1
|
Tissaoui G, Suchentrunk F, Awadi A, Smith S, Weber A, Ben Slimen H. Evolutionary characteristics of the mitochondrial NADH dehydrogenase subunit 6 gene in some populations of four sympatric Mustela species (Mustelidae, Mammalia) from central Europe. Mol Biol Rep 2024; 51:575. [PMID: 38664260 DOI: 10.1007/s11033-024-09505-6] [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: 02/08/2024] [Accepted: 04/02/2024] [Indexed: 04/30/2024]
Abstract
BACKGROUND Selection on or reticulate evolution of mtDNA is documented in various mammalian taxa and could lead to misleading phylogenetic conclusions if not recognized. We sequenced the MT-ND6 gene of four sympatric Mustelid species of the genus Mustela from some central European populations. We hypothesised positive selection on MT-ND6, given its functional importance and the different body sizes and life histories of the species, even though climatic differences may be unimportant for adaptation in sympatry. METHODS AND RESULTS MT-ND6 genes were sequenced in 187 sympatric specimens of weasels, Mustela nivalis, stoats, M. erminea, polecats, M. putorius, and steppe polecats, M. eversmannii, from eastern Austria and of fourteen allopatric polecats from eastern-central Germany. Median joining networks, neighbour joining and maximum likelihood analyses as well as Bayesian inference grouped all species according to earlier published phylogenetic models. However, polecats and steppe polecats, two very closely related species, shared the same two haplotypes. We found only negative selection within the Mustela sequences, including 131 downloaded ones covering thirteen species. Positive selection was observed on three MT-ND6 codons of other mustelid genera retrieved from GenBank. CONCLUSIONS Negative selection for MT-ND6 within the genus Mustela suggests absence of both environmental and species-specific effects of cellular energy metabolism despite large species-specific differences in body size. The presently found shared polymorphism in European polecats and steppe polecats may result from ancestral polymorphism before speciation and historical or recent introgressive hybridization; it may indicate mtDNA capture of steppe polecats by M. putorius in Europe.
Collapse
Affiliation(s)
- Ghada Tissaoui
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Jendouba, Tunisia
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, Vienna, 1160, Austria
| | - Asma Awadi
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Jendouba, Tunisia
| | - Steve Smith
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, Vienna, 1160, Austria
| | - Antje Weber
- Landesamt für Umweltschutz Sachsen-Anhalt, Dez. 44 WZI, Lindenstraße 18, 39606, Iden, Germany
| | - Hichem Ben Slimen
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Jendouba, Tunisia.
| |
Collapse
|
2
|
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.
Collapse
|
3
|
Thulin CG, Winiger A, Tallian A, Kindberg J. Hunting harvest data in Sweden indicate precipitous decline in the native mountain hare subspecies Lepus timidus sylvaticus (heath hare). J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
4
|
Kraatz B, Belabbas R, Fostowicz-Frelik Ł, Ge DY, Kuznetsov AN, Lang MM, López-Torres S, Mohammadi Z, Racicot RA, Ravosa MJ, Sharp AC, Sherratt E, Silcox MT, Słowiak J, Winkler AJ, Ruf I. Lagomorpha as a Model Morphological System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.636402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.
Collapse
|
5
|
Buglione M, Petrelli S, de Filippo G, Troiano C, Rivieccio E, Notomista T, Maselli V, di Martino L, Carafa M, Gregorio R, Latini R, Fortebraccio M, Romeo G, Biliotti C, Fulgione D. Contribution to the ecology of the Italian hare (Lepus corsicanus). Sci Rep 2020; 10:13071. [PMID: 32753640 PMCID: PMC7403147 DOI: 10.1038/s41598-020-70013-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/06/2020] [Indexed: 11/09/2022] Open
Abstract
The Italian hare (Lepus corsicanus) is endemic to Central-Southern Italy and Sicily, classified as vulnerable due to habitat alterations, low density and fragmented populations and ecological competition with the sympatric European hare (Lepus europaeus). Despite this status, only few and local studies have explored its ecological features. We provided some key traits of the ecological niche of the Italian hare as well as its potential distribution in the Italian peninsula. All data derived from genetically validated presences. We generated a habitat suitability model using maximum entropy distribution model for the Italian hare and its main competitor, the European hare. The dietary habits were obtained for the Italian hare with DNA metabarcoding and High-Throughput Sequencing on faecal pellets. The most relevant environmental variables affecting the potential distribution of the Italian hare are shared with the European hare, suggesting a potential competition. The variation in the observed altitudinal distribution is statistically significant between the two species.The diet of the Italian hare all year around includes 344 plant taxa accounted by 62 families. The Fagaceae, Fabaceae, Poaceae, Rosaceae and Solanaceae (counts > 20,000) represented the 90.22% of the total diet. Fabaceae (60.70%) and Fagaceae (67.47%) were the most abundant plant items occurring in the Spring/Summer and Autumn/Winter diets, respectively. The Spring/Summer diet showed richness (N = 266) and diversity index values (Shannon: 2.329, Evenness: 0.03858, Equitability: 0.4169) higher than the Autumn/Winter diet (N = 199, Shannon: 1.818, Evenness: 0.03096, Equitability: 0.3435). Our contribution adds important information to broaden the knowledge on the environmental (spatial and trophic) requirements of the Italian hare, representing effective support for fitting management actions in conservation planning.
