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Sharko F, Slobodova N, Boulygina E, Cheprasov M, Gladysheva-Azgari M, Tsygankova S, Rastorguev S, Novgorodov G, Boeskorov G, Grigorieva L, Hwang WS, Tikhonov A, Nedoluzhko A. Ancient DNA of the Don-Hares Assumes the Existence of Two Distinct Mitochondrial Clades in Northeast Asia. Genes (Basel) 2023; 14:genes14030700. [PMID: 36980972 PMCID: PMC10047931 DOI: 10.3390/genes14030700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/14/2023] Open
Abstract
Paleoclimatic changes during the Pleistocene–Holocene transition is suggested as a main factor that led to species extinction, including the woolly mammoth (Mammuthus primigenius), Steller’s sea cow (Hydrodamalis gigas) and the Don-hare (Lepus tanaiticus). These species inhabited the territory of Eurasia during the Holocene, but eventually went extinct. The Don-hare is an extinct species of the genus Lepus (Leporidae, Lagomorpha), which lived in the Late Pleistocene–Early Holocene in Eastern Europe and Northern Asia. For a long time, the Don-hare was considered a separate species, but at the same time, its species status was disputed, taking into account both morphological data and mitochondrial DNA. In this study, mitochondrial genomes of five Don-hares, whose remains were found on the territory of Northeastern Eurasia were reconstructed. Firstly, we confirm the phylogenetic proximity of the “young” specimens of Don-hare and mountain or white hare, and secondly, that samples older than 39 Kya form a completely distinct mitochondrial clade.
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Affiliation(s)
- Fedor Sharko
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Natalia Slobodova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Faculty of Biology and Biotechnology, HSE University, 101000 Moscow, Russia
| | - Eugenia Boulygina
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Maksim Cheprasov
- Lazarev Mammoth Museum, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
- Federal Research Centre “The Yakut Scientific Centre of the Siberian Branch of the Russian Academy of Sciences”, 677980 Yakutsk, Russia
| | - Maria Gladysheva-Azgari
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Svetlana Tsygankova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Sergey Rastorguev
- Laboratory of Experimental Embryology, Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Gavril Novgorodov
- Lazarev Mammoth Museum, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of the Russian Academy of Sciences, 677007 Yakutsk, Russia
| | - Lena Grigorieva
- Center of Molecular Paleontology, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Woo Suk Hwang
- UAE Biotech Research Center, Abu Dhabi 30310, United Arab Emirates
- Department of Biology, North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Alexei Tikhonov
- Lazarev Mammoth Museum, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
- Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | - Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint Petersburg, Russia
- Correspondence:
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Cano-Sánchez E, Rodríguez-Gómez F, Ruedas LA, Oyama K, León-Paniagua L, Mastretta-Yanes A, Velazquez A. Using Ultraconserved Elements to Unravel Lagomorph Phylogenetic Relationships. J MAMM EVOL 2022. [DOI: 10.1007/s10914-021-09595-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Ferreira MS, Jones MR, Callahan CM, Farelo L, Tolesa Z, Suchentrunk F, Boursot P, Mills LS, Alves PC, Good JM, Melo-Ferreira J. The Legacy of Recurrent Introgression during the Radiation of Hares. Syst Biol 2021; 70:593-607. [PMID: 33263746 PMCID: PMC8048390 DOI: 10.1093/sysbio/syaa088] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 12/30/2022] Open
Abstract
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1-4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation. [Adaptation; ancient introgression; hybridization; Lepus; phylogenomics.].
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Affiliation(s)
- Mafalda S Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Zelalem Tolesa
- Department of Biology, Hawassa University, Hawassa, Ethiopia
| | - Franz Suchentrunk
- Department for Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Pierre Boursot
- Institut des Sciences de l’Évolution Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, France
| | - L Scott Mills
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
- Office of Research and Creative Scholarship, University of Montana, Missoula, Montana, United States of America; Jeffrey M. Good and José Melo-Ferreira shared the senior authorship
| | - 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 da Universidade do Porto, Porto, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - 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 da Universidade do Porto, Porto, Portugal
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4
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Analysis of fecal samples from Amami rabbits (Pentalagus furnessi) indicates low levels of antimicrobial resistance in Escherichia coli. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-01424-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Hamada F, Mizuta T. Unique reproductive traits of the Amami rabbit Pentalagus furnessi: an endangered endemic species from southwestern Japan. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00497-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Orimoto A, Katayama M, Tani T, Ito K, Eitsuka T, Nakagawa K, Inoue-Murayama M, Onuma M, Kiyono T, Fukuda T. Primary and immortalized cell lines derived from the Amami rabbit (Pentalagus furnessi) and evolutionally conserved cell cycle control with CDK4 and Cyclin D1. Biochem Biophys Res Commun 2020; 525:1046-1053. [PMID: 32178875 DOI: 10.1016/j.bbrc.2020.03.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/06/2020] [Indexed: 10/24/2022]
Abstract
The Amami rabbit (Pentagulus furnessi) is a dark brown-furred rabbit classified as an endangered species and only found in the Amami Islands of Japan. They are often called living fossils because they retain primitive characteristics of ancient rabbits that lived approximately 1 million years ago, such as short feet and hind legs and small ears. Although the ancient rabbit has disappeared due to the competition with European rabbit (Oryctolagus cuniculus) in the most of the Asian area, Amami rabbit survived since Amami Islands has isolated from Japan and Taiwan. Although Amari rabbit is one of the protected animals, their population decreases each year due to human activities, such as deforestation and roadkill. In this study, we collected roadkill samples of Amami rabbits and established primary and immortalized fibroblast cell lines. Combined expression of human-derived mutant Cyclin-dependent kinase 4, Cyclin D1, and hTERT allowed us to immortalize fibroblasts successfully in three individuals of Amami rabbits. The immortalized fibroblasts dramatically extended the cell culture period, when it was compared with the cell culture period of wild type cells. Furthermore, the immortalized cells maintained their normal chromosomal pattern (2n = 46). Our results suggest that cellular senescence which mainly regulated by p16-RB signaling pathway is conserved in animal evolution at least from 1 million years ago.
