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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Stefanović M, Djan M, Veličković N, Beuković D, Lavadinović V, Zhelev CD, Demirbaş Y, Paule L, Gedeon CI, Mamuris Z, Posautz A, Beiglböck C, Kübber-Heiss A, Suchentrunk F. Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective. PLoS One 2019; 14:e0224902. [PMID: 31703111 PMCID: PMC6839855 DOI: 10.1371/journal.pone.0224902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/23/2019] [Indexed: 11/28/2022] Open
Abstract
Previous studies in hares and jackrabbits have indicated that positive selection has shaped the genetic diversity of mitochondrial genes involved in oxidative phosphorylation, which may affect cellular energy production and cause regional adaptation to different environmental (climatic) pressures. In the present study, we sequenced the NADH dehydrogenase subunit 6 (MT-ND6) gene of 267 brown hares (L. europaeus) from Europe and Asia Minor and tested for positive selection and adaptations acting on amino acid sequences (protein variants). Molecular diversity indices and spatial clustering were assessed by DnaSP, Network, and Geneland, while the presence of selection signals was tested by codeml in PAML, and by using the Datamonkey Adaptive Evolution web server. The SPSS software was used to run multinomial regression models to test for possible effects of climate parameters on the currently obtained protein variants. Fifty-eight haplotypes were revealed with a haplotype diversity of 0.817, coding for 17 different protein variants. The MT-ND6 phylogeographic pattern as determined by the nucleotide sequences followed the earlier found model based on the neutrally evolving D-loop sequences, and reflected the earlier found phylogeographic Late Pleistocene scenario. Based on several selection tests, only one codon position consistently proved to be under positive selection. It did occur exclusively in the evolutionarily younger hares from Europe and it gave rise to several protein variants from the southeastern and south-central Balkans. The occurrence of several of those variants was significantly favored under certain precipitation conditions, as proved by our multinomial regression models. Possibly, the great altitudinal variation in the Balkans may have lead to bigger changes in precipitation across that region and this may have imposed an evolutionarily novel selective pressure on the protein variants and could have led to regional adaptation.
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Affiliation(s)
- Milomir Stefanović
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
- * E-mail:
| | - Mihajla Djan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Nevena Veličković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Dejan Beuković
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | | | | | - Yasin Demirbaş
- Faculty of Science and Arts, University of Kırıkkale, Kırıkkale, Turkey
| | - Ladislav Paule
- Faculty of Forestry, Technical University, Zvolen, Slovakia
| | - Csongor István Gedeon
- Institute for Soil Sciences and Agricultural Chemistry, Hungarian Academy of Sciences, Budapest, Hungary
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, University of Thessaly, Larrisa, Greece
| | - Annika Posautz
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Beiglböck
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Anna Kübber-Heiss
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
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Stalder GL, Pinior B, Zwirzitz B, Loncaric I, Jakupović D, Vetter SG, Smith S, Posautz A, Hoelzl F, Wagner M, Hoffmann D, Kübber-Heiss A, Mann E. Gut microbiota of the European Brown Hare (Lepus europaeus). Sci Rep 2019; 9:2738. [PMID: 30804494 PMCID: PMC6390100 DOI: 10.1038/s41598-019-39638-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/21/2019] [Indexed: 12/14/2022] Open
Abstract
Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive demographic and phylogeographic research, little is known about the composition of its gut microbiota and how it might vary based on potential environmental or host factors. We analysed the intestinal and faecal microbiota of 3 hare populations by Illumina MiSeq 16S rRNA gene amplicon sequencing. The phyla and OTU abundance composition differed significantly between intestinal and faecal samples (PERMANOVA: P = 0.002 and P = 0.031, respectively), but in both sample types Firmicutes and Bacteroidetes dominated the microbial community composition (45.51% and 19.30% relative abundance). Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71-fold change, P < 0.001). At OTU level, a significant enrichment with best BLAST hits to the Escherichia-Shigella group, Eubacterium limosum, Sphingomonas kyeonggiensis, Flintibacter butyricus and Blautia faecis were detected in intestinal samples (P < 0.05). In our statistical model, geographic location and possibly associated environmental factors had a greater impact on the microbiota composition than host factors. Population had a significant effect on the composition of abundant intestinal and faecal OTUs, and on the abundance of potential pathogenic bacteria of the family Enterobacteriaceae, regularly associated with intestinal dysbiosis in hares, in faecal samples. Our study is the first to describe the microbiota in brown hares and provides a foundation to generate hypothesis aiming to test the role of gut health in population fluctuations of the species.