Collapse
Affiliation(s)
- Maria Buglione
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Simona Petrelli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Claudia Troiano
- Department of Humanities, University of Naples Federico II, Napoli, Italy
| | | | - Tommaso Notomista
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | | | - Romano Gregorio
- Cilento, Vallo di Diano e Alburni National Park, Salerno, Italy
| | - Roberta Latini
- Abruzzo, Lazio and Molise National Park, Pescasseroli, Aquila, Italy
| | | | - Giorgia Romeo
- Wildlife Section, Tuscan Regional Council, Grosseto, Italy
| | - Claudia Biliotti
- SOS Animali Onlus, Wildlife Rescue Center, Semproniano, Grosseto, Italy
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Naples, Italy.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Natola L, Burg TM. Population Genetics and Speciation of Yellow-Bellied, Red-Naped, and Red-Breasted Sapsuckers (Sphyrapicus varius, S. nuchalis, and S. ruber). J Hered 2019; 109:663-674. [PMID: 30010809 DOI: 10.1093/jhered/esy034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/11/2018] [Indexed: 12/11/2022] Open
Abstract
The root of understanding speciation lies in determining the forces which drive it. In many closely-related species, including Sphyrapicus varius, S. nuchalis, and S. ruber, it is assumed that speciation occurred due to isolation in multiple Pleistocene refugia. We used genetic data from 457 samples at the control region (CR), cytochrome oxidase I (COI), and chromo-helicase DNA binding protein (CHD1Z) to examine range-wide population genetic structure and differentiation amongst these 3 species across each species' breeding range. In addition, we modeled these species' ecological niches for the Holocene (~6000 years ago), Last Glacial Maximum (~22000 years ago), and Last Interglacial (~120000-140000 years ago) to determine if Pleistocene glaciations could have contributed to allopatric distributions, therefore allowing these groups to differentiate. Population genetic data show a potential Pleistocene refugium in Haida Gwaii, an east-west split among S. varius, and low genetic differentiation within each species. Our CR data show some polyphyly, while COI and CHD1Z data show differentiation among species using composite genotypes. Ecological Niche Modeling shows a large amount of niche overlap at each time period suggesting that S. varius, S. nuchalis, and S. ruber may not have been completely allopatric, and these species likely had repeated intermittent contact. Our data support the growing body of research that suggests differentiation despite gene flow.
Collapse
Affiliation(s)
- Libby Natola
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Theresa M Burg
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| |
Collapse
|
8
|
Unidirectional Introgression and Evidence of Hybrid Superiority over Parental Populations in Eastern Iranian Plateau Population of Hares (Mammalia: Lepus Linnaeus, 1758). J MAMM EVOL 2019. [DOI: 10.1007/s10914-019-09478-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
9
|
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.
