kolenda
- Department of Evolutionary Biology and Conservation of Vertebrates, Institute of Environmental Biology, University of Wrocław, Wrocław, Poland
| | - Nazar Smirnov
- Department of Nature, Chernivtsi Regional Museum, Chernivtsi, Ukraine
| | - Philippe Géniez
- CEFE, EPHE-PSL, CNRS, University of Montpellier, University Paul Valéry Montpellier 3, IRD, Montpellier, France
| | - Simeon Lukanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Pierre-André Crochet
- CEFE, CNRS, University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Sylvain Dubey
- Hintermann & Weber SA, Montreux, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Agrosustain SA, Nyon, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.,Department of Zoology and Physiology, Dagestan State University, Makhachkala, Russia
| | - Mathieu Denoël
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Group, Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
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14
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15
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Martincová I, Ďureje Ľ, Kreisinger J, Macholán M, Piálek J. Phenotypic effects of the Y chromosome are variable and structured in hybrids among house mouse recombinant lines. Ecol Evol 2019; 9:6124-6137. [PMID: 31161024 PMCID: PMC6540687 DOI: 10.1002/ece3.5196] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/03/2019] [Indexed: 12/12/2022] Open
Abstract
Hybrid zones between divergent populations sieve genomes into blocks that introgress across the zone, and blocks that do not, depending on selection between interacting genes. Consistent with Haldane's rule, the Y chromosome has been considered counterselected and hence not to introgress across the European house mouse hybrid zone. However, recent studies detected massive invasion of M. m. musculus Y chromosomes into M. m. domesticus territory. To understand mechanisms facilitating Y spread, we created 31 recombinant lines from eight wild-derived strains representing four localities within the two mouse subspecies. These lines were reciprocally crossed and resulting F1 hybrid males scored for five phenotypic traits associated with male fitness. Molecular analyses of 51 Y-linked SNPs attributed ~50% of genetic variation to differences between the subspecies and 8% to differentiation within both taxa. A striking proportion, 21% (frequencies of sperm head abnormalities) and 42% (frequencies of sperm tail dissociations), of phenotypic variation was explained by geographic Y chromosome variants. Our crossing design allowed this explanatory power to be examined across a hierarchical scale from subspecific to local intrastrain effects. We found that divergence and variation were expressed diversely in different phenotypic traits and varied across the whole hierarchical scale. This finding adds another dimension of complexity to studies of Y introgression not only across the house mouse hybrid zone but potentially also in other contact zones.
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Affiliation(s)
- Iva Martincová
- Research Facility Studenec, Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
- Department of Botany and Zoology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Ľudovít Ďureje
- Research Facility Studenec, Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of ScienceCharles University in PraguePragueCzech Republic
| | - Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and GeneticsCzech Academy of SciencesBrnoCzech Republic
| | - Jaroslav Piálek
- Research Facility Studenec, Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
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16
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Tarnowska E, Niedziałkowska M, Jędrzejewska B. Genetic structure of bank vole populations in the contact zone of two lineages in north-eastern Poland. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Cortés-Ortiz L, Baiz MD, Hermida-Lagunes J, García-Orduña F, Rangel-Negrín A, Kitchen DM, Bergman TJ, Dias PAD, Canales-Espinosa D. Reduced Introgression of Sex Chromosome Markers in the Mexican Howler Monkey ( Alouatta palliata × A. pigra) Hybrid Zone. INT J PRIMATOL 2019; 40:114-131. [PMID: 30880850 PMCID: PMC6394575 DOI: 10.1007/s10764-018-0056-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/07/2018] [Indexed: 01/12/2023]
Abstract
Interspecific hybridization allows the introgression or movement of alleles from one genome to another. While some genomic regions freely exchange alleles during hybridization, loci associated with reproductive isolation do not intermix. In many model organisms, the X chromosome displays limited introgression compared to autosomes owing to the presence of multiple loci associated with hybrid sterility or inviability (the "large X-effect"). Similarly, if hybrids are produced, the heterogametic sex is usually inviable or sterile, a pattern known as Haldane's rule. We analyzed the patterns of introgression of genetic markers located in the mitochondrial (control region) and nuclear (autosomal microsatellites and sex chromosome genes) genomes of two howler monkey species (Alouatta palliata and A. pigra) that form a natural hybrid zone in southern Mexico, to evaluate whether the large X-effect and Haldane's rule affect the outcomes of hybridization between these sister species. To identify the level of admixture of each individual in the hybrid zone (N = 254) we analyzed individuals sampled outside the hybrid zone (109 A. pigra and 39 A. palliata) to determine allele frequencies of parental species and estimated a hybrid index based on nuclear markers. We then performed a cline analysis using individuals in the hybrid zone to determine patterns of introgression for each locus. Our analyses show that although the hybrid zone is bimodal (with no known F1 s and few recent generation hybrids) and quite narrow, there has been extensive introgression in both directions, and there is a large array of admixed individuals in the hybrid zone. Mitochondrial and most autosomal markers showed bidirectional introgression, but some had biased introgression toward one species or the other. All markers on the sex chromosomes and a few autosomal markers showed highly restricted introgression. This pattern is consistent with the hypothesis that the sex chromosomes make a disproportionate contribution to reproductive isolation, and our results broaden the taxonomic representation of these patterns across animal taxa.