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Affiliation(s)
- G L Stalder
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria.
| | - B Pinior
- Department for Farm Animals and Veterinary Public Health, Institute for Veterinary Public Health, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria
| | - B Zwirzitz
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - I Loncaric
- Department of Pathobiology, Institute of Microbiology, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria
| | - D Jakupović
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - S G Vetter
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - S Smith
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - A Posautz
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - F Hoelzl
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - M Wagner
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - D Hoffmann
- Game Conservancy Deutschland e. V., Schloßstrasse 1, 86732, Oettingen, Germany
| | - A Kübber-Heiss
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - E Mann
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria
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Giannoulis T, Plageras D, Stamatis C, Chatzivagia E, Tsipourlianos A, Birtsas P, Billinis C, Suchentrunk F, Mamuris Z. Islands and hybrid zones: combining the knowledge from "Natural Laboratories" to explain phylogeographic patterns of the European brown hare. BMC Evol Biol 2019; 19:17. [PMID: 30630408 PMCID: PMC6329171 DOI: 10.1186/s12862-019-1354-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 01/02/2019] [Indexed: 12/30/2022] Open
Abstract
Background The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocations, spontaneous and human-mediated, local adaptation and the genetic drift in the shaping of the phylogeographic patterns of the species. For this purpose, we used molecular markers, both nuclear and mitochondrial, that are indicative for local adaptation as well as neutral markers to elucidate the patterns of population differentiation based on geographic isolation and the clade of origin. To broaden our analysis, we included data from our previous studies concerning mainland populations, to explore the genetic differentiation in the base of the geographic origin (mainland/island) of the populations. Results Our results suggest that local adaptation shapes the differentiation in both genomes, favoring specific alleles in nuclear genes (e.g. DQA) or haplotypes in mtDNA (e.g. Control Region, CR). mtDNA variation was found to be in a higher level and was able to give a phylogeographic signal for the populations. Furthermore, the degree of variation was influenced not only by the geographic origin, but also by the clade of origin, since specific island populations of Anatolian origin showed a greater degree of variation compared to specific mainland populations of the European clade. Concerning the hybrid population, we confirmed the existence of both clades in the territory and we provided a possible explanation for the lack of introgression between the clades. Conclusion Our results indicate that the Quaternary’s climatic oscillations played a major role in the shaping of the phylogeographic patterns of the species, by isolating populations in the distinct refugia, where they adapted and differentiate in allopatry, leading to genome incompatibilities observed nowadays. Electronic supplementary material The online version of this article (10.1186/s12862-019-1354-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Themistoklis Giannoulis
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Dimitrios Plageras
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Costas Stamatis
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Eleni Chatzivagia
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Andreas Tsipourlianos
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Periklis Birtsas
- Department of Forestry and Natural Environment Administration, TEI of Thessaly, Larissa, Greece
| | | | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece.
