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Awadi A, Ben Slimen H, Smith S, Makni M, Suchentrunk F. Patterns of evolution in MHC class II DQA and DQB exon 2 genes of Alpine mountain hares, Lepus timidus varronis, and sympatric and parapatric brown hares, L. europaeus, from Switzerland. Immunogenetics 2024; 76:37-50. [PMID: 38114658 DOI: 10.1007/s00251-023-01328-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
In natural populations, hybridization is known to occur between a wide range of species. However, its evolutionary significance is less clear. Genes involved in fighting pathogens are considered excellent candidates for studying adaptive introgression, although both introgression and balancing selection can generate similar patterns of diversity and differentiation. Here, we compared DQA and DQB MHC class II and microsatellite allelic diversity of sympatric and parapatric mountain (Lepus timidus) and brown hare (L. europaeus) populations from Switzerland. We detected higher genetic diversity in brown hares compared to mountain hares at both MHC and microsatellite loci. We consider the observed patterns of microsatellite diversity both for L. europaeus and L. timidus as result of stochastic demographic processes while the pattern of MHC polymorphism of the studied hare populations can be explained by pathogen-driven selection. Rare bidirectional gene flow between both hare species seems to occur specifically for MHC alleles. However, the high number of shared alleles showing similar high frequency in both species suggests that reciprocally exchanged MHC alleles are being maintained via balancing selection. Adaptation to similar pathogen communities can also lead to parallel selection of MHC alleles. Positive selection, recombination and mutations have played different roles in shaping the patterns of MHC allelic diversity in and differentiation between both species. Results for the latter evolutionary forces do not show a better matching between the sympatric populations compared to the parapatric ones, suggesting a minor role of introgression for the observed evolutionary patterns of the studied hare species.
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Affiliation(s)
- A Awadi
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Béja, 9000, Tunisia
| | - H Ben Slimen
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Béja, 9000, Tunisia.
| | - S Smith
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, Vienna, 1160, Austria
| | - M Makni
- Faculty of Sciences of Tunis, LR01ES05 Biochimie et Biotechnologie, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - F Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, Vienna, 1160, Austria
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2
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Nikelski E, Rubtsov AS, Irwin D. High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression. Heredity (Edinb) 2023; 130:1-13. [PMID: 36463372 PMCID: PMC9814147 DOI: 10.1038/s41437-022-00580-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.
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Affiliation(s)
- Ellen Nikelski
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada.
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
| | | | - Darren Irwin
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada
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3
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Characterising Mitochondrial Capture in an Iberian Shrew. Genes (Basel) 2022; 13:genes13122228. [PMID: 36553495 PMCID: PMC9777731 DOI: 10.3390/genes13122228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/08/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Mitochondrial introgression raises questions of biogeography and of the extent of reproductive isolation and natural selection. Previous phylogenetic work on the Sorex araneus complex revealed apparent mitonuclear discordance in Iberian shrews, indicating past hybridisation of Sorex granarius and the Carlit chromosomal race of S. araneus, enabling introgression of the S. araneus mitochondrial genome into S. granarius. To further study this, we genetically typed 61 Sorex araneus/coronatus/granarius from localities in Portugal, Spain, France, and Andorra at mitochondrial, autosomal, and sex-linked loci and combined our data with the previously published sequences. Our data are consistent with earlier data indicating that S. coronatus and S. granarius are the most closely related of the three species, confirming that S. granarius from the Central System mountain range in Spain captured the mitochondrial genome from a population of S. araneus. This mitochondrial capture event can be explained by invoking a biogeographical scenario whereby S. araneus was in contact with S. granarius during the Younger Dryas in central Iberia, despite the two species currently having disjunct distributions. We discuss whether selection favoured S. granarius with an introgressed mitochondrial genome. Our data also suggest recent hybridisation and introgression between S. coronatus and S. granarius, as well as between S. araneus and S. coronatus.
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4
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Gaertner K, Michell C, Tapanainen R, Goffart S, Saari S, Soininmäki M, Dufour E, Pohjoismäki JLO. Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares (
Lepus
spp., Lagomorpha: Leporidae). Mol Ecol 2022. [PMID: 36320183 DOI: 10.1111/mec.16755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/16/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
Abstract
Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological and behavioural differences. Each species has travelled its own evolutionary trajectory, influenced by random drift and driven by various types of natural selection, making the association of genetic differences between the species with the phenotypic differences extremely complex to dissect. In the present study, we have used an in vitro model to analyse in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare (Lepus timidus Linnaeus) and the temperate steppe-climate adapted brown hare (Lepus europaeus Pallas). We discovered the existence of a species-specific expression pattern of 1623 genes, manifesting in differences in cell growth, cell cycle control, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest that speciation acts on fundamental cellular processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on a cellular level, which could contribute to the maintenance of the species boundary.
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Affiliation(s)
- Kateryna Gaertner
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Craig Michell
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Riikka Tapanainen
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Sina Saari
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Manu Soininmäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
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5
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Reid N, Hughes MF, Hynes RA, Montgomery WI, Prodöhl PA. Bidirectional hybridisation and introgression between introduced European brown hare, Lepus europaeus and the endemic Irish hare, L. timidus hibernicus. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01471-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractIntroduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus, and the endemic Irish hare, L. timidus hibernicus. Roadkill hares (n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin (Tf) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus. Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus, 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.
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6
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Bailey NP, Stevison LS. Mitonuclear conflict in a macaque species exhibiting phylogenomic discordance. J Evol Biol 2021; 34:1568-1579. [PMID: 34379829 DOI: 10.1111/jeb.13914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/28/2021] [Indexed: 12/19/2022]
Abstract
Speciation and hybridization are intertwined processes in the study of evolution. Hybridization between sufficiently diverged populations can result in genomic conflict within offspring, causing reduced viability and fertility, thus increasing divergence between populations. Conflicts between mitochondrial and nuclear genes are increasingly found to play a role in this process in various systems. We examine the possibility of this conflict in the bear macaque, Macaca arctoides (Primates: Cercopithecidae), a primate species exhibiting mitonuclear discordance due to extensive hybridization with species in the sinica and fascicularis groups. Here, divergence, introgression and natural selection of mitonuclear genes (N = 160) relative to nuclear control genes (N = 144) were analysed to determine whether there are evolutionary processes involved in resolving the potential conflict caused by mitonuclear discordance. Nucleotide divergence of mitonuclear genes is increased relative to control nuclear genes between M. arctoides and the species sharing its nuclear ancestry (p = 0.007), consistent with genetic conflict. However, measures of introgression and selection do not identify large-scale co-introgression or co-evolution as means to resolve mitonuclear conflict. Nonetheless, mitochondrial tRNA synthetases stand out in analyses using dN/dS and extended branch lengths as potential targets of selection. The methodology implemented provides a framework that can be used to examine the effects of mitonuclear co-introgression and co-evolution on a genomic scale in a variety of systems.
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Affiliation(s)
- Nick P Bailey
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Laurie S Stevison
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
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7
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Mengüllüoğlu D, Ambarlı H, Barlow A, Paijmans JLA, Sayar AO, Emir H, Kandemir İ, Hofer H, Fickel J, Förster DW. Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx. Genes (Basel) 2021; 12:genes12081216. [PMID: 34440390 PMCID: PMC8392285 DOI: 10.3390/genes12081216] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022] Open
Abstract
Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.
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Affiliation(s)
- Deniz Mengüllüoğlu
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Correspondence:
| | - Hüseyin Ambarlı
- Department of Wildlife Ecology and Management, Faculty of Forestry, Düzce University, Düzce 81620, Turkey;
| | - Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK;
| | - Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany;
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ali Onur Sayar
- Department of Game and Wildlife, Cankiri Karatekin University, Cankiri 18100, Turkey;
| | - Hasan Emir
- Wildlife Department of General Directorate of Nature Conservation and National Parks, Turkish Ministry of Agriculture and Forestry, Ankara 06000, Turkey;
| | - İrfan Kandemir
- Department of Biology, Ankara University, Ankara 06000, Turkey;
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 10315 Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, 10315 Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany;
| | - Daniel W. Förster
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
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8
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Lukicheva S, Mardulyn P. Whole-genome sequencing reveals asymmetric introgression between two sister species of cold-resistant leaf beetles. Mol Ecol 2021; 30:4077-4089. [PMID: 34097806 DOI: 10.1111/mec.16011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/02/2023]
Abstract
A large number of genetic variation studies have identified cases of mitochondrial genome introgression in animals, indicating that reproductive barriers among closely related species are often permeable. Because of its sheer size, the impact of hybridization on the evolution of the nuclear genome is more difficult to apprehend. Only a few studies have explored it recently thanks to recent progress in DNA sequencing and genome assembly. Here, we analysed whole-genome sequence variation among multiple individuals of two sister species of leaf beetles inside their hybrid zone, in which asymmetric mitochondrial genome introgression had previously been established. We used a machine learning approach based on computer simulations for training to identify regions of the nuclear genome that were introgressed. We inferred asymmetric introgression of ≈2% of the genome, in the same direction that was observed for the mitochondrial genome. Because a previous study based on a reduced-representation sequencing approach was not able to detect this introgression, we conclude that whole-genome sequencing is necessary when the fraction of the introgressed genome is small. We also analysed the whole-genome sequence of a hybrid individual, demonstrating that hybrids have the capacity to backcross with the species for which virtually no introgression was observed. Our data suggest that one species has recently invaded the range of the other and/or some alleles that where transferred from the invaded into the invading species could be under positive selection and may have favoured the adaptation of the invading species to the Alpine environment.