Collapse
|
10
|
Spatial genetics of brown hares (Lepus europaeus Pallas, 1778) from Turkey: Different gene pool architecture on either side of the Bosphorus? Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
11
|
Iacolina L, Corlatti L, Buzan E, Safner T, Šprem N. Hybridisation in European ungulates: an overview of the current status, causes, and consequences. Mamm Rev 2018. [DOI: 10.1111/mam.12140] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Laura Iacolina
- Department of Chemistry and Bioscience; Aalborg University; Frederik Bajers Vej 7H 9220 Aalborg Denmark
- Aalborg Zoo; Mølleparkvej 63 9000 Aalborg Denmark
| | - Luca Corlatti
- Wildlife Ecology and Management; University of Freiburg; Tennenbacher Straße 4 79106 Freiburg Germany
- Institute of Wildlife Biology and Game Management; University of Natural Resources and Life Sciences Vienna; Gregor-Mendel-Straße 33 1180 Vienna Austria
| | - Elena Buzan
- Department of Biodiversity; Faculty of Mathematics, Natural Sciences and Information Technologies; University of Primorska; Glagoljaška 8 6000 Koper Slovenia
| | - Toni Safner
- Faculty of Agriculture; Department of Plant Breeding, Genetics and Biometrics; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
| | - Nikica Šprem
- Faculty of Agriculture; Department of Fisheries, Beekeeping, Game Management and Special Zoology; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
| |
Collapse
|
12
|
Large-scale mitochondrial DNA analysis reveals new light on the phylogeography of Central and Eastern-European Brown hare (Lepus europaeus Pallas, 1778). PLoS One 2018; 13:e0204653. [PMID: 30286121 PMCID: PMC6171851 DOI: 10.1371/journal.pone.0204653] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 09/12/2018] [Indexed: 01/29/2023] Open
Abstract
European brown hare, Lepus europaeus, from Central and Eastern European countries (Hungary, Poland, Serbia, Lithuania, Romania, Georgia and Italy) were sampled, and phylogenetic analyses were carried out on two datasets: 1.) 137 sequences (358 bp) of control region mtDNA; and 2.) 105 sequences of a concatenated fragment (916 bp), including the cytochrome b, tRNA-Thr, tRNA-Pro and control region mitochondrial DNA. Our sequences were aligned with additional brown hare sequences from GenBank. A total of 52 and 51 haplotypes were detected within the two datasets, respectively, and assigned to two previously described major lineages: Anatolian/Middle Eastern (AME) and European (EUR). Furthermore, the European lineage was divided into two subclades including South Eastern European (SEE) and Central European (CE). Sympatric distribution of the lineages of the brown hare in South-Eastern and Eastern Europe revealed contact zones there. BAPS analysis assigned sequences from L. europaeus to five genetic clusters, whereas CE individuals were assigned to only one cluster, and AME and SEE sequences were each assigned to two clusters. Our findings uncover numerous novel haplotypes of Anatolian/Middle Eastern brown hare outside their main range, as evidence for the combined influence of Late Pleistocene climatic fluctuations and anthropogenic activities in shaping the phylogeographic structure of the species. Our results support the hypothesis of a postglacial brown hare expansion from Anatolia and the Balkan Peninsula to Central and Eastern Europe, and suggest some slight introgression of individual haplotypes from L. timidus to L. europaeus.
Collapse
|
13
|
Ben Slimen H, Awadi A, Tolesa ZG, Knauer F, Alves PC, Makni M, Suchentrunk F. Positive selection on the mitochondrial ATP synthase 6and the NADH dehydrogenase 2genes across 22 hare species (genus Lepus). J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hichem Ben Slimen
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique; Faculty of Sciences of Tunis; University of Tunis El Manar; Tunis Tunisia
- Institut Supérieur de Biotechnologie de Béja; University of Jendouba; Béja Tunisia
| | - Asma Awadi
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique; Faculty of Sciences of Tunis; University of Tunis El Manar; Tunis Tunisia
| | | | - Felix Knauer
- Research Institute of Wildlife Ecology; University of Veterinary Medicine Vienna; Vienna Austria
| | - Paulo Célio Alves
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - Mohamed Makni
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique; Faculty of Sciences of Tunis; University of Tunis El Manar; Tunis Tunisia
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology; University of Veterinary Medicine Vienna; Vienna Austria
| |
Collapse
|
14
|
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
| |
Collapse
|
15
|
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.