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Demirbaş Y, Albayrak İ, Özkan Koca A, Stefanović M, Knauer F, Suchentrunk F. Spatial genetics of brown hares (Lepus europaeus Pallas, 1778) from Turkey: Different gene pool architecture on either side of the Bosphorus? Mamm Biol 2019; 94:77-85. [DOI: 10.1016/j.mambio.2018.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Neumann K, Yiğit N, Fritzsche P, Çolak E, Feoktistova N, Surov A, Michaux J. Genetic structure of the Turkish hamster ( Mesocricetus brandti ). Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Koutsogiannouli EA, Moutou KA, Stamatis C, Walter L, Mamuris Z. Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas. Immunogenetics 2014; 66:379-92. [DOI: 10.1007/s00251-014-0772-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/31/2014] [Indexed: 10/25/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Mamuris Z, Moutou KA, Stamatis C, Sarafidou T, Suchentrunk F. Y DNA and mitochondrial lineages in European and Asian populations of the brown hare (Lepus europaeus). Mamm Biol 2010. [DOI: 10.1016/j.mambio.2009.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Koutsogiannouli EA, Moutou KA, Sarafidou T, Stamatis C, Spyrou V, Mamuris Z. Major histocompatibility complex variation at class II DQA locus in the brown hare (Lepus europaeus). Mol Ecol 2009; 18:4631-49. [PMID: 19845856 DOI: 10.1111/j.1365-294x.2009.04394.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The major histocompatability complex (MHC) is a multigene family of receptors that bind and present antigenic peptides to T-cells. Genes of the MHC are characterized by an outstanding genetic polymorphism, which is considered to be maintained by positive selection. Sites involved in peptide binding form binding pockets (P) that are collectively termed the peptide-binding region (PBR). In this study, we examined the level of MHC genetic diversity within and among natural populations of brown hare (Lepus europaeus) from Europe and Anatolia choosing for analysis of the second exon of the DQA locus, one of the most polymorphic class II loci. We aimed at an integrated population genetic analysis of L. europeaus by (i) correlating MHC polymorphism to genetic variability and phylogenetic status estimated previously from maternally (mtDNA) and biparentally (allozymes, microsatellites) inherited loci; and (ii) comparing full-length exon amino acid polymorphism with functional polymorphism in the PBR and the binding pockets P1, P6 and P9. A substantial level of DQA exon 2 polymorphism was detected with two completely different set of alleles between the Anatolian and European populations. However, the phylogeny of full-length exon 2 Leeu-DQA alleles did not show a strong phylogeographic signal. The presence of balancing selection was supported by a statistically significant excess of nonsynonymous substitutions over synonymous in the PBR and a trans-species pattern of evolution detected after phylogenetic reconstruction. The differentiating patterns detected between genetic and functional polymorphism, i.e. the number and the distribution of pocket variants within and among populations, indicated a hierarchical action of selection pressures.
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Affiliation(s)
- E A Koutsogiannouli
- Department of Biochemistry & Biotechnology, University of Thessaly, 26 Ploutonos St., 41221 Larissa, Greece
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Goüy de Bellocq J, Suchentrunk F, Baird SJE, Schaschl H. Evolutionary history of an MHC gene in two leporid species: characterisation of Mhc-DQA in the European brown hare and comparison with the European rabbit. Immunogenetics 2008; 61:131-44. [PMID: 19104797 DOI: 10.1007/s00251-008-0349-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 12/02/2008] [Indexed: 10/21/2022]
Abstract
We surveyed the genetic diversity of the expressed major histocompatibility complex class II DQA locus in natural populations of European brown hares, Lepus europaeus, from Austria and Belgium (267 individuals in total). Based on cDNA sequences, we designed hare-specific primers to amplify the highly variable second exon of the DQA gene. Using cloning-sequencing methodology and capillary electrophoresis single-strand conformation polymorphism, we found ten alleles of the DQA exon 2 locus across these two European regions, of which eight are described for the first time. To search for signals of selection and recombination in the evolution of the DQA gene within the leporids, we augmented our sample with orthologous DQA alleles from the European rabbit, Oryctolagus cuniculus, in order to carry out a species level, species pairwise comparison. We found evidence of recombination in the history of the DQA sequences in leporids with some recombinant alleles bridging the species divide. In both species, selection on peptide binding site codons can be detected, though stronger for the rabbit. This result suggests that there may be a differential selection pressure in the deeper evolutionary history of these two species due to differences in several demographic and ecological traits likely subjecting them to differential selection by parasites. Finally, evolutionary relationships show a widespread and statistically significant intermingling of alleles from the two species. The many macroparasites shared between hares and rabbits may explain this pattern of trans-species polymorphism.