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Affiliation(s)
- Svitlana Lukicheva
- Evolutionary Biology and Ecology, Interuniversity Institute of Bioinformatics in Brussels - (IB)², Université libre de Bruxelles, Brussels, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Interuniversity Institute of Bioinformatics in Brussels - (IB)², Université libre de Bruxelles, Brussels, Belgium
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9
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Schwartz JH. Evolution, systematics, and the unnatural history of mitochondrial DNA. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:126-151. [PMID: 33818247 DOI: 10.1080/24701394.2021.1899165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The tenets underlying the use of mtDNA in phylogenetic and systematic analyses are strict maternal inheritance, clonality, homoplasmy, and difference due to mutation: that is, there are species-specific mtDNA sequences and phylogenetic reconstruction is a matter of comparing these sequences and inferring closeness of relatedness from the degree of sequence similarity. Yet, how mtDNA behavior became so defined is mysterious. Even though early studies of fertilization demonstrated for most animals that not only the head, but the sperm's tail and mitochondria-bearing midpiece penetrate the egg, the opposite - only the head enters the egg - became fact, and mtDNA conceived as maternally transmitted. When midpiece/tail penetration was realized as true, the conceptions 'strict maternal inheritance', etc., and their application to evolutionary endeavors, did not change. Yet there is mounting evidence of paternal mtDNA transmission, paternal and maternal combination, intracellular recombination, and intra- and intercellular heteroplasmy. Clearly, these phenomena impact the systematic and phylogenetic analysis of mtDNA sequences.
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Affiliation(s)
- Jeffrey H Schwartz
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
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10
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Cadenillas R, D'Elía G. The number of species of degus (genus Octodon) is currently underestimated: An appraisal of species limits and their phylogenetic relationships (Rodentia: Hystricomorpha: Octodontidae). Mol Phylogenet Evol 2021; 159:107111. [PMID: 33607277 DOI: 10.1016/j.ympev.2021.107111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 01/04/2023]
Abstract
As currently understood, the genus Octodon contains five species degus, lunatus, bridgesii, pacificus, and ricardojeda. Previous phylogenetic studies suggest that genus specific diversity is underestimated. In order to evaluate the taxonomic diversity of Octodon, we implemented unilocus (cytochrome-b) and multilocus (cytochrome-b + 4 nuclear genes) species delimitation methods. Octodon degus was recovered as a sister of the other species of the genus. The unilocus bGMYC and mPTP methods, based on cytochrome-b sequences, delimits 11 and 7 candidate species respectively, and both methods fail to recognize O. pacificus from O. ricardojeda. Results of the multilocus analysis (BPP) vary as a function of the dataset used. When the five genes are used 11 species are delimited, while eight species are delimited when only the nuclear genes are used. Octodon bridgesii is shown as comprising at least two species (one on the Pacific coast and the typical form found on the Andean slopes), while O. ricardojeda may comprise two species (one on the Chilean side of the Andes and the other in Argentina). Likewise, both multilocus matrices recover O. pacificus as a distinct species. This shows that species diversity of Octodon is underestimated. Remarkably, many of the delimited species based on genetic data are morphologically differentiated in cranio-dental characteristics. However, a pair of species has not achieved morphological differentiation, being cryptic species. Finally, the incongruence between mitochondrial and nuclear phylogenies suggests that processes such as incomplete lineage sorting and/or introgression have been present during the radiation of the genus.
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Affiliation(s)
- Richard Cadenillas
- Doctorado en Ciencias, Mención Ecología y Evolución, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia 5090000, Chile; Instituto de Paleontología, Universidad Nacional de Piura, Piura 20002, Peru.
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia 5090000, Chile.
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11
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Zolotareva KI, Belokon MM, Belokon YS, Rutovskaya MV, Hlyap LA, Starykov VP, Politov DV, Lebedev VS, Bannikova AA. Genetic diversity and structure of the hedgehogs Erinaceus europaeus and Erinaceus roumanicus: evidence for ongoing hybridization in Eastern Europe. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Secondary contact zones between related species are key to understanding speciation mechanisms. The Central European sympatry zone of West European (Erinaceus europaeus) and northern white-breasted (Erinaceus roumanicus) hedgehogs is well studied, whereas data on the Eastern European sympatry zone are scarce. We examined the genetic variation in Russian populations using the mitochondrial Cytb gene, TTR intron 1 and 11 microsatellites to assess genetic variability and distribution patterns. In contrast to the Central European sympatry zone, we found evidence of ongoing hybridization between the two species in the sympatry zone of European Russia, where the proportion of individuals with mixed ancestry was c. 20%. Our data indicate bi-directional mtDNA introgression, but with a higher frequency of E. europaeus haplotypes in hybrids. The proportion of pure specimens with introgressed mitotypes is higher in E. roumanicus than in E. europaeus. Nuclear data showed the prevalence of the genetic contribution from E. roumanicus in admixed individuals. Demographic analyses indicated recent population growth in E. europaeus and little change in E. roumanicus, suggesting that E. europaeus colonized East Europe later than E. roumanicus.
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Affiliation(s)
| | - Mariana M Belokon
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Yuri S Belokon
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Marina V Rutovskaya
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Ludmila A Hlyap
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | | | - Dmitry V Politov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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12
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Marques JP, Seixas FA, Farelo L, Callahan CM, Good JM, Montgomery WI, Reid N, Alves PC, Boursot P, Melo-Ferreira J. An Annotated Draft Genome of the Mountain Hare (Lepus timidus). Genome Biol Evol 2020; 12:3656-3662. [PMID: 31834364 PMCID: PMC6951464 DOI: 10.1093/gbe/evz273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2019] [Indexed: 12/25/2022] Open
Abstract
Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated 24,578 protein coding genes by combining ab-initio predictions, homology search, and transcriptome data, of which 683 were solely derived from hare-specific transcriptome data. The hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Similar estimates of heterozygosity and inferred demographic history profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. Our results validate previous reference-based strategies and suggest that the chromosome-scale hare draft genome should enable chromosome-wide analyses and genome scans on hares.
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Affiliation(s)
- João P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências do Porto, Portugal.,Institut des Sciences de l'Evolution Montpellier (ISEM), Univ Montpellier, CNRS, IRD, EPHE, France
| | - Fernando A Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências do Porto, Portugal.,Institut des Sciences de l'Evolution Montpellier (ISEM), Univ Montpellier, CNRS, IRD, EPHE, France
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | | | - Jeffrey M Good
- Division of Biological Sciences, University of Montana.,Wildlife Biology Program, University of Montana
| | - W Ian Montgomery
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, United Kingdom
| | - Neil Reid
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, United Kingdom
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências do Porto, Portugal.,Wildlife Biology Program, University of Montana
| | - Pierre Boursot
- Institut des Sciences de l'Evolution Montpellier (ISEM), Univ Montpellier, CNRS, IRD, EPHE, France
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências do Porto, Portugal
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13
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Abstract
Introgressive hybridization can affect the evolution of populations in several important ways. It may retard or reverse divergence of species, enable the development of novel traits, enhance the potential for future evolution by elevating levels of standing variation, create new species, and alleviate inbreeding depression in small populations. Most of what is known of contemporary hybridization in nature comes from the study of pairs of species, either coexisting in the same habitat or distributed parapatrically and separated by a hybrid zone. More rarely, three species form an interbreeding complex (triad), reported in vertebrates, insects, and plants. Often, one species acts as a genetic link or conduit for the passage of genes (alleles) between two others that rarely, if ever, hybridize. Demographic and genetic consequences are unknown. Here we report results of a long-term study of interbreeding Darwin's finches on Daphne Major island, Galápagos. Geospiza fortis acted as a conduit for the passage of genes between two others that have never been observed to interbreed on Daphne: Geospiza fuliginosa, a rare immigrant, and Geospiza scandens, a resident. Microsatellite gene flow from G. fortis into G. scandens increased in frequency during 30 y of favorable ecological conditions, resulting in genetic and morphological convergence. G. fortis, G. scandens, and the derived dihybrids and trihybrids experienced approximately equal fitness. Especially relevant to young adaptive radiations, where species differ principally in ecology and behavior, these findings illustrate how new combinations of genes created by hybridization among three species can enhance the potential for evolutionary change.