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Affiliation(s)
- Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA
| | - Marcella D Baiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA
| | | | | | | | - Dawn M Kitchen
- Department of Anthropology, The Ohio State University, Columbus, OH 43210 USA
| | - Thore J Bergman
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA.,Department of Psychology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Pedro A D Dias
- Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico
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Stojak J, Borowik T, Górny M, Mcdevitt AD, Wójcik JM. Climatic influences on the genetic structure and distribution of the common vole and field vole in Europe. MAMMAL RES 2019; 64:19-29. [DOI: 10.1007/s13364-018-0395-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Abstract
Relationships between phylogenetic relatedness, hybrid zone spatial structure, the amount of interspecific gene flow and population demography were investigated, with the newt genus Triturus as a model system. In earlier work, a bimodal hybrid zone of two distantly related species combined low interspecific gene flow with hybrid sterility and heterosis was documented. Apart from that, a suite of unimodal hybrid zones in closely related Triturus showed more or less extensive introgressive hybridization with no evidence for heterosis. We here report on population demography and interspecific gene flow in two Triturus species (T. macedonicus and T. ivanbureschi in Serbia). These are two that are moderately related, engage in a heterogeneous uni-/bimodal hybrid zone and hence represent an intermediate situation. This study used 13 diagnostic nuclear genetic markers in a population at the species contact zone. This showed that all individuals were hybrids, with no parentals detected. Age, size and longevity and the estimated growth curves are not exceeding that of the parental species, so that we conclude the absence of heterosis in T. macedonicus-T. ivanbureschi. Observations across the genus support the hypothesis that fertile hybrids allocate resources to reproduction and infertile hybrids allocate resources to growth. Several Triturus species hybrid zones not yet studied allow the testing of this hypothesis.
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Affiliation(s)
| | - Nazan Üzüm
- Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, Aydin, Turkey
| | - Maja D. Ajduković
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Ana Ivanović
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Slender AL, Louter M, Gardner MG, Kleindorfer S. Thick-billed grasswren (Amytornis modestus) songs differ across subspecies and elicit different subspecific behavioural responses. T ROY SOC SOUTH AUST 2018. [DOI: 10.1080/03721426.2018.1483185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Amy L. Slender
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Marina Louter
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Michael G. Gardner
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- Evolutionary Biology Unit, Adelaide, SA, Australia
| | - Sonia Kleindorfer
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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23
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Sciuchetti L, Dufresnes C, Cavoto E, Brelsford A, Perrin N. Dobzhansky-Muller incompatibilities, dominance drive, and sex-chromosome introgression at secondary contact zones: A simulation study. Evolution 2018; 72:1350-1361. [PMID: 29806172 DOI: 10.1111/evo.13510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 05/08/2018] [Indexed: 11/28/2022]
Abstract
Dobzhansky-Muller (DM) incompatibilities involving sex chromosomes have been proposed to account for Haldane's rule (lowered fitness among hybrid offspring of the heterogametic sex) as well as Darwin's corollary (asymmetric fitness costs with respect to the direction of the cross). We performed simulation studies of a hybrid zone to investigate the effects of different types of DM incompatibilities on cline widths and positions of sex-linked markers. From our simulations, X-Y incompatibilities generate steep clines for both X-linked and Y-linked markers; random effects may produce strong noise in cline center positions when migration is high relative to fitness costs, but X- and Y-centers always coincide strictly. X-autosome and Y-autosome incompatibilities also generate steep clines, but systematic shifts in cline centers occur when migration is high relative to selection, as a result of a dominance drive linked to Darwin's corollary. Interestingly, sex-linked genes always show farther introgression than the associated autosomal genes. We discuss ways of disentangling the potentially confounding effects of sex biases in migration, we compare our results to those of a few documented contact zones, and we stress the need to study independent replicates of the same contact zone.