Collapse
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:
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Beugin MP, Letty J, Kaerle C, Guitton JS, Muselet L, Queney G, Pontier D. A single multiplex of twelve microsatellite markers for the simultaneous study of the brown hare (Lepus europaeus) and the mountain hare (Lepus timidus). Ecol Evol 2017. [DOI: 10.1002/ece3.2943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Marie-Pauline Beugin
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
- Univ Lyon; Université Lyon 1; CNRS; Laboratoire de Biométrie et Biologie Evolutive UMR5558; F-69622 Villeurbanne France
| | - Jérôme Letty
- Research Department; National Hunting and Wildlife Agency (ONCFS); Juvignac Nantes France
| | - Cécile Kaerle
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
| | - Jean-Sébastien Guitton
- Research Department; National Hunting and Wildlife Agency (ONCFS); Juvignac Nantes France
| | - Lina Muselet
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
| | - Guillaume Queney
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
| | - Dominique Pontier
- Univ Lyon; Université Lyon 1; CNRS; Laboratoire de Biométrie et Biologie Evolutive UMR5558; F-69622 Villeurbanne France
| |
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
Awadi A, Suchentrunk F, Makni M, Ben Slimen H. Variation of partial transferrin sequences and phylogenetic relationships among hares (Lepus capensis, Lagomorpha) from Tunisia. Genetica 2016; 144:497-512. [PMID: 27485731 DOI: 10.1007/s10709-016-9916-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 07/11/2016] [Indexed: 10/21/2022]
Abstract
North African hares are currently included in cape hares, Lepus capensis sensu lato, a taxon that may be considered a superspecies or a complex of closely related species. The existing molecular data, however, are not unequivocal, with mtDNA control region sequences suggesting a separate species status and nuclear loci (allozymes, microsatellites) revealing conspecificity of L. capensis and L. europaeus. Here, we study sequence variation in the intron 6 (468 bp) of the transferrin nuclear gene, of 105 hares with different coat colour from different regions in Tunisia with respect to genetic diversity and differentiation, as well as their phylogenetic status. Forty-six haplotypes (alleles) were revealed and compared phylogenetically to all available TF haplotypes of various Lepus species retrieved from GenBank. Maximum Likelihood, neighbor joining and median joining network analyses concordantly grouped all currently obtained haplotypes together with haplotypes belonging to six different Chinese hare species and the African scrub hare L. saxatilis. Moreover, two Tunisian haploypes were shared with L. capensis, L timidus, L. sinensis, L. yarkandensis, and L. hainanus from China. These results indicated the evolutionary complexity of the genus Lepus with the mixing of nuclear gene haplotypes resulting from introgressive hybridization or/and shared ancestral polymorphism. We report the presence of shared ancestral polymorphism between North African and Chinese hares. This has not been detected earlier in the mtDNA sequences of the same individuals. Genetic diversity of the TF sequences from the Tunisian populations was relatively high compared to other hare populations. However, genetic differentiation and gene flow analyses (AMOVA, FST, Nm) indicated little divergence with the absence of geographically meaningful phylogroups and lack of clustering with coat colour types. These results confirm the presence of a single hare species in Tunisia, but a sound inference on its phylogenetic position would require additional nuclear markers and numerous geographically meaningful samples from Africa and Eurasia.
Collapse
Affiliation(s)
- Asma Awadi
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique, Université de Tunis El Manar, Tunis, Tunisia.
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mohamed Makni
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique, Université de Tunis El Manar, Tunis, Tunisia
| | - Hichem Ben Slimen
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique, Université de Tunis El Manar, Tunis, Tunisia
| |
Collapse
|
20
|
González E, Gállego M, Molina R, Abras A, Alcover MM, Ballart C, Fernández A, Jiménez M. Identification of blood meals in field captured sand flies by a PCR-RFLP approach based on cytochrome b gene. Acta Trop 2015; 152:96-102. [PMID: 26342793 DOI: 10.1016/j.actatropica.2015.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/21/2015] [Accepted: 08/31/2015] [Indexed: 11/29/2022]
Abstract
Leishmaniasis is a vector-borne disease transmitted by phlebotomine sand flies. Information about blood meal preferences in sand flies is essential to understand the epidemiology of the disease to adopt control measures. In previous studies, a polymerase chain reaction (PCR) of 359bp fragment of the conserved gene cytochrome b (cyt b) and further sequencing were applied in the study of blood meal sources in sand flies collected in the area of a leishmaniasis outbreak in southwest Madrid, Spain, providing significant information about blood meal preferences in the focus. In this work, a PCR-restriction fragment length polymorphism (RFLP) targeting a fragment of 359bp of vertebrate cyt b gene was developed. Restriction endonucleases HaeIII and HinfI generated specific patterns consistent with the blood meal sources found in sand flies. The protocol has been validated with twenty six engorged females collected in the field with CDC traps. Blood meals from nine vertebrates were identified based on PCR-cyt b and sequencing-human, dog, cat, horse, hare, rabbit, sheep, goat and chicken - and mixed blood meals (sheep/human; sheep/goat) - and successfully distinguished by PCR-RFLP. Therefore, this approach is an efficient and reliable alternative method to be applied in entomological surveys.