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14
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Mynhardt S, Bennett NC, Bloomer P. New insights from RADseq data on differentiation in the Hottentot golden mole species complex from South Africa. Mol Phylogenet Evol 2019; 143:106667. [PMID: 31676418 DOI: 10.1016/j.ympev.2019.106667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/28/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
Abstract
Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub-Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have relatively wide ranges. We recently uncovered cryptic diversity within A. hottentotus, through a phylogeographic analysis of this taxon using two mitochondrial gene regions and a nuclear intron. To further investigate this cryptic diversity, we generated nuclear SNP data from across the genome of A. hottentotus, by means of double-digest restriction-site associated DNA sequencing (ddRADSeq), and mapped reads to the Cape golden mole genome. We conducted a phylogenetic analysis and investigated population differentiation. Our results support the distinctiveness of A. h. meesteri. Furthermore, we provide evidence from nuclear SNPs in support of our previous finding that Central coastal samples represent a unique cryptic lineage that is highly divergent from A. h. pondoliae farther south. Although mtDNA suggests that Umtata may represent a unique lineage sister to A. h. longiceps, mito-nuclear discordance from our RADseq data indicate that these samples may instead be closer to A. h. pondoliae, and therefore may not represent a distinct lineage. We stress the importance of recognizing that understudied populations, such as that of Umtata, may represent populations or ESUs under threat and in need of conservation attention. We present a high-quality filtered SNP dataset, comprising thousands of SNPs, which may serve as a useful resource for future golden mole studies. We have thus added to the growing body of research demonstrating the power and utility of RADseq to investigate population differentiation.
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Affiliation(s)
- Samantha Mynhardt
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
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15
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Kim BM, Lee WY, Rhee JS. Complete mitochondrial genome of the Arctic hare, Lepus arcticus. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3621-3623. [PMID: 33366112 PMCID: PMC7707595 DOI: 10.1080/23802359.2019.1677193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we report on the complete mitochondrial genome of the Arctic hare, Lepus arcticus (Leporidae; Lagomorpha) a large lagomorph endemic to the northernmost regions of Greenland. The complete mitogenome of L. arcticus was 16,972 bp long and was typical of genus Lepus mitogenomes in genomic content and structure, as the entire mitogenome contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one control region. The phylogenetic analysis of the Arctic hare within Leporidae confirmed the sister relationship among Lepus species. This mitogenome sequence will provide a useful resource for investigations of biogeography, phylogenetic distance, and evolutionary history in lagomorphs.
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Affiliation(s)
- Bo-Mi Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Won Young Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, South Korea.,Research Institute of Basic Sciences, Incheon National University, Incheon, South Korea
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16
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The evolutionary history of the Cape hare (Lepus capensis sensu lato): insights for systematics and biogeography. Heredity (Edinb) 2019; 123:634-646. [PMID: 31073237 DOI: 10.1038/s41437-019-0229-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/11/2019] [Accepted: 04/19/2019] [Indexed: 12/27/2022] Open
Abstract
Inferring the phylogeography of species with large distributions helps deciphering major diversification patterns that may occur in parallel across taxa. Here, we infer the evolutionary history of the Cape hare, Lepus capensis sensu lato, a species distributed from southern Africa to Asia, by analyzing variation at 18 microsatellites and 9 DNA (1 mitochondrial and 8 nuclear) sequenced loci, from field and museum-collected samples. Using a combination of assignment and coalescent-based methods, we show that the Cape hare is composed of five evolutionary lineages, distributed in distinct biogeographic regions-north-western Africa, eastern Africa, southern Africa, the Near East and the Arabian Peninsula. A deep phylogenetic break possibly dating to the Early Pleistocene was inferred between the African and Asian L. capensis groups, and the latter appear more closely related to other Eurasian hare species than to African Cape hares. The inferred phylogeographic structure is shared by numerous taxa distributed across the studied range, suggesting that environmental changes, such as the progressive aridification of the Saharo-Arabian desert and the fluctuations of savannah habitats in Sub-Saharan Africa, had comparable impacts across species. Fine-scale analyses of the western Sahara-Sahel populations showed rich fragmentation patterns for mitochondrial DNA but not for microsatellites, compatible with the environmental heterogeneity of the region and female philopatry. The complex evolutionary history of L. capensis sensu lato, which possibly includes interspecific gene flow, is not reflected by taxonomy. Integrating evolutionary inference contributes to an improved characterization of biodiversity, which is fundamental to foster the conservation of relevant evolutionary units.
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17
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Hill GE. Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression. Integr Comp Biol 2019; 59:912-924. [DOI: 10.1093/icb/icz019] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.
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Affiliation(s)
- Geoffrey E Hill
- Department of Biological Sciences, 331 Funchess Hall, Auburn University, Auburn, AL 36849-5414, USA
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18
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Kinoshita G, Nunome M, Kryukov AP, Kartavtseva IV, Han SH, Yamada F, Suzuki H. Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus). Mol Phylogenet Evol 2019; 136:65-75. [PMID: 30951923 DOI: 10.1016/j.ympev.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 01/16/2023]
Abstract
Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleotide sequences of one mitochondrial DNA and eight nuclear gene loci were examined, adding sequences of hares in China from databases. All nuclear DNA analyses supported the clear separation of three phylogroups: L. timidus, L. brachyurus, and the L. mandshuricus complex containing L. coreanus. On the other hand, massive mitochondrial introgression from two L. timidus lineages to the L. mandshuricus complex was suggested in continental East Asia. The northern population of the L. mandshuricus complex was mainly associated with introgression from the continental lineage of L. timidus, possibly since the last glacial period, whereas the southern population of the L. mandshuricus complex experienced introgression from another L. timidus lineage related to the Hokkaido population, possibly before the last glacial period. In contrast to continental hares, no evidence of introgression was found in L. brachyurus in the Japanese Archipelago, which showed the oldest divergence amongst East Asian hare lineages. Our findings suggest that glacial-interglacial climate changes in the circum-Japan Sea region promoted distribution shifts and introgressive hybridization among continental hare species, while the geographic structure of the region contributed to long-term isolation of hares on the islands, preventing inter-species gene flow.
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Affiliation(s)
- Gohta Kinoshita
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan; Laboratory of Forest Biology Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyoku, Kyoto 606-8502, Japan.
| | - Mitsuo Nunome
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Alexey P Kryukov
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Irina V Kartavtseva
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - San-Hoon Han
- Inter-Korea Wildlife Institute, Namtong-dong, Gumi-si, Kyeongsang-Bukdo 39301, Republic of Korea
| | - Fumio Yamada
- Laboratory of Wildlife Ecology, Forestry and Forest Products Research Institute (FFPRI), Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Hitoshi Suzuki
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan
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19
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Zinner D, Chuma IS, Knauf S, Roos C. Inverted intergeneric introgression between critically endangered kipunjis and yellow baboons in two disjunct populations. Biol Lett 2018; 14:rsbl.2017.0729. [PMID: 29343565 DOI: 10.1098/rsbl.2017.0729] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/20/2017] [Indexed: 11/12/2022] Open
Abstract
Intergeneric hybridization and introgression was reported from one of two populations of the recently discovered kipunji (Rungwecebus kipunji), a critically endangered African monkey species of southern Tanzania. Kipunjis of the introgressed population (from Mount Rungwe) carry a mitochondrial DNA (mtDNA) haplotype closely related to those of parapatric yellow baboons (Papio cynocephalus), whereas the second kipunji population, in the Udzungwa Mountains, carries the original kipunji mtDNA haplotypes, which diverged from the baboon lineage about 3 million years ago. Interestingly, in our study of yellow baboons in Tanzania, we found that baboons from the southeastern boundary of the Udzungwa Mountains carry mtDNA haplotypes closely related to the original kipunji haplotype, whereas baboons from the northern boundary, as expected, carry mtDNA haplotypes of the northern yellow baboon clade. These findings provide evidence for a case of inverted intergeneric admixture in primates: (i) a baboon mtDNA haplotype introgressed the Mount Rungwe kipunji population by mitochondrial capture and (ii) an Udzungwa Mountains kipunji mtDNA haplotype introgressed a small subpopulation of yellow baboons by either mitochondrial capture or nuclear swamping. The baboon-kipunji example therefore constitutes an interesting system for further studies of the effects of genetic admixture on fitness and speciation.