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Affiliation(s)
- Joëlle Goüy de Bellocq
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Vienna, Austria.
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Ben Slimen H, Suchentrunk F, Stamatis C, Mamuris Z, Sert H, Alves PC, Kryger U, Shahin AB, Ben Ammar Elgaaied A. Population genetics of cape and brown hares (Lepus capensis and L. europaeus): A test of Petter's hypothesis of conspecificity. BIOCHEM SYST ECOL 2008. [DOI: 10.1016/j.bse.2007.06.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Stamatis C, Giannouli S, Suchentrunk F, Sert H, Stathopoulos C, Mamuris Z. Recruitment of mitochondrial tRNA genes as auxiliary variability markers for both intra- and inter-species analysis: The paradigm of brown hare (Lepus europaeus). Gene 2007; 410:154-64. [PMID: 18249075 DOI: 10.1016/j.gene.2007.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Revised: 11/27/2007] [Accepted: 12/06/2007] [Indexed: 10/22/2022]
Abstract
We sequenced and analyzed the mitochondrial tRNA(Thr) and tRNA(Pro) genes from brown hare (Lepus europaeus) individuals of different geographic distribution and we investigated the role of various nucleotide substitutions that were detected. We compared these tRNAs with the respective available mitochondrial tRNA genes sequences within Lepus species and among mammals. The mutations that were detected represent specific and conserved polymorphisms that do not seem to affect the structural and functional features that are required for participation of tRNA molecules in mitochondrial protein synthesis. These changes however, possibly reflect on the evolutionary background of the species, which is based on the high intra-genomic variability and the evolutionary dynamic of the mitochondrial DNA. In an attempt to compare the phylogeny that is based on these specific tRNA genes with the phylogeny that is produced from sequencing data of the mitochondrial variable loop, we came up with results that indicate similar phylogeographic clusters. This observation implies that the tRNA mutations that were used for the present study have been well tolerated during evolution and they define an additional genetic and biochemical tag that can be used for such studies. Based on this notion and according to our results, we propose that mitochondrial tRNA genes can be used as valuable auxiliary molecular markers for contemporaneous and linked biochemical and genetic analyses.
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Affiliation(s)
- Costas Stamatis
- Department of Biochemistry & Biotechnology, University of Thessaly, 26 Ploutonos st., 41 221 Larissa, Greece
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Suchentrunk F, Flux J, Flux MM, Ben Slimen H. Multivariate discrimination between East African cape hares (Lepus capensis) and savanna hares (L. victoriae) based on occipital bone shape. Mamm Biol 2007. [DOI: 10.1016/j.mambio.2006.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ben Slimen H, Suchentrunk F, Shahin A, Ben Ammar Elgaaied A. Phylogenetic analysis of mtCR-1 sequences of Tunisian and Egyptian hares (Lepus sp. or spp., Lagomorpha) with different coat colours. Mamm Biol 2007; 72:224-39. [DOI: 10.1016/j.mambio.2006.03.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Gündüz I, Jaarola M, Tez C, Yeniyurt C, Polly PD, Searle JB. Multigenic and morphometric differentiation of ground squirrels (Spermophilus, Scuiridae, Rodentia) in Turkey, with a description of a new species. Mol Phylogenet Evol 2007; 43:916-35. [PMID: 17500011 DOI: 10.1016/j.ympev.2007.02.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 01/09/2007] [Accepted: 02/01/2007] [Indexed: 10/23/2022]
Abstract
This study reports on the molecular phylogenetics of ground squirrels, genus Spermophilus, in Turkey using cytochrome b (1140bp), part of the D-loop and flanking tRNAs (572bp), X chromosome (867-1051bp) and Y chromosome (983-989bp) DNA sequences. Individuals also were characterized by karyotype and with geometric morphometric analyses of mandibles and skulls. Two hundred fourteen individuals from 91 localities were studied. All the data support the recognition of a new species in SW Anatolia: the Taurus ground squirrel Spermophilus taurensis sp. nov. The new species has a small distribution in the Taurus Mountains in an area that is a hotspot for biodiversity. Molecular clock analysis suggests that the new species diverged from the European ground squirrel, Spermophilus citellus, about 2.5 million years ago and that the ancestor of these two species diverged from the widespread Anatolian ground squirrel, Spermophilus xanthoprymnus, about 5 million years ago. Morphometric differentiation in skull and mandible shape among the three species is incomplete, but statistically significant. S. xanthoprymnus is subdivided into five cytochrome b phylogroups and we use these data to infer the location of glacial refugia where the species lived during the last glacial maximum. This study illustrates the potential of combined molecular and morphometric studies to uncover new Anatolian species and to reconstruct their phylogeographic history. The new species is important for squirrel taxonomy and for understanding Eurasian mammal evolution.