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Affiliation(s)
- Luca Sciuchetti
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
- Department of Animal & Plant Sciences, University of Sheffield, Alfred Denny building, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Elisa Cavoto
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Alan Brelsford
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
- Biology Department, University of California, Riverside, CA, 92521
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
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24
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Dufresnes C, Lymberakis P, Kornilios P, Savary R, Perrin N, Stöck M. Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic. BMC Evol Biol 2018; 18:67. [PMID: 29720079 PMCID: PMC5930823 DOI: 10.1186/s12862-018-1179-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 04/16/2018] [Indexed: 11/18/2022] Open
Abstract
Background Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs. Results We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids. Conclusions The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia. Electronic supplementary material The online version of this article (10.1186/s12862-018-1179-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Knosos Av, P.O. Box 2208, 71409, Irakleio, Crete, Greece
| | - Panagiotis Kornilios
- Section of Animal Biology, Department of Biology, School of Natural Sciences, University of Patras, GR-26500, Patras, Greece.,Department of Biology, University of Washington, Box 351800, Seattle, WA, 98195-1800, USA
| | - Romain Savary
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587, Berlin, Germany.
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Barbosa S, Paupério J, Pavlova SV, Alves PC, Searle JB. The Microtus voles: Resolving the phylogeny of one of the most speciose mammalian genera using genomics. Mol Phylogenet Evol 2018; 125:85-92. [PMID: 29574272 DOI: 10.1016/j.ympev.2018.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/03/2018] [Accepted: 03/14/2018] [Indexed: 11/24/2022]
Abstract
Sequential rapid radiations pose some of the greatest difficulties in phylogenetics, especially when analysing only a small number of genetic markers. Given that most of the speciation events occur in quick succession at various points in time, this creates particular challenges in determining phylogenetic relationships, i.e. branching order and divergence times. With the development of high throughput sequencing, thousands of markers can now readily be used to tackle these issues. Microtus is a speciose genus currently composed of 65 species that evolved over the last 2 million years. Although it is a well-studied group, there is still phylogenetic uncertainty at various divergence levels. Building upon previous studies that generally used small numbers of mitochondrial and/or nuclear loci, in this genomic-scale study we used both mitochondrial and nuclear data to study the rapid radiation within Microtus, using partial mitogenomes and genotyping-by-sequencing (GBS) on seven species representing five Microtus subgenera and the main biogeographic ranges where this group occurs. Both types of genome (mitochondrial and nuclear) generated similar tree topologies, with a basal split of the Nearctic (M. ochrogaster) and Holarctic (M. oeconomus) species, and then a subdivision of the five Palearctic species into two subgroups. These data support the occurrence of two European radiations, one North American radiation, and a later expansion of M. oeconomus from Asia to both Europe and North America. We further resolved the positioning of M. cabrerae as sister group of M. agrestis and refute the claim that M. cabrerae should be elevated to its own genus (Iberomys). Finally, the data support ongoing speciation events, especially within M. agrestis, with high levels of genetic divergence between the three Evolutionarily Significant Units (ESUs) previously identified. Similar high levels of divergence were also found among ESUs within M. oeconomus and M. arvalis.
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Grabenstein KC, Taylor SA. Breaking Barriers: Causes, Consequences, and Experimental Utility of Human-Mediated Hybridization. Trends Ecol Evol 2018; 33:198-212. [DOI: 10.1016/j.tree.2017.12.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 11/08/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022]
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Abstract
Hybridization with invasive species is one of the major threats to the phenotypic and genetic persistence of native organisms worldwide. Arion vulgaris (syn. lusitanicus) is a major agricultural pest slug that successfully invaded many European countries in recent decades, but its impact on closely related native species remains unclear. Here, we hypothesized that the regional decline of native A. rufus is connected with the spread of invasive A. vulgaris, and tested whether this can be linked to hybridization between the two species by analyzing 625 Arion sp. along altitudinal transects in three regions in Switzerland. In each region, we observed clear evidence of different degrees of genetic admixture, suggesting recurrent hybridization beyond the first generation. We found spatial differences in admixture patterns that might reflect distinct invasion histories among the regions. Our analyses provide a landscape level perspective for the genetic interactions between invasive and native animals during the invasion. We predict that without specific management action, A. vulgaris will further expand its range, which might lead to local extinction of A. rufus and other native slugs in the near future. Similar processes are likely occurring in other regions currently invaded by A. vulgaris.