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Affiliation(s)
- Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Göttingen, Germany
| | - Idrissa S Chuma
- Work Group Neglected Tropical Diseases, German Primate Center, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Göttingen, Germany.,Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, German Primate Center, Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
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20
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Baca M, Popović D, Panagiotopoulou H, Marciszak A, Krajcarz M, Krajcarz MT, Makowiecki D, Węgleński P, Nadachowski A. Human-mediated dispersal of cats in the Neolithic Central Europe. Heredity (Edinb) 2018; 121:557-563. [PMID: 29588507 PMCID: PMC6221894 DOI: 10.1038/s41437-018-0071-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 11/09/2022] Open
Abstract
Archeological and genetic evidence suggest that all domestic cats derived from the Near Eastern wildcat (Felis silvestris lybica) and were first domesticated in the Near East around 10,000 years ago. The spread of the domesticated form in Europe occurred much later, primarily mediated by Greek and Phoenician traders and afterward by Romans who introduced cats to Western and Central Europe around 2000 years ago. We investigated mtDNA of Holocene Felis remains and provide evidence of an unexpectedly early presence of cats bearing the Near Eastern wildcat mtDNA haplotypes in Central Europe, being ahead of Roman period by over 2000 years. The appearance of the Near Eastern wildcats in Central Europe coincides with the peak of Neolithic settlement density, moreover most of those cats belonged to the same mtDNA lineages as those domesticated in the Near East. Thus, although we cannot fully exclude that the Near Eastern wildcats appeared in Central Europe as a result of introgression with European wildcat, our findings support the hypothesis that the Near Eastern wildcats spread across Europe together with the first farmers, perhaps as commensal animals. We also found that cats dated to the Neolithic period belonged to different mtDNA lineages than those brought to Central Europe in Roman times, this supports the hypothesis that the gene pool of contemporary European domestic cats might have been established from two different source populations that contributed in different periods.
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Affiliation(s)
- Mateusz Baca
- Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-079, Warsaw, Poland.
| | - Danijela Popović
- Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-079, Warsaw, Poland
| | - Hanna Panagiotopoulou
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Adrian Marciszak
- Department of Paleozoology, Institute of Environmental Biology, University of Wroclaw, Sienkiewicza 21, 50-335, Wrocław, Poland
| | - Magdalena Krajcarz
- Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Szosa Bydgoska 44/48, 87-100, Torun, Poland
| | - Maciej T Krajcarz
- Institute of Geological Sciences, Polish Academy of Sciences, Research Centre in Warsaw, Twarda 51/55, 00-818, Warsaw, Poland
| | - Daniel Makowiecki
- Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Szosa Bydgoska 44/48, 87-100, Torun, Poland
| | - Piotr Węgleński
- Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-079, Warsaw, Poland
| | - Adam Nadachowski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Krakow, Poland
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21
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Neimanis AS, Ahola H, Larsson Pettersson U, Lopes AM, Abrantes J, Zohari S, Esteves PJ, Gavier-Widén D. Overcoming species barriers: an outbreak of Lagovirus europaeus GI.2/RHDV2 in an isolated population of mountain hares (Lepus timidus). BMC Vet Res 2018; 14:367. [PMID: 30477499 PMCID: PMC6258167 DOI: 10.1186/s12917-018-1694-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 11/12/2018] [Indexed: 12/19/2022] Open
Abstract
Background Prior to 2010, the lagoviruses that cause rabbit hemorrhagic disease (RHD) in European rabbits (Oryctolagus cuniculus) and European brown hare syndrome (EBHS) in hares (Lepus spp.) were generally genus-specific. However, in 2010, rabbit hemorrhagic disease virus 2 (RHDV2), also known as Lagovirus europaeus GI.2, emerged and had the distinguishing ability to cause disease in both rabbits and certain hare species. The mountain hare (Lepus timidus) is native to Sweden and is susceptible to European brown hare syndrome virus (EBHSV), also called Lagovirus europaeus GII.1. While most mountain hare populations are found on the mainland, isolated populations also exist on islands. Here we investigate a mortality event in mountain hares on the small island of Hallands Väderö where other leporid species, including rabbits, are absent. Results Post-mortem and microscopic examination of three mountain hare carcasses collected from early November 2016 to mid-March 2017 revealed acute hepatic necrosis consistent with pathogenic lagovirus infection. Using immunohistochemistry, lagoviral capsid antigen was visualized within lesions, both in hepatocytes and macrophages. Genotyping and immunotyping of the virus independently confirmed infection with L. europaeus GI.2, not GII.1. Phylogenetic analyses of the vp60 gene grouped mountain hare strains together with a rabbit strain from an outbreak of GI.2 in July 2016, collected approximately 50 km away on the mainland. Conclusions This is the first documented infection of GI.2 in mountain hares and further expands the host range of GI.2. Lesions and tissue distribution mimic those of GII.1 in mountain hares. The virus was most likely initially introduced from a concurrent, large-scale GI.2 outbreak in rabbits on the adjacent mainland, providing another example of how readily this virus can spread. The mortality event in mountain hares lasted for at least 4.5 months in the absence of rabbits, which would have required virus circulation among mountain hares, environmental persistence and/or multiple introductions. This marks the fourth Lepus species that can succumb to GI.2 infection, suggesting that susceptibility to GI.2 may be common in Lepus species. Measures to minimize the spread of GI.2 to vulnerable Lepus populations therefore are prudent. Electronic supplementary material The online version of this article (10.1186/s12917-018-1694-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aleksija S Neimanis
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden. .,Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Box 7028, 750 07, Uppsala, Sweden.
| | - Harri Ahola
- Department of Microbiology, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden
| | - Ulrika Larsson Pettersson
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden
| | - Ana M Lopes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Siamak Zohari
- Department of Microbiology, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden
| | - Pedro J Esteves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007, Porto, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Dolores Gavier-Widén
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden.,Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Box 7028, 750 07, Uppsala, Sweden
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22
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Seixas FA, Boursot P, Melo-Ferreira J. The genomic impact of historical hybridization with massive mitochondrial DNA introgression. Genome Biol 2018; 19:91. [PMID: 30056805 PMCID: PMC6065068 DOI: 10.1186/s13059-018-1471-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. RESULTS Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions. CONCLUSIONS General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.
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Affiliation(s)
- Fernando A Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France.
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal.
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23
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Levänen R, Kunnasranta M, Pohjoismäki J. Mitochondrial DNA Introgression at the Northern Edge of the Brown Hare (Lepus europaeus) Range. ANN ZOOL FENN 2018. [DOI: 10.5735/086.055.0103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Natural Resources Institute Finland (Luke), Yliopistokatu 6, FI-80100, Joensuu, Finland
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
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Angers B, Leung C, Vétil R, Deremiens L, Vergilino R. The effects of allospecific mitochondrial genome on the fitness of northern redbelly dace ( Chrosomus eos). Ecol Evol 2018; 8:3311-3321. [PMID: 29607026 PMCID: PMC5869299 DOI: 10.1002/ece3.3922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/17/2018] [Accepted: 01/23/2018] [Indexed: 11/07/2022] Open
Abstract
Instantaneous mitochondrial introgression events allow the disentangling of the effects of hybridization from those of allospecific mtDNA. Such process frequently occurred in the fish Chrosomus eos, resulting in cybrid individuals composed of a C. eos nuclear genome but with a C. neogaeus mtDNA. This provides a valuable model to address the fundamental question: How well do introgressed individuals perform in their native environment? We infer where de novo production of cybrids occurred to discriminate native environments from those colonized by cybrids in 25 sites from two regions (West-Qc and East-Qc) in Quebec (Canada). We then compared the relative abundance of wild types and cybrids as a measure integrating both fitness and de novo production of cybrids. According to mtDNA variation, 12 introgression events are required to explain the diversity of cybrids. Five cybrid lineages could not be associated with in situ introgression events. This includes one haplotype carried by 93% of the cybrids expected to have colonized West-Qc. These cybrids also displayed a nearly complete allopatric distribution with wild types. We still inferred de novo production of cybrids at seven sites, that accounted for 70% of the cybrids in East-Qc. Wild-type and cybrid individuals coexist in all East-Qc sites while cybrids were less abundant. Allopatry of cybrids restricted to the postglacial expansion suggests the existence of higher fitness for cybrids in specific conditions, allowing for the colonization of different environments and expanding the species' range. However, allospecific mtDNA does not provide a higher fitness to cybrids in their native environment compared to wild types, making the success of an introgressed lineage uncertain.