Collapse
Affiliation(s)
- Estela González
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo s/n, 28220 Majadahonda, Madrid, Spain
| | - Montserrat Gállego
- Laboratori de Parasitologia, Facultat de Farmàcia, Universitat de Barcelona (UB), Spain; ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ricardo Molina
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo s/n, 28220 Majadahonda, Madrid, Spain
| | - Alba Abras
- Laboratori de Parasitologia, Facultat de Farmàcia, Universitat de Barcelona (UB), Spain; ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - M Magdalena Alcover
- Laboratori de Parasitologia, Facultat de Farmàcia, Universitat de Barcelona (UB), Spain; ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Cristina Ballart
- Laboratori de Parasitologia, Facultat de Farmàcia, Universitat de Barcelona (UB), Spain; ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Anna Fernández
- Laboratori de Parasitologia, Facultat de Farmàcia, Universitat de Barcelona (UB), Spain
| | - Maribel Jiménez
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo s/n, 28220 Majadahonda, Madrid, Spain.
| |
Collapse
|
21
|
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]
|
22
|
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
| |
Collapse
|
23
|
Cheng E, Hodges KE, Melo-Ferreira J, Alves PC, Mills LS. Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare. Mol Ecol 2014; 23:2929-42. [PMID: 24814937 DOI: 10.1111/mec.12790] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 05/05/2014] [Accepted: 05/05/2014] [Indexed: 11/27/2022]
Abstract
With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of the microsatellite data suggests initial subdivision in two groups, Boreal and southwestern. The southwestern group further splits into Greater Pacific Northwest and U.S. Rockies. The genealogical information retrieved from mtDNA is congruent with the three highly differentiated and divergent groups of snowshoe hares. These groups can correspond with evolutionarily significant units that might have evolved in separate refugia south and east of the Pleistocene ice sheets. Genetic diversity was highest at mid-latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mtDNA and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mtDNA lineage were more closely related to black-tailed jackrabbits (Lepus californicus) than to other snowshoe hares, which may result from secondary introgression or shared ancestral polymorphism. Given the genetic distinctiveness of southern populations and minimal gene flow with their northern neighbours, fragmentation and loss of southern boreal habitats could mean loss of many unique alleles and reduced evolutionary potential.
Collapse
Affiliation(s)
- Ellen Cheng
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | | | | | | | | |
Collapse
|
24
|
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
| |
Collapse
|
25
|
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
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Puggioni G, Cavadini P, Maestrale C, Scivoli R, Botti G, Ligios C, Le Gall-Reculé G, Lavazza A, Capucci L. The new French 2010 Rabbit Hemorrhagic Disease Virus causes an RHD-like disease in the Sardinian Cape hare (Lepus capensis mediterraneus). Vet Res 2013; 44:96. [PMID: 24099575 PMCID: PMC3853023 DOI: 10.1186/1297-9716-44-96] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 09/26/2013] [Indexed: 11/10/2022] Open
Abstract
Lagovirus is an emerging genus of Caliciviridae, which includes the Rabbit Hemorrhagic Disease Virus (RHDV) of rabbits and the European brown hare syndrome virus (EBHSV) of hares that cause lethal hepatitis. In 2010, a new RHDV related virus (RHDV2) with a unique genetic and antigenic profile and lower virulence was identified in France in rabbits. Here we report the identification of RHDV2 as the cause in Sardinia of several outbreaks of acute hepatitis in rabbits and Cape hare (Lepus capensis mediterraneus). This is the first account of a lagovirus that causes fatal hepatitis in both rabbits and hares.
Collapse
Affiliation(s)
- Giantonella Puggioni
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, OIE Reference Laboratory for RHD, via Bianchi 9, 25124 Brescia, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
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.
Collapse
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:
| |
Collapse
|
29
|
Jiménez M, González E, Iriso A, Marco E, Alegret A, Fúster F, Molina R. Detection of Leishmania infantum and identification of blood meals in Phlebotomus perniciosus from a focus of human leishmaniasis in Madrid, Spain. Parasitol Res 2013; 112:2453-9. [PMID: 23535889 DOI: 10.1007/s00436-013-3406-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 03/15/2013] [Indexed: 11/26/2022]
Abstract
Since 2010, the number of cases of both human visceral leishmaniasis and cutaneous leishmaniasis in southwestern Madrid region (Spain) and more specifically in the town of Fuenlabrada has increased. Direct xenodiagnosis of leishmaniasis proved that hares (Lepus granatensis) from this focus are able to infect with Leishmania infantum colonized Phlebotomus perniciosus. To a better understanding of this focus of leishmaniasis, we conducted an entomological survey using CDC light traps, at the end of the seasonal transmission period of 2011 before the beginning of control measures of the disease, to study the phlebotomine sand flies species involved. Detection of Leishmania DNA in the sand flies captured was studied by kDNA-PCR and cpb-PCR. In addition, blood fed and gravid female P. perniciosus were analysed by a PCR based in vertebrate cytochrome b (cyt b) gene. Taxonomic identification of captured sand flies (n = 174) as P. perniciosus (n = 171) and Sergentomyia minuta (n = 3) together with the analysis of blood feeding in ten sand flies that shows a high preference for hares (n = 6), followed by humans (n = 3), and cats (n = 1) confirm a strong association between P. perniciosus hares and humans in the focus. Moreover, 79 out of 135 (58.5 %) P. perniciosus were positive to L. infantum by PCR approaches. These data support the increase of human leishmaniasis cases in the area and the existence of an unusual sylvatic cycle alternative to the classical domestic one, where the dog is the main reservoir of L. infantum.