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Armella Sierra AB, Castillo ER, Labaroni C, Barrandeguy ME, Martí DA, Ojeda R, Lanzone C. Genetic studies in the recently divergent Eligmodontia puerulus and E. moreni (Rodentia, Cricetidae, Sigmodontinae) from Puna and Monte deserts of South America. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Delahaie B, Cornuault J, Masson C, Bertrand JAM, Bourgeois YXC, Milá B, Thébaud C. Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex. J Evol Biol 2017; 30:2132-2145. [DOI: 10.1111/jeb.13177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/26/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023]
Affiliation(s)
- B. Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
- Centre d'Ecologie Fonctionnelle et Evolutive; CNRS-UMR5175 CEFE; Montpellier France
| | - J. Cornuault
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - C. Masson
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - J. A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - Y. X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - B. Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | - C. Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
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Barbosa S, Paupério J, Herman JS, Ferreira CM, Pita R, Vale-Gonçalves HM, Cabral JA, Garrido-García JA, Soriguer RC, Beja P, Mira A, Alves PC, Searle JB. Endemic species may have complex histories: within-refugium phylogeography of an endangered Iberian vole. Mol Ecol 2017; 26:951-967. [DOI: 10.1111/mec.13994] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 11/18/2016] [Accepted: 12/13/2016] [Indexed: 01/18/2023]
Affiliation(s)
- S. Barbosa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Department of Ecology and Evolutionary Biology; Corson Hall, Cornell University; Ithaca NY 14853-2701 USA
| | - J. Paupério
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
| | - J. S. Herman
- Department of Natural Sciences; National Museums Scotland; Chambers Street Edinburgh EH1 1JF UK
| | - C. M. Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
| | - R. Pita
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade de Évora; 7000-890 Évora Portugal
| | - H. M. Vale-Gonçalves
- CITAB, Centro de Investigação e Tecnologias Agroambientais e Biológicas; Universidade de Trás-os-Montes e Alto Douro (UTAD); 5001-801 Vila Real Portugal
| | - J. A. Cabral
- CITAB, Centro de Investigação e Tecnologias Agroambientais e Biológicas; Universidade de Trás-os-Montes e Alto Douro (UTAD); 5001-801 Vila Real Portugal
| | - J. A. Garrido-García
- Estación Biológica de Doñana (CSIC); Avda Américo Vespucio s/n, Isla de la Cartuja 41092 Sevilla Spain
| | - R. C. Soriguer
- Estación Biológica de Doñana (CSIC); Avda Américo Vespucio s/n, Isla de la Cartuja 41092 Sevilla Spain
| | - P. Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - A. Mira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade de Évora; 7000-890 Évora Portugal
| | - P. C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM); 13005 Ciudad Real Spain
| | - J. B. Searle
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO Laboratório Associado; Universidade do Porto; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Department of Ecology and Evolutionary Biology; Corson Hall, Cornell University; Ithaca NY 14853-2701 USA
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Slender AL, Louter M, Gardner MG, Kleindorfer S. Plant community predicts the distribution and occurrence of thick-billed grasswren subspecies (Amytornis modestus) in a region of parapatry. AUST J ZOOL 2017. [DOI: 10.1071/zo17081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Habitat heterogeneity can have considerable effects on gene flow and migration across a region of parapatry. Describing habitat across a region of parapatry is important for the development of eco-evolutionary theory. Two subspecies of thick-billed grasswren (Amytornis modestus) share a region of parapatry between the South Australian salt lakes, Lake Eyre and Lake Torrens. While the two subspecies remain morphologically diverged outside the region of parapatry, it is not known what factors within the region of parapatry may affect migration and gene flow. In this study, we test associations between habitat differences and subspecies distributions and discuss whether ecological barriers could play a role in mitigating gene flow between the subspecies. We compare dominant plant species (1) between the allopatric ranges of the subspecies and within their region of parapatry, and (2) in relation to presence or absence of grasswrens within their region of parapatry. We found that the dominant plant species differed between grasswren subspecies in their allopatric range and in their region of parapatry, and also differed in the region of parapatry at sites with or without grasswrens. Specifically, grasswrens were absent in vegetation that is typical of sand dunes. These findings are discussed in light of evidence for secondary contact and hybridisation between A. m. indulkanna and A. m. raglessi, and susceptibility to introgression.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Engebretsen KN, Barrow LN, Rittmeyer EN, Brown JM, Moriarty Lemmon E. Quantifying the spatiotemporal dynamics in a chorus frog (Pseudacris) hybrid zone over 30 years. Ecol Evol 2016; 6:5013-31. [PMID: 27547330 PMCID: PMC4979724 DOI: 10.1002/ece3.2232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/11/2016] [Accepted: 05/16/2016] [Indexed: 12/14/2022] Open