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Affiliation(s)
- Bernard Angers
- Department of Biological Sciences Université de Montréal Montreal QC Canada
| | - Christelle Leung
- Department of Biological Sciences Université de Montréal Montreal QC Canada
| | - Romain Vétil
- Department of Biological Sciences Université de Montréal Montreal QC Canada
| | - Léo Deremiens
- Department of Biological Sciences Université de Montréal Montreal QC Canada
| | - Roland Vergilino
- Department of Biological Sciences Université de Montréal Montreal QC Canada
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Levänen R, Thulin CG, Spong G, Pohjoismäki JLO. Widespread introgression of mountain hare genes into Fennoscandian brown hare populations. PLoS One 2018; 13:e0191790. [PMID: 29370301 PMCID: PMC5784980 DOI: 10.1371/journal.pone.0191790] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/11/2018] [Indexed: 11/29/2022] Open
Abstract
In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.
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Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Carl-Gustaf Thulin
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Spong
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
- * E-mail:
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La Morgia V, Venturino E. Understanding hybridization and competition processes between hare species: Implications for conservation and management on the basis of a mathematical model. Ecol Modell 2017. [DOI: 10.1016/j.ecolmodel.2017.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tolesa Z, Bekele E, Tesfaye K, Ben Slimen H, Valqui J, Getahun A, Hartl GB, Suchentrunk F. Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia. PLoS One 2017; 12:e0180137. [PMID: 28767659 PMCID: PMC5540492 DOI: 10.1371/journal.pone.0180137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/10/2017] [Indexed: 11/28/2022] Open
Abstract
For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals. For the hares from Ethiopia, genotype composition at twelve microsatellite loci (n = 107) was used to explore both interspecific gene pool separation and levels of current hybridization, as has been observed in some other Lepus species. For phylogenetic analyses ATP6 and TF sequences of Lepus species from South and North Africa (L. capensis, L. saxatilis), the Anatolian peninsula and Europe (L. europaeus, L. timidus) were also produced and additional TF sequences of 18 Lepus species retrieved from GenBank were included as well. Median joining networks, neighbour joining, maximum likelihood analyses, as well as Bayesian inference resulted in similar models of evolution of the three species from Ethiopia for the ATP6 and TF sequences, respectively. The Ethiopian species are, however, not monophyletic, with signatures of contemporary uni- and bidirectional mitochondrial introgression and/ or shared ancestral polymorphism. Lepus habessinicus carries mtDNA distinct from South African L. capensis and North African L. capensis sensu lato; that finding is not in line with earlier suggestions of its conspecificity with L. capensis. Lepus starcki has mtDNA distinct from L. capensis and L. europaeus, which is not in line with earlier suggestions to include it either in L. capensis or L. europaeus. Lepus fagani shares mitochondrial haplotypes with the other two species from Ethiopia, despite its distinct phenotypic and microsatellite differences; moreover, it is not represented by a species-specific mitochondrial haplogroup, suggesting considerable mitochondrial capture by the other species from Ethiopia or species from other parts of Africa. Both mitochondrial and nuclear sequences indicate close phylogenetic relationships among all three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. TF sequences suggest close evolutionary relationships between the three Ethiopian species and Cape hares from South and North Africa; they further suggest that hares from Ethiopia hold a position ancestral to many Eurasian and North American species.
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Affiliation(s)
- Zelalem Tolesa
- Department of Biology, Hawassa University, Hawassa, Ethiopia
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Endashaw Bekele
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Centre of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hichem Ben Slimen
- Institut Supérieur de Biotechnologie de Béja, Avenue Habib Bourguiba, Béja, Tunisia
| | - Juan Valqui
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Abebe Getahun
- Department of Zoological Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Günther B. Hartl
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
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Pérez T, Fernández M, Hammer SE, Domínguez A. Multilocus Intron Trees Reveal Extensive Male-Biased Homogenization of Ancient Populations of Chamois (Rupicapra spp.) across Europe during Late Pleistocene. PLoS One 2017; 12:e0170392. [PMID: 28146581 PMCID: PMC5287467 DOI: 10.1371/journal.pone.0170392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/04/2017] [Indexed: 11/19/2022] Open
Abstract
The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms.
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Affiliation(s)
- Trinidad Pérez
- Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, Oviedo, Spain
| | - Margarita Fernández
- Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, Oviedo, Spain
| | - Sabine E. Hammer
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, Vienna, Austria
| | - Ana Domínguez
- Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, Oviedo, Spain
- * E-mail:
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Smith S, Sandoval-Castellanos E, Lagerholm VK, Napierala H, Sablin M, Von Seth J, Fladerer FA, Germonpré M, Wojtal P, Miller R, Stewart JR, Dalén L. Nonreceding hare lines: genetic continuity since the Late Pleistocene in European mountain hares (Lepus timidus). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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30
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Koju NP, He K, Chalise MK, Ray C, Chen Z, Zhang B, Wan T, Chen S, Jiang X. Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China. Mol Phylogenet Evol 2016; 107:239-245. [PMID: 27838310 DOI: 10.1016/j.ympev.2016.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 11/30/2022]
Abstract
The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity. Our study supported O. syrinx (O. huangensis) as a distinct clade from all named subgenera. Relationships among subgenera were not fully resolved, which may be due to a rapid diversification in the middle Miocene (∼13.90Ma). Conflicting gene trees implied mitochondrial introgression from O. cansus to O. curzoniae. We uncovered three cryptic species from Shaanxi, Sichuan and Yunnan with strong support, suggesting an underestimation of species diversity in the "sky-island" mountains of southwest China.
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Affiliation(s)
- Narayan Prasad Koju
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China; Central Department of Zoology, Tribhuvan University, Kathmandu, Nepal
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Smithsonian Institution, National Museum of Natural History, Washington, DC 20004, USA; The Kyoto University Museum, Kyoto University, Kyoto 606-8501, Japan.
| | | | - Chris Ray
- Department of Ecology and Evolutionary Biology and Institute of Arctic and Alpine Research, University of Colorado-Boulder, 450 UCB, Boulder, CO 80309-0450, USA
| | - Zhongzheng Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Bin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Tao Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Shunde Chen
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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31
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Mastrantonio V, Porretta D, Urbanelli S, Crasta G, Nascetti G. Dynamics of mtDNA introgression during species range expansion: insights from an experimental longitudinal study. Sci Rep 2016; 6:30355. [PMID: 27460445 PMCID: PMC4962091 DOI: 10.1038/srep30355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/30/2016] [Indexed: 11/23/2022] Open
Abstract
Introgressive hybridization represents one of the long-lasting debated genetic consequences of species range expansion. Mitochondrial DNA has been shown to heavily introgress between interbreeding animal species that meet in new sympatric areas and, often, asymmetric introgression from local to the colonizing populations has been observed. Disentangling among the evolutionary and ecological processes that might shape this pattern remains difficult, because they continuously act across time and space. In this context, long-term studies can be of paramount importance. Here, we investigated the dynamics of mitochondrial introgression between two mosquito species (Aedes mariae and Ae. zammitii ) during a colonization event that started in 1986 after a translocation experiment. By analyzing 1,659 individuals across 25 years, we showed that introgression occurred earlier and at a higher frequency in the introduced than in the local species, showing a pattern of asymmetric introgression. Throughout time, introgression increased slowly in the local species, becoming reciprocal at most sites. The rare opportunity to investigate the pattern of introgression across time during a range expansion along with the characteristics of our study-system allowed us to support a role of demographic dynamics in determining the observed introgression pattern.
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Affiliation(s)
- V Mastrantonio
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - D Porretta
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - S Urbanelli
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - G Crasta
- Department of Mathematics, Sapienza University of Rome, Rome, Italy
| | - G Nascetti
- Department of Ecological and Biological Sciences, Tuscia University, Viterbo, Italy
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Fontanesi L, Di Palma F, Flicek P, Smith AT, Thulin CG, Alves PC. LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order. J Hered 2016; 107:295-308. [PMID: 26921276 DOI: 10.1093/jhered/esw010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 02/02/2016] [Indexed: 01/07/2023] Open
Abstract
The order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important economically and scientifically as major human food resources, valued game species, pests of agricultural significance, model laboratory animals, and key elements in food webs. A quarter of the lagomorph species are listed as threatened. They are native to all continents except Antarctica, and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range of environmental conditions. The order has notable taxonomic problems presenting significant difficulties for defining a species due to broad phenotypic variation, overlap of morphological characteristics, and relatively recent speciation events. At present, only the genomes of 2 species, the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been sequenced and assembled. Starting from a paucity of genome information, the main scientific aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of the European COST Action "A Collaborative European Network on Rabbit Genome Biology-RGB-Net" and the World Lagomorph Society (WLS), is to provide an international framework for the sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration.
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Affiliation(s)
- Luca Fontanesi
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves).
| | - Federica Di Palma
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves)
| | - Paul Flicek
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves)
| | - Andrew T Smith
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves)
| | - Carl-Gustaf Thulin
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves)
| | - Paulo C Alves
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves).