Collapse
Affiliation(s)
- Maribel Jiménez
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo s/n, 28220 Majadahonda, Madrid, Spain.
| | | | | | | | | | | | | |
Collapse
|
30
|
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.
Collapse
Affiliation(s)
- Gohta Kinoshita
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo, Japan.
| | | | | | | | | |
Collapse
|
31
|
Antoniou A, Magoulas A, Platis P, Kotoulas G. Assessing the genetic landscape of a contact zone: the case of European hare in northeastern Greece. Genetica 2013; 141:23-40. [PMID: 23381134 DOI: 10.1007/s10709-013-9703-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 01/30/2013] [Indexed: 12/28/2022]
Abstract
The European hare populations of the Balkan Peninsula comprise two divergent phylogenetic lineages with discrete geographical distribution slightly overlapping in the area of northeastern Greece and Bulgaria. Here we elucidate their contact zone, by defining the spatial distributional pattern of the two highly divergent groups, detecting individuals of hybrid origin, and identifying genetic barriers present in the area of their co-existence. Specimens from northeastern Greece were assayed for lineage assignment and population genetic inference based on a 511 bp fragment of mitochondrial DNA control region and allelic data from 10 microsatellite loci. Bayesian analyses on original and simulated genotypes were performed allowing for the contact zone delineation. Our results indicate high genetic diversity in both nuclear and mitochondrial DNA, strong population structure and non random spatial distribution of the differentiated gene pools. The information provided by the two types of molecular markers yielded consistent results. This study comprises a fine scale analysis of the contact zone between the two evolutionary lineages of European brown hares in northeastern Greece. Specific questions on the spatial patterns where addressed for the first time. Furthermore, hypotheses regarding the presence of hybrids were also tested. As a result, interpretive power to the diversity patterns observed today in the Balkans was added and previously overlooked aspects of the species biology were highlighted.
Collapse
Affiliation(s)
- Aglaia Antoniou
- Department of Biology, University of Crete, Herakleio, Crete, Greece.
| | | | | | | |
Collapse
|
32
|
Acevedo P, Melo-Ferreira J, Real R, Alves PC. Past, present and future distributions of an Iberian Endemic, Lepus granatensis: ecological and evolutionary clues from species distribution models. PLoS One 2012; 7:e51529. [PMID: 23272115 PMCID: PMC3521729 DOI: 10.1371/journal.pone.0051529] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 11/05/2012] [Indexed: 01/21/2023] Open
Abstract
The application of species distribution models (SDMs) in ecology and conservation biology is increasing and assuming an important role, mainly because they can be used to hindcast past and predict current and future species distributions. However, the accuracy of SDMs depends on the quality of the data and on appropriate theoretical frameworks. In this study, comprehensive data on the current distribution of the Iberian hare (Lepus granatensis) were used to i) determine the species' ecogeographical constraints, ii) hindcast a climatic model for the last glacial maximum (LGM), relating it to inferences derived from molecular studies, and iii) calibrate a model to assess the species future distribution trends (up to 2080). Our results showed that the climatic factor (in its pure effect and when it is combined with the land-cover factor) is the most important descriptor of the current distribution of the Iberian hare. In addition, the model's output was a reliable index of the local probability of species occurrence, which is a valuable tool to guide species management decisions and conservation planning. Climatic potential obtained for the LGM was combined with molecular data and the results suggest that several glacial refugia may have existed for the species within the major Iberian refugium. Finally, a high probability of occurrence of the Iberian hare in the current species range and a northward expansion were predicted for future. Given its current environmental envelope and evolutionary history, we discuss the macroecology of the Iberian hare and its sensitivity to climate change.