Abstract
Although theory suggests that hybrid zones can move or change structure over time, studies supported by direct empirical evidence for these changes are relatively limited. We present a spatiotemporal genetic study of a hybrid zone between Pseudacris nigrita and P. fouquettei across the Pearl River between Louisiana and Mississippi. This hybrid zone was initially characterized in 1980 as a narrow and steep “tension zone,” in which hybrid populations were inferior to parentals and were maintained through a balance between selection and dispersal. We reanalyzed historical tissue samples and compared them to samples of recently collected individuals using microsatellites. Clinal analyses indicate that the cline has not shifted in roughly 30 years but has widened significantly. Anthropogenic and natural changes may have affected selective pressure or dispersal, and our results suggest that the zone may no longer best be described as a tension zone. To the best of our knowledge, this study provides the first evidence of significant widening of a hybrid cline but stasis of its center. Continued empirical study of dynamic hybrid zones will provide insight into the forces shaping their structure and the evolutionary potential they possess for the elimination or generation of species.
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Affiliation(s)
- Kristin N Engebretsen
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee Florida 32306
| | - Lisa N Barrow
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee Florida 32306
| | - Eric N Rittmeyer
- Department of Biological Sciences Museum of Natural Science Louisiana State University 202 Life Sciences Building Baton Rouge Louisiana 70803; Research School of Biology The Australian National University Gould Building 116 Canberra ACT 2601 Australia
| | - Jeremy M Brown
- Department of Biological Sciences Museum of Natural Science Louisiana State University 202 Life Sciences Building Baton Rouge Louisiana 70803
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee Florida 32306
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Duarte MA, Heckel G, da Luz Mathias M, Bastos-silveira C. Olfactory receptors and behavioural isolation: a study on Microtus voles. MAMMAL RES 2016; 61:399-407. [DOI: 10.1007/s13364-016-0266-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rougemont Q, Gaigher A, Lasne E, Côte J, Coke M, Besnard AL, Launey S, Evanno G. Low reproductive isolation and highly variable levels of gene flow reveal limited progress towards speciation between European river and brook lampreys. J Evol Biol 2015; 28:2248-63. [PMID: 26348652 DOI: 10.1111/jeb.12750] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 09/02/2015] [Accepted: 09/02/2015] [Indexed: 01/10/2023]
Abstract
Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here, we used a combination of mating trials, experimental crosses and population genetic analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000 individuals of the migratory parasitic river lamprey (Lampetra fluviatilis) and freshwater-resident nonparasitic brook lamprey (Lampetra planeri) distributed in 10 sympatric and parapatric population pairs in France. Mating trials, parentage analyses and artificial fertilizations demonstrated a low level of reproductive isolation between species even though size-assortative mating may contribute to isolation. Most parapatric population pairs were strongly differentiated due to the joint effects of geographic distance and barriers to migration. In contrast, we found variable levels of gene flow between sympatric populations ranging from panmixia to moderate differentiation, which indicates a gradient of divergence with some population pairs that may correspond to alternative morphs or ecotypes of a single species and others that remain partially isolated. Ecologically based divergent selection may explain these variable levels of divergence among sympatric population pairs, but incomplete genome swamping following secondary contact could have also played a role. Overall, this study illustrates how highly differentiated phenotypes can be maintained despite high levels of gene flow that limit the progress towards speciation.