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Mengoni C, Mucci N, Randi E. Genetic diversity and no evidences of recent hybridization in the endemic Italian hare (Lepus corsicanus). CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0674-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Silva TL, Godinho R, Castro D, Abáigar T, Brito JC, Alves PC. Genetic identification of endangered North African ungulates using noninvasive sampling. Mol Ecol Resour 2014; 15:652-61. [PMID: 25256349 DOI: 10.1111/1755-0998.12335] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/28/2022]
Abstract
North African ungulates include several threatened and emblematic species, yet are poorly studied mainly due to their remoteness and elusiveness. Noninvasive sampling provides a useful approach to obtain ecological and genetic information essential to guide conservation actions. The very first and most important step in conservation planning is to accurately identify species, and molecular genetics has been proved to be a useful tool. Several molecular genetics protocols are available for species identification, even for samples with poor quality DNA, such as faeces, hairs or bones. Most of these protocols use mitochondrial DNA for barcoding despite this marker being especially prone to problems, including mtDNA introgression, nuclear insert copies, high intraspecific diversity or heteroplasmy. In this work, we developed a molecular method based on polymorphisms in small fragments of the mitochondrial cytochrome b (cytb, mtDNA) and the nuclear kappa casein genes (KCAS, nDNA) for identifying endangered North African ungulates. These fragments revealed polymorphisms, including species-specific variation, which allowed species identification of nine ungulate species that co-occur in North Africa. The method was validated across more than 400 samples, including different types of noninvasive samples collected in the field. The simplicity, high reliability and relative low cost of the described method make it a promising tool to improve ecological studies of the North African ungulates and consequently, the implementation of more efficient management and conservation plans for these endangered ungulates.
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Affiliation(s)
- Teresa Luísa Silva
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Porto, 4169-007, Portugal; Estación Experimental de Zonas Áridas (EEZA), CSIC, Carretera de Sacramento s/n, Almería, Spain
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Dong J, Mao X, Sun H, Irwin DM, Zhang S, Hua P. Introgression of mitochondrial DNA promoted by natural selection in the Japanese pipistrelle bat (Pipistrellus abramus). Genetica 2014; 142:483-94. [DOI: 10.1007/s10709-014-9794-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
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36
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Ding L, Chen M, Pan T, Zhang B, Zhou Y, Wang H. Complete mitochondrial DNA sequence of Lepus sinensis (Leporidae: Lepus). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1711-2. [PMID: 25242179 DOI: 10.3109/19401736.2014.961134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, we determined the complete nucleotide sequence of the mitochondrial (mt) genome of Chinese hare, Lepus sinensis (Leporidae: Lepus) by using polymerase chain reaction (PCR) technique. The entire mtDNA sequence is 17438 nucleotides long and contains 13 protein-coding genes, 2 ribosomal tRNA 22 transfer RNA gens and one long non-coding region known as the control region. The mt gene arrangement of L. sinensis is identical to those typical for vertebrates.
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Affiliation(s)
- Ling Ding
- a School of Life Science, Anhui University , Hefei , Anhui , People's Republic of China
| | - Maochang Chen
- a School of Life Science, Anhui University , Hefei , Anhui , People's Republic of China
| | - Tao Pan
- a School of Life Science, Anhui University , Hefei , Anhui , People's Republic of China
| | - Baowei Zhang
- a School of Life Science, Anhui University , Hefei , Anhui , People's Republic of China
| | - Yongrong Zhou
- a School of Life Science, Anhui University , Hefei , Anhui , People's Republic of China
| | - Hui Wang
- a School of Life Science, Anhui University , Hefei , Anhui , People's Republic of China
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37
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Melo-Ferreira J, Seixas FA, Cheng E, Mills LS, Alves PC. The hidden history of the snowshoe hare,Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation. Mol Ecol 2014; 23:4617-30. [DOI: 10.1111/mec.12886] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 01/09/2023]
Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Fernando A. Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; 4099-002 Porto Portugal
| | - Ellen Cheng
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
- Ugyen Wangchuck Institute for Conservation and Environment; Lamai Goempa Bumthang Bhutan
| | - L. Scott Mills
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
- Fisheries, Wildlife and Conservation Biology Program; North Carolina State University; Raleigh NC 27695-7617 USA
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; 4099-002 Porto Portugal
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
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38
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Andújar C, Arribas P, Ruiz C, Serrano J, Gómez-Zurita J. Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation ofMesocarabus(Coleoptera: Carabidae). Mol Ecol 2014; 23:4344-61. [DOI: 10.1111/mec.12793] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 04/23/2014] [Accepted: 05/01/2014] [Indexed: 11/30/2022]
Affiliation(s)
- C. Andújar
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; Murcia 30100 Spain
| | - P. Arribas
- Departamento de Ecología e Hidrología; Facultad de Biología; Universidad de Murcia; Murcia 30100 Spain
| | - C. Ruiz
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; Murcia 30100 Spain
- Departamento de Ciencias Naturales; Universidad Técnica Particular de Loja; San Cayetano Alto s/n C.P. 11 01 608 Loja Ecuador
| | - J. Serrano
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; Murcia 30100 Spain
| | - J. Gómez-Zurita
- Animal Biodiversity and Evolution; Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra); Pg. Marítim de la Barceloneta 37 Barcelona 08003 Spain
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39
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Sanz-Martín MJ, Estonba A, Manzano C, Iriondo M, Pérez-Suárez G, Fernández A, Palacios F. Genetic structure of brown and Iberian hare populations in northern Iberia: Implications for conservation of genetic diversity. J Wildl Manage 2014. [DOI: 10.1002/jwmg.713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- María J. Sanz-Martín
- Department of Genetics; Physical Anthropology and Animal Physiology; Faculty of Science and Technology; University of the Basque Country UPV/EHU; Leioa E-48940 Bizkaia Spain
- Department of Life Sciences; University of Alcalá; Alcalá de Henares E-28801 Madrid Spain
| | - Andone Estonba
- Department of Genetics; Physical Anthropology and Animal Physiology; Faculty of Science and Technology; University of the Basque Country UPV/EHU; Leioa E-48940 Bizkaia Spain
| | - Carmen Manzano
- Department of Genetics; Physical Anthropology and Animal Physiology; Faculty of Science and Technology; University of the Basque Country UPV/EHU; Leioa E-48940 Bizkaia Spain
| | - Mikel Iriondo
- Department of Genetics; Physical Anthropology and Animal Physiology; Faculty of Science and Technology; University of the Basque Country UPV/EHU; Leioa E-48940 Bizkaia Spain
| | - Gonzalo Pérez-Suárez
- Department of Life Sciences; University of Alcalá; Alcalá de Henares E-28801 Madrid Spain
| | - Alfonso Fernández
- Institute of Agrobiotechnology; Public University of Navarre; Pamplona E-31006 Navarre Spain
| | - Fernando Palacios
- Department of Biodiversity and Evolutionary Biology; National Museum of Natural Sciences/CSIC; Madrid E-28006 Spain
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40
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Melo-Ferreira J, Vilela J, Fonseca MM, da Fonseca RR, Boursot P, Alves PC. The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression. Genome Biol Evol 2014; 6:886-96. [PMID: 24696399 PMCID: PMC4007550 DOI: 10.1093/gbe/evu059] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2014] [Indexed: 12/21/2022] Open
Abstract
Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive.