Collapse
Affiliation(s)
- Pelayo Acevedo
- Biogeography, Diversity and Conservation Research Team, University of Malaga, Malaga, Spain.
| | | | | | | |
Collapse
|
33
|
Koutsogiannouli EA, Moutou KA, Stamatis C, Mamuris Z. Analysis of MC1R genetic variation in Lepus species in Mediterranean refugia. Mamm Biol 2012. [DOI: 10.1016/j.mambio.2012.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
34
|
Bastos-Silveira C, Santos SM, Monarca R, Mathias MDL, Heckel G. Deep mitochondrial introgression and hybridization among ecologically divergent vole species. Mol Ecol 2012; 21:5309-23. [DOI: 10.1111/mec.12018] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 12/23/2022]
Affiliation(s)
| | - Sara M. Santos
- Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; Campo Grande; 1749-016; Lisbon; Portugal
| | - Rita Monarca
- Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; Campo Grande; 1749-016; Lisbon; Portugal
| | | | | |
Collapse
|
35
|
Canu A, Suchentrunk F, Cossu A, Foddai R, Iacolina L, Ben Slimen H, Apollonio M, Scandura M. Differentiation under isolation and genetic structure of Sardinian hares as revealed by craniometric analysis, mitochondrial DNA and microsatellites. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00671.x] [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]
|
36
|
FREEDBERG STEVEN, MYERS ERINM. Cytonuclear equilibrium following interspecific introgression in a turtle lacking sex chromosomes. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01862.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
37
|
Melo-Ferreira J, Boursot P, Carneiro M, Esteves PJ, Farelo L, Alves PC. Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) Revealed by Species-Tree Inference and Coalescent Simulations. Syst Biol 2011; 61:367-81. [DOI: 10.1093/sysbio/syr114] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J. Melo-Ferreira
- CIBIO, 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 da Universidade do Porto, 4099−002 Porto, Portugal
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution, 34095 Montpellier cedex 5, France
| | - P. Boursot
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution, 34095 Montpellier cedex 5, France
| | - M. Carneiro
- CIBIO, 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 da Universidade do Porto, 4099−002 Porto, Portugal
| | - P. J. Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- CITS—Centro de Investigação em Tecnologias da Saúde, IPSN, Gandra, CESPU, Portugal
| | - L. Farelo
- CIBIO, 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 da Universidade do Porto, 4099−002 Porto, Portugal
| | - P. C. Alves
- CIBIO, 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 da Universidade do Porto, 4099−002 Porto, Portugal
- University of Montana, Wildlife Biology Program, College of Forestry and Conservation, Missoula, MT 59812, USA
| |
Collapse
|
38
|
Affiliation(s)
- Quinn R. Shurtliff
- Department of Biological Sciences; Idaho State University; Idaho; 83209; USA
| |
Collapse
|
39
|
Santos CG, Melo VS, Amaral JS, Estevinho L, Oliveira MBPP, Mafra I. Identification of hare meat by a species-specific marker of mitochondrial origin. Meat Sci 2011; 90:836-41. [PMID: 22133589 DOI: 10.1016/j.meatsci.2011.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/26/2011] [Accepted: 10/26/2011] [Indexed: 10/15/2022]
Abstract
Meat species identification in food has gained increasing interest in recent years due to public health, economic and legal concerns. Following the consumer trend towards high quality products, game meat has earned much attention. The aim of the present work was to develop a DNA-based technique able to identify hare meat. Mitochondrial cytochrome b gene was used to design species-specific primers for hare detection. The new primers proved to be highly specific to Lepus species, allowing the detection of 0.01% of hare meat in pork meat by polymerase chain reaction (PCR). A real-time PCR assay with the new intercalating EvaGreen dye was further proposed as a specific and fast tool for hare identification with increased sensitivity (1pg) compared to end-point PCR (10pg). It can be concluded that the proposed new primers can be used by both species-specific end-point PCR or real-time PCR to accurately authenticate hare meat.
Collapse
Affiliation(s)
- Cristina G Santos
- REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Aníbal Cunha, 164, 4099-030 Porto, Portugal
| | | | | | | | | | | |
Collapse
|
40
|
Liu J, Yu L, Arnold ML, Wu CH, Wu SF, Lu X, Zhang YP. Reticulate evolution: frequent introgressive hybridization among Chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci. BMC Evol Biol 2011; 11:223. [PMID: 21794180 PMCID: PMC3155923 DOI: 10.1186/1471-2148-11-223] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/28/2011] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. RESULTS Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. CONCLUSION This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.