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Affiliation(s)
- Q Rougemont
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - A Gaigher
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France.,Laboratory for Conservation Biology, Department of Ecology and Evolution, University of Lausanne, Biophore, Switzerland
| | - E Lasne
- Muséum National d'Histoire Naturelle, CRESCO, Dinard, France.,UMR CARRTEL, INRA, Thonon-les-Bains, France
| | - J Côte
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - M Coke
- Unité Expérimentale d'Ecologie et d'Ecotoxicologie Aquatique, INRA, Rennes, France
| | - A-L Besnard
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - S Launey
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - G Evanno
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dufresnes C, Brelsford A, Crnobrnja-Isailović J, Tzankov N, Lymberakis P, Perrin N. Timeframe of speciation inferred from secondary contact zones in the European tree frog radiation (Hyla arborea group). BMC Evol Biol 2015; 15:155. [PMID: 26253600 DOI: 10.1186/s12862-015-0385-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/20/2015] [Indexed: 12/02/2022] Open
Abstract
Background Hybridization between incipient species is expected to become progressively limited as their genetic divergence increases and reproductive isolation proceeds. Amphibian radiations and their secondary contact zones are useful models to infer the timeframes of speciation, but empirical data from natural systems remains extremely scarce. Here we follow this approach in the European radiation of tree frogs (Hyla arborea group). We investigated a natural hybrid zone between two lineages (Hyla arborea and Hyla orientalis) of Mio-Pliocene divergence (~5 My) for comparison with other hybrid systems from this group. Results We found concordant geographic distributions of nuclear and mitochondrial gene pools, and replicated narrow transitions (~30 km) across two independent transects, indicating an advanced state of reproductive isolation and potential local barriers to dispersal. This result parallels the situation between H. arborea and H. intermedia, which share the same amount of divergence with H. orientalis. In contrast, younger lineages show much stronger admixture at secondary contacts. Conclusions Our findings corroborate the negative relationship between hybridizability and divergence time in European tree frogs, where 5 My are necessary to achieve almost complete reproductive isolation. Speciation seems to progress homogeneously in this radiation, and might thus be driven by gradual genome-wide changes rather than single speciation genes. However, the timescale differs greatly from that of other well-studied amphibians. General assumptions on the time necessary for speciation based on evidence from unrelated taxa may thus be unreliable. In contrast, comparative hybrid zone analyses within single radiations such as our case study are useful to appreciate the advance of speciation in space and time. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0385-2) contains supplementary material, which is available to authorized users.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Fischer MC, Foll M, Heckel G, Excoffier L. Continental-scale footprint of balancing and positive selection in a small rodent (Microtus arvalis). PLoS One 2014; 9:e112332. [PMID: 25383542 DOI: 10.1371/journal.pone.0112332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Jing M, Yu HT, Bi X, Lai YC, Jiang W, Huang L. Phylogeography of Chinese house mice (Mus musculus musculus/castaneus): distribution, routes of colonization and geographic regions of hybridization. Mol Ecol 2014; 23:4387-405. [PMID: 25065953 DOI: 10.1111/mec.12873] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 11/27/2022]
Abstract
House mice (Mus musculus) are human commensals and have served as a primary model in biomedical, ecological and evolutionary research. Although there is detailed knowledge of the biogeography of house mice in Europe, little is known of the history of house mice in China, despite the fact that China encompasses an enormous portion of their range. In the present study, 535 house mice caught from 29 localities in China were studied by sequencing the mitochondrial D-loop and genotyping 10 nuclear microsatellite markers distributed on 10 chromosomes. Phylogenetic analyses revealed two evolutionary lineages corresponding to Mus musculus castaneus and Mus musculus musculus in the south and north, respectively, with the Yangtze River approximately representing the boundary. More detailed analyses combining published sequence data from mice sampled in neighbouring countries revealed the migration routes of the two subspecies into China: M. m. castaneus appeared to have migrated through a southern route (Yunnan and Guangxi), whereas M. m. musculus entered China from Kazakhstan through the north-west border (Xinjiang). Bayesian analysis of mitochondrial sequences indicated rapid population expansions in both subspecies, approximately 4650-9300 and 7150-14 300 years ago for M. m. castaneus and M. m. musculus, respectively. Interestingly, the migration routes of Chinese house mice coincide with the colonization routes of modern humans into China, and the expansion times of house mice are consistent with the development of agriculture in southern and northern China, respectively. Finally, our study confirmed the existence of a hybrid zone between M. m. castaneus and M. m. musculus in China. Further study of this hybrid zone will provide a useful counterpart to the well-studied hybrid zone between M. m. musculus and Mus musculus domesticus in central Europe.
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Affiliation(s)
- Meidong Jing
- College of Life Sciences, Ludong University, Yantai, Shandong, 264025, China
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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