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Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
| | - Joana Vilela
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto, Portugal
| | - Miguel M. Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Spain
| | - Rute R. da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal
| | - Pierre Boursot
- Institut des Sciences de l’Evolution, Université Montpellier 2, CNRS, IRD, France
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula
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41
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Nunome M, Kinoshita G, Tomozawa M, Torii H, Matsuki R, Yamada F, Matsuda Y, Suzuki H. Lack of association between winter coat colour and genetic population structure in the Japanese hare,Lepus brachyurus(Lagomorpha: Leporidae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mitsuo Nunome
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Gohta Kinoshita
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
| | | | - Harumi Torii
- Center for Natural Environment Education; Nara University of Education; Takabatake-cho Nara 630-8528 Japan
| | - Rikyu Matsuki
- Environmental Science Research Laboratory; Central Research Institute of Electric Power Industry; 1646 Abiko Chiba 270-1194 Japan
| | - Fumio Yamada
- Forestry and Forest Products Research Institute; PO Box 16 Tsukuba Norin Ibaraki 305-8687 Japan
| | - Yoichi Matsuda
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
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42
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Seixas FA, Juste J, Campos PF, Carneiro M, Ferrand N, Alves PC, Melo-Ferreira J. Colonization history of Mallorca Island by the European rabbit,Oryctolagus cuniculus, and the Iberian hare,Lepus granatensis(Lagomorpha: Leporidae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Fernando A. Seixas
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; InBIO; Laboratório Associado; Campus Agrário de Vairão; 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; Rua Campo Alegre s/n 4169-007 Porto Portugal
| | - Javier Juste
- Estación Biológica de Doñana (CSIC); Avda. Americo Vespucio s/n Sevilla 41092 Spain
| | - Paula F. Campos
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
| | - Miguel Carneiro
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; InBIO; Laboratório Associado; Campus Agrário de Vairão; 4485-661 Vairão Portugal
| | - Nuno Ferrand
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; InBIO; Laboratório Associado; Campus Agrário de Vairão; 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; Rua Campo Alegre s/n 4169-007 Porto Portugal
| | - Paulo C. Alves
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; InBIO; Laboratório Associado; Campus Agrário de Vairão; 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; Rua Campo Alegre s/n 4169-007 Porto Portugal
- Wildlife Biology Program; College of Forestry and Conservation; University of Montana; Missoula MT 59812 USA
| | - José Melo-Ferreira
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; InBIO; Laboratório Associado; Campus Agrário de Vairão; 4485-661 Vairão Portugal
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43
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Kohli BA, Speer KA, Kilpatrick CW, Batsaikhan N, Damdinbazar D, Cook JA. Multilocus systematics and non-punctuated evolution of Holarctic Myodini (Rodentia: Arvicolinae). Mol Phylogenet Evol 2014; 76:18-29. [PMID: 24594062 DOI: 10.1016/j.ympev.2014.02.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 02/06/2014] [Accepted: 02/18/2014] [Indexed: 11/17/2022]
Abstract
The tribe Myodini consists of five genera of forest and alpine voles (Alticola, Caryomys, Eothenomys, Hyperacrius and Myodes) distributed throughout the Holarctic. Because mitochondrial evidence has revealed paraphyly and polyphyly among genera, we apply the first multilocus tests to clarify taxonomy and phylogenetic relationships. Our analyses of 28 of 36 species within Myodini, including three not previously sequenced (A. montosa, A. albicaudus, and H. fertilis), identify four distinct clades and provide the first molecular evidence that Hyperacrius may not belong in Myodini. Myodes is paraphyletic, while polyphyly of Alticola reflects apparent ancient mitochondrial introgression. Diversification in this tribe was hypothesized to be tightly linked to Late Cenozoic climatic events, however, lineage through time analysis indicates diversification over the last 4 My was gradual and not strongly punctuated.
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Affiliation(s)
- Brooks A Kohli
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131-1051, USA.
| | - Kelly A Speer
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131-1051, USA
| | | | - Nyamsuren Batsaikhan
- Department of Zoology, Faculty of Biology, National University of Mongolia, Ulaan Bataar, Mongolia
| | - Darmaa Damdinbazar
- Department of Zoology, Faculty of Biology, National University of Mongolia, Ulaan Bataar, Mongolia
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131-1051, USA
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44
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Melo-Ferreira J, Farelo L, Freitas H, Suchentrunk F, Boursot P, Alves PC. Home-loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing. Heredity (Edinb) 2013; 112:265-73. [PMID: 24149657 DOI: 10.1038/hdy.2013.102] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/23/2013] [Accepted: 09/09/2013] [Indexed: 01/02/2023] Open
Abstract
Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove because the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mitochondrial DNA (mtDNA) across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X- and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation results from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecology-driven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home-loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones.
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Affiliation(s)
- J Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Vairão, Portugal
| | - L Farelo
- 1] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Vairão, Portugal [2] Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - H Freitas
- 1] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Vairão, Portugal [2] Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - F Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - P Boursot
- Institut des Sciences de l'Evolution, Université Montpellier 2, CNRS IRD, Montpellier, France
| | - P C Alves
- 1] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Vairão, Portugal [2] Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal [3] Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
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45
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Yuan SL, Jiang XL, Li ZJ, He K, Harada M, Oshida T, Lin LK. A mitochondrial phylogeny and biogeographical scenario for Asiatic water shrews of the genus Chimarrogale: implications for taxonomy and low-latitude migration routes. PLoS One 2013; 8:e77156. [PMID: 24124605 PMCID: PMC3790732 DOI: 10.1371/journal.pone.0077156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 09/01/2013] [Indexed: 11/18/2022] Open
Abstract
The six species and three subspecies in the genus Chimarrogale (Soricomorpha: Soricidae) are commonly referred to as Asiatic water shrews. The Chimarrogale are the most widely distributed group of Nectogaline shrews, extending throughout the Oriental region and Japan. Because of the limited numbers of specimens available for study, the phylogenetic relationships and biogeographical history of this genus have not been comprehensively discussed. We used mitochondrial cytochrome b gene sequences to estimate phylogenetic relationships and divergence times among four Chimarrogale species, including all three subspecies of Chimarrogale himalayica. We also conducted a species delimitation analysis and tested two alternative migration scenarios in Asia through species distribution modeling and a reconstruction of the ancestral distribution. Here, we present the first proposed hypothesis regarding the Asiatic water shrew phylogeny and reveal ten putative species within the four recognized species. Distinct phylogenetic statuses of Chimarrogale phaeura, Chimarrogale platycephala, and Chimarrogale styani were confirmed. Chimarrogale himalayica was strongly supported as paraphyletic. We suggest that three subspecies of Chimarrogale himalayica should be reconsidered as distinct species. However, these suggestions must be considered with caution because only a single locus of a mtDNA gene was used. Four additional putative species, possibly distributed in central southwestern China and Taiwan, are currently undescribed; therefore, comprehensive morphological analyses are warranted to test their taxonomic statuses. The estimated molecular divergence times indicated that rapid speciation occurred during the early Pliocene, and current distribution patterns may have been affected by global cooling during the Pliocene/Pleistocene boundary. Reconstruction of the ancestral distribution and species distribution modeling for Asiatic water shrews revealed a low-latitude migration route over which ancestral Chimarrogale migrated from Europe via Central Asia to their current distribution. Our results demonstrated that Asiatic water shrews could have evolved throughout the low-latitude migration route from Europe to East and Southeast Asia.
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Affiliation(s)
- Shou-Li Yuan
- Laboratory of Wildlife Ecology, Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Xue-Long Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhen-Ji Li
- College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Biological Sciences department, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Masashi Harada
- Laboratory Animal Center, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Tatsuo Oshida
- Laboratory of Wildlife Ecology, Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Liang-Kong Lin
- Laboratory of Wildlife Ecology, Department of Life Science, Tunghai University, Taichung, Taiwan
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46
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Iacovakis C, Mamuris Z, Moutou KA, Touloudi A, Hammer AS, Valiakos G, Giannoulis T, Stamatis C, Spyrou V, Athanasiou LV, Kantere M, Asferg T, Giannakopoulos A, Salomonsen CM, Bogdanos D, Birtsas P, Petrovska L, Hannant D, Billinis C. Polarisation of major histocompatibility complex II host genotype with pathogenesis of European Brown Hare syndrome virus. PLoS One 2013; 8:e74360. [PMID: 24069299 PMCID: PMC3778001 DOI: 10.1371/journal.pone.0074360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/31/2013] [Indexed: 11/18/2022] Open
Abstract
A study was conducted in order to determine the occurrence of European Brown Hare Syndrome virus (EBHSV) in Denmark and possible relation between disease pathogenesis and Major Histocompatibility Complex (MHC) host genotype. Liver samples were examined from 170 brown hares (hunted, found sick or dead), collected between 2004 and 2009. Macroscopical and histopathological findings consistent with EBHS were detected in 24 (14.1%) hares; 35 (20.6%) had liver lesions not typical of the syndrome, 50 (29.4%) had lesions in other tissues and 61 (35.9%) had no lesions. Sixty five (38.2%) of 170 samples were found to be EBHSV-positive (RT-PCR, VP60 gene). In order to investigate associations between viral pathogenesis and host genotype, variation within the exon 2 DQA gene of MHC was assessed. DQA exon 2 analysis revealed the occurrence of seven different alleles in Denmark. Consistent with other populations examined so far in Europe, observed heterozygosity of DQA (Ho = 0.1180) was lower than expected (He = 0.5835). The overall variation for both nucleotide and amino acid differences (2.9% and 14.9%, respectively) were lower in Denmark than those assessed in other European countries (8.3% and 16.9%, respectively). Within the peptide binding region codons the number of nonsynonymous substitutions (dN) was much higher than synonymous substitutions (dS), which would be expected for MHC alleles under balancing selection. Allele frequencies did not significantly differ between EBHSV-positive and -negative hares. However, allele Leeu-DQA*30 was detected in significantly higher (P = 0.000006) frequency among the positive hares found dead with severe histopathological lesions than among those found sick or apparently healthy. In contrast, the latter group was characterized by a higher frequency of the allele Leeu-DQA*14 as well as the proportion of heterozygous individuals (P = 0.000006 and P = 0.027). These data reveal a polarisation between EBHSV pathogenesis and MHC class II genotype within the European brown hare in Denmark.