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Affiliation(s)
- Islam Gündüz
- Department of Biology, Faculty of Arts and Sciences, University of Ondokuz Mayis, Samsun, Turkey.
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Ben Slimen H, Suchentrunk F, Memmi A, Sert H, Kryger U, Alves P, Ben Ammar Elgaaied A. Evolutionary relationships among hares from North Africa (Lepus sp. or Lepus spp.), cape hares (L. capensis) from South Africa, and brown hares (L. europaeus), as inferred from mtDNA PCR-RFLP and allozyme data. J ZOOL SYST EVOL RES 2006. [DOI: 10.1111/j.1439-0469.2005.00345.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ben Slimen H, Suchentrunk F, Memmi A, Ben Ammar Elgaaied A. Biochemical Genetic Relationships Among Tunisian Hares (Lepus sp.), South African Cape Hares (L. capensis), and European Brown Hares (L. europaeus). Biochem Genet 2005; 43:577-96. [PMID: 16382363 DOI: 10.1007/s10528-005-9115-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Accepted: 02/14/2005] [Indexed: 11/25/2022]
Abstract
Tunisian hares (n = 45), currently assigned to Lepus capensis, were assayed for allelic variation at 40 allozyme loci, and allele frequencies at 32 loci were directly compared with earlier data of South African cape hares (L. capensis, n = 9) and European brown hares (L. europaeus, n = 244) to reveal genetic relationships among them. European mountain hares (L. timidus, n = 200) were used for outgroup comparison. In the Tunisian hares 27.5% of the loci were polymorphic with 2-4 alleles. Among all alleles at polymorphic loci, 15.1% occurred exclusively in Tunisian hares, 5.7% exclusively in cape hares, and 7.5% exclusively in brown hares at low frequencies. Not a single locus showed alternately fixed alleles between the samples of the L. capensis/L. europaeus complex. Levels of absolute and relative genetic differentiation among the samples of the L. capensis/L. europaeus complex were low, relative to pairwise comparisons involving mountain hares. Diverse cluster analyses and multidimensional scaling of various pairwise genetic distance matrices concordantly grouped Tunisian hares with brown hares, and South African cape hares clustered only slightly farther apart, whereas mountain hares were distinctly separate. These results suggest regionally distinct phylogenetic units within an overall cohesive gene pool in the L. capensis/L. europaeus complex, supporting Petter's view that all North African hares belong to L. capensis except for one local population of savanna hares, and that cape hares and brown hares are conspecific.
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Affiliation(s)
- Hichem Ben Slimen
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Campus Universitaire El Manar, 2029, Tunis, Tunisia.
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Sert H, Suchentrunk F, Ludescher B, Hackländer K. Developmental stability and canalization of limb bones of brown haresLepus europaeus with varying levels of heterozygosity. ACTA ACUST UNITED AC 2005; 50:213-26. [DOI: 10.1007/bf03194485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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