Collapse
Affiliation(s)
- Jiang Liu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Li Yu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Michael L Arnold
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Chun-Hua Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
- Utah State University Department of Animal, Dairy & Veterinary Sciences Old Main Hill 4700 Center for Integrated Biosystems Rm315 Logan, UT 84322-4700, USA
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Xin Lu
- Department of Zoology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ya-Ping Zhang
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| |
Collapse
|
41
|
Wu Y, Xia L, Zhang Q, Yang Q, Meng X. Bidirectional introgressive hybridization between Lepus capensis and Lepus yarkandensis. Mol Phylogenet Evol 2011; 59:545-55. [DOI: 10.1016/j.ympev.2011.03.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 03/10/2011] [Accepted: 03/24/2011] [Indexed: 11/29/2022]
|
42
|
Melo-Ferreira J, Alves PC, Rocha J, Ferrand N, Boursot P. Interspecific X-chromosome and mitochondrial DNA introgression in the Iberian hare: selection or allele surfing? Evolution 2011; 65:1956-68. [PMID: 21729051 DOI: 10.1111/j.1558-5646.2011.01261.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introgression from a resident species into an invading one is predicted to occur through the demographic process of "allele surfing," and to particularly affect genomic regions transmitted by the lower migrating sex, such as mtDNA. This could explain that northern Iberian populations of Lepus granatensis harbor high frequencies of mtDNA from L. timidus, an arctic hare it replaced there after deglaciation. We report that variation of introgressed timidus-like mtDNA reflects several predicted effects of this process: increasing frequency and diversity in the direction of expansion, strong perpendicular phylogeographic structure and signs of postglacial demographic growth. However, demographic inferences for the granatensis and timidus-like mtDNA lineages suggest the latter may have outcompeted the former in northern Iberia. Autosomal introgression occurs at low frequencies and species-wide rather than only in the north. If this difference with mtDNA resulted from sex-biased migration, an intermediate pattern should prevail for the X-chromosome, but we report species-wide and high-frequency introgression of an X-fragment. Either selection favored this ubiquitous X-introgression, or more complex postglacial expansion patterns prevailed, with different consequences depending on the genomic and geographic region. This illustrates the difficulty of distinguishing demographic and selective effects and the need for genome and species-wide based demographic models.
Collapse
Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | | | | | | | | |
Collapse
|
43
|
Hares in Corsica: high prevalence of Lepus corsicanus and hybridization with introduced L. europaeus and L. granatensis. EUR J WILDLIFE RES 2010. [DOI: 10.1007/s10344-010-0430-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
44
|
Zachos FE, Ben Slimen H, Hackländer K, Giacometti M, Suchentrunk F. Regional genetic
in situ
differentiation despite phylogenetic heterogeneity in Alpine mountain hares. J Zool (1987) 2010. [DOI: 10.1111/j.1469-7998.2010.00710.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. E. Zachos
- Zoological Institute, Christian‐Albrechts‐University, Kiel, Germany
| | - H. Ben Slimen
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Campus Universitaire El Manar, Tunis, Tunisia
| | - K. Hackländer
- Department of Integrative Biology and Biodiversity Research, Institute of Wildlife Biology and Game Management, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | | | - F. Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| |
Collapse
|
45
|
PROST S, KNAPP M, FLEMMIG J, HUFTHAMMER AK, KOSINTSEV P, STILLER M, HOFREITER M. SHORT COMMUNICATION: A phantom extinction? New insights into extinction dynamics of the Don-hare Lepus tanaiticus. J Evol Biol 2010; 23:2022-9. [DOI: 10.1111/j.1420-9101.2010.02062.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
46
|
Kral LG. Multiple Nuclear Gene Analysis of the Divergence between Populations of the Tallapoosa Darter, Etheostoma tallapoosae. SOUTHEAST NAT 2010. [DOI: 10.1656/058.009.0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
47
|
Bogdanowicz W, Van Den Bussche RA, Gajewska M, Postawa T, Harutyunyan M. Ancient and Contemporary DNA Sheds Light on the History of Mouse-Eared Bats in Europe and the Caucasus. ACTA CHIROPTEROLOGICA 2009. [DOI: 10.3161/150811009x485530] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
48
|
Keck BP, Near TJ. GEOGRAPHIC AND TEMPORAL ASPECTS OF MITOCHONDRIAL REPLACEMENT INNOTHONOTUSDARTERS (TELEOSTEI: PERCIDAE: ETHEOSTOMATINAE). Evolution 2009; 64:1410-28. [DOI: 10.1111/j.1558-5646.2009.00901.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
49
|
Sert H, Slimen HB, Erdoğan A, Suchentrunk F. Mitochondrial HVI sequence variation in Anatolian hares (Lepus europaeus Pallas, 1778). Mamm Biol 2009. [DOI: 10.1016/j.mambio.2008.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
50
|
Petit RJ, Excoffier L. Gene flow and species delimitation. Trends Ecol Evol 2009; 24:386-93. [PMID: 19409650 DOI: 10.1016/j.tree.2009.02.011] [Citation(s) in RCA: 473] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/19/2009] [Accepted: 02/23/2009] [Indexed: 10/20/2022]
|