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Affiliation(s)
- Christos Iacovakis
- Faculty of Veterinary Medicine, University of Thessaly, Karditsa, Greece
- Institute for Research & Technology-Thessaly, Larissa, Greece
| | - Zissis Mamuris
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - Katerina A. Moutou
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - Antonia Touloudi
- Faculty of Veterinary Medicine, University of Thessaly, Karditsa, Greece
- Institute for Research & Technology-Thessaly, Larissa, Greece
| | - Anne Sofie Hammer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences University of Copenhagen, Copenhagen, Denmark
| | - George Valiakos
- Faculty of Veterinary Medicine, University of Thessaly, Karditsa, Greece
- Institute for Research & Technology-Thessaly, Larissa, Greece
| | - Themis Giannoulis
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - Costas Stamatis
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - Vassiliki Spyrou
- Department of Animal Production, Technological Education Institute of Larissa, Larissa, Greece
| | - Labrini V. Athanasiou
- Faculty of Veterinary Medicine, University of Thessaly, Karditsa, Greece
- Institute for Research & Technology-Thessaly, Larissa, Greece
| | - Maria Kantere
- Faculty of Veterinary Medicine, University of Thessaly, Karditsa, Greece
| | - Tommy Asferg
- Institute for Bioscience, Aarhus University, Aarhus, Denmark
| | | | - Charlotte M. Salomonsen
- Section for Fur Animal and Wildlife Diseases, National Veterinary Institute, Technical University of Denmark, Aarhus, Denmark
| | - Dimitrios Bogdanos
- Department of Medicine, University of Thessaly, Larissa, Greece
- Institute of Liver Studies, King’s College London, London, United Kingdom
| | - Periklis Birtsas
- Department of Forestry and Natural Environment Administration, Technological Education Institute of Larissa, Karditsa, Greece
| | - Liljana Petrovska
- Department of Bacteriology, Veterinary Laboratories Agency, Weybridge, United Kingdom
| | - Duncan Hannant
- School of Veterinary Medicine & Science, University of Nottingham, Nottingham, United Kingdom
| | - Charalambos Billinis
- Faculty of Veterinary Medicine, University of Thessaly, Karditsa, Greece
- Institute for Research & Technology-Thessaly, Larissa, Greece
- * E-mail:
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Lawson LP, Vernesi C, Ricci S, Rovero F. Evolutionary history of the grey-faced Sengi, Rhynchocyon udzungwensis, from Tanzania: a molecular and species distribution modelling approach. PLoS One 2013; 8:e72506. [PMID: 24015252 PMCID: PMC3754996 DOI: 10.1371/journal.pone.0072506] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/10/2013] [Indexed: 11/18/2022] Open
Abstract
Rhynchocyon udzungwensis is a recently described and poorly understood sengi (giant elephant-shrew) endemic to two small montane forests in Southern Tanzania, and surrounded in lower forests by R. cirnei reichardi. In this study, we investigate the molecular genetic relationship between R. udzungwensis and R. c. reichardi, and the possible role that shifting species distributions in response to climate fluctuations may have played in shaping their evolutionary history. Rhynchocyon udzungwensis and R. c. reichardi individuals were sampled from five localities for genetic analyses. Three mitochondrial and two nuclear loci were used to construct species trees for delimitation and to determine whether introgression was detectable either from ancient or ongoing hybridization. All species-tree results show R. udzungwensis and R. c. reichardi as distinct lineages, though mtDNA shows evidence of introgression in some populations. Nuclear loci of each species were monophyletic, implying introgression is exclusively historical. Because we found evidence of introgression, we used distribution data and species distribution modelling for present, glacial, and interglacial climate cycles to predict how shifting species distributions may have facilitated hybridization in some populations. Though interpretations are affected by the limited range of these species, a likely scenario is that the mtDNA introgression found in eastern mid-elevation populations was facilitated by low numbers of R. udzungwensis that expanded into lowland heavily occupied R. c. reichardi areas during interglacial climate cycles. These results imply that relationships within the genus Rhynchocyon may be confounded by porous species boundaries and introgression, even if species are not currently sympatric.
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Affiliation(s)
- Lucinda P. Lawson
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Centre for Research and Innovation, Michele all’Adige, Italy
| | - Silvia Ricci
- Tropical Biodiversity Section, Museo delle Scienze, Trento, Italy
| | - Francesco Rovero
- Tropical Biodiversity Section, Museo delle Scienze, Trento, Italy
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Capa M, Pons J, Hutchings P. Cryptic diversity, intraspecific phenetic plasticity and recent geographical translocations inBranchiomma(Sabellidae, Annelida). ZOOL SCR 2013. [DOI: 10.1111/zsc.12028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Maria Capa
- Australian Museum; Sydney; NSW; 2010; Australia
| | - Joan Pons
- Instituto Mediterráneo de Estudios Avanzados; c/-Miquel Marquès, 21; 07190-Esporles; Balearic Islands; Spain
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Jezkova T, Leal M, Rodríguez-Robles JA. Genetic drift or natural selection? Hybridization and asymmetric mitochondrial introgression in two Caribbean lizards (Anolis pulchellus and Anolis krugi). J Evol Biol 2013; 26:1458-71. [PMID: 23663090 DOI: 10.1111/jeb.12149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 11/28/2022]
Abstract
Hybridization and gene introgression can occur frequently between closely related taxa, but appear to be rare phenomena among members of the species-rich West Indian radiation of Anolis lizards. We investigated the pattern and possible mechanism of introgression between two sister species from Puerto Rico, Anolis pulchellus and Anolis krugi, using mitochondrial (ND2) and nuclear (DNAH3, NKTR) DNA sequences. Our findings demonstrated extensive introgression of A. krugi mtDNA (k-mtDNA) into the genome of A. pulchellus in western Puerto Rico, to the extent that k-mtDNA has mostly or completely replaced the native mtDNA of A. pulchellus on this part of the island. We proposed two not mutually exclusive scenarios to account for the interspecific matings between A. pulchellus and A. krugi. We inferred that hybridization events occurred independently in several populations, and determined that k-mtDNA haplotypes harboured in individuals of A. pulchellus can be assigned to four of the five major mtDNA clades of A. krugi. Further, the spatial distribution of k-mtDNA clades in the two species is largely congruent. Based on this evidence, we concluded that natural selection was the probable driving mechanism for the extensive k-mtDNA introgression into A. pulchellus. Our two nuclear data sets yielded different results. DNAH3 showed reciprocal monophyly of A. pulchellus and A. krugi, indicating no effect of hybridization on this marker. In contrast, the two species shared nine NKTR alleles, probably due to incomplete lineage sorting. Our study system will provide an excellent opportunity to experimentally assess the behavioural and ecological mechanisms that can lead to hybridization in closely related taxa.
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Affiliation(s)
- T Jezkova
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
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Kinoshita G, Nunome M, Han SH, Hirakawa H, Suzuki H. Ancient colonization and within-island vicariance revealed by mitochondrial DNA phylogeography of the mountain hare (Lepus timidus) in Hokkaido, Japan. Zoolog Sci 2013; 29:776-85. [PMID: 23106564 DOI: 10.2108/zsj.29.776] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We examined the phylogenetic status and history of the mountain hare Lepus timidus in and around Hokkaido using mitochondrial cytochrome b (cyt b) sequences from 158 samples from Hokkaido and 14 from Sakhalin, as well as four samples from the Korean hare, L. coreanus. The phylogenetic analysis of the cyt b sequences generated in this study and obtained from DNA databases showed the clear genetic specificity of the Hokkaido lineage as a clade. The Hokkaido lineage was estimated to have diverged from the other conspecific and L. coreanus lineages 0.46 and 0.30 million years ago (Mya), respectively. These results suggest that the common ancestor of the mitochondrial lineage in Hokkaido and Korea inhabited Far East Asia before colonization by the present continental lineages of L. timidus, including the Sakhalin population. We estimated the time of the most recent common ancestor of the Hokkaido population to be 0.17 Mya, and found two distinct haplogroups within the island. One group had greater genetic diversity (mean number of pairwise differences: π = 0.0188 ± 0.0108) and appears to have expanded from the west to the entire island of Hokkaido. The other had lower genetic diversity (π = 0.0038 ± 0.0037) and its distribution was concentrated in the east. These contrasting west/east trends indicate that the Hokkaido population was fragmented in the past, and then subsequently expanded. Our study suggests that Hokkaido was an important refugium for boreal species in the far eastern region, and allowed the formation of various population genetic structures within the island.
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Affiliation(s)
- Gohta Kinoshita
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo, Japan.
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