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Affiliation(s)
- Ai Orimoto
- Graduate School of Science and Engineering, Iwate University, Morioka, Japan
| | - Masafumi Katayama
- Ecological Risk Assessment and Control Section, Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan; Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Japan
| | - Tetsuya Tani
- Laboratory of Animal Reproduction, Department of Agriculture, Kindai University, Nara, Japan
| | - Keiko Ito
- Amami Dog and Cat Animal Hospital, Amami Island, Japan
| | - Takahiro Eitsuka
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Kiyotaka Nakagawa
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan; Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Japan
| | - Manabu Onuma
- Ecological Risk Assessment and Control Section, Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan; Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Japan
| | - Tohru Kiyono
- Division of Carcinogenesis and Prevention, National Cancer Center Research Institute, Tokyo, Japan.
| | - Tomokazu Fukuda
- Graduate School of Science and Engineering, Iwate University, Morioka, Japan; Soft-Path Engineering Research Center (SPERC), Iwate University, Morioka, Japan; Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Japan.
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7
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Kinoshita G, Nunome M, Kryukov AP, Kartavtseva IV, Han SH, Yamada F, Suzuki H. Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus). Mol Phylogenet Evol 2019; 136:65-75. [PMID: 30951923 DOI: 10.1016/j.ympev.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 01/16/2023]
Abstract
Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleotide sequences of one mitochondrial DNA and eight nuclear gene loci were examined, adding sequences of hares in China from databases. All nuclear DNA analyses supported the clear separation of three phylogroups: L. timidus, L. brachyurus, and the L. mandshuricus complex containing L. coreanus. On the other hand, massive mitochondrial introgression from two L. timidus lineages to the L. mandshuricus complex was suggested in continental East Asia. The northern population of the L. mandshuricus complex was mainly associated with introgression from the continental lineage of L. timidus, possibly since the last glacial period, whereas the southern population of the L. mandshuricus complex experienced introgression from another L. timidus lineage related to the Hokkaido population, possibly before the last glacial period. In contrast to continental hares, no evidence of introgression was found in L. brachyurus in the Japanese Archipelago, which showed the oldest divergence amongst East Asian hare lineages. Our findings suggest that glacial-interglacial climate changes in the circum-Japan Sea region promoted distribution shifts and introgressive hybridization among continental hare species, while the geographic structure of the region contributed to long-term isolation of hares on the islands, preventing inter-species gene flow.
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Affiliation(s)
- Gohta Kinoshita
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan; Laboratory of Forest Biology Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyoku, Kyoto 606-8502, Japan.
| | - Mitsuo Nunome
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Alexey P Kryukov
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Irina V Kartavtseva
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - San-Hoon Han
- Inter-Korea Wildlife Institute, Namtong-dong, Gumi-si, Kyeongsang-Bukdo 39301, Republic of Korea
| | - Fumio Yamada
- Laboratory of Wildlife Ecology, Forestry and Forest Products Research Institute (FFPRI), Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Hitoshi Suzuki
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan
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Silva SM, Ruedas LA, Santos LH, e Silva JDS, Aleixo A. Illuminating the obscured phylogenetic radiation of South American SylvilagusGray, 1867 (Lagomorpha: Leporidae). J Mammal 2019. [DOI: 10.1093/jmammal/gyy186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Sofia Marques Silva
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
| | - Luis A Ruedas
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
| | - Larissa Hasnah Santos
- Portland State University, Department of Biology and Museum of Natural History, SRTC-246, Portland, OR, USA
| | - José de Sousa e Silva
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
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9
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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.
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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
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10
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Adaptive Gene Loss? Tracing Back the Pseudogenization of the Rabbit CCL8 Chemokine. J Mol Evol 2016; 83:12-25. [PMID: 27306379 DOI: 10.1007/s00239-016-9747-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
Abstract
Studies of the process of pseudogenization have widened our understanding of adaptive evolutionary change. In Rabbit, an alteration at the second extra-cellular loop of the CCR5 chemokine receptor was found to be associated with the pseudogenization of one of its prime ligands, the chemokine CCL8. This relationship has raised questions about the existence of a causal link between both events, which would imply adaptive gene loss. This hypothesis is evaluated here by tracing back the history of the genetic modifications underlying the chemokine pseudogenization. The obtained data indicate that mutations at receptor and ligand genes occurred after the lineage split of New World Leporids versus Old World Leporids and prior to the generic split of the of Old World species studied, which occurred an estimated 8-9 million years ago. More important, they revealed the emergence, before this zoographical split, of a "slippery" nucleotide motif (CCCCGGG) at the 3' region of CCL8-exon2. Such motives are liable of generating +1G or -1G frameshifts, which could, however, be overcome by "translesion" synthesis or somatic reversion. The CCL8 pseudogenization in the Old World lineage was apparently initiated by three synapomorphic point mutations at the exon2-intron2 boundary which provide at short range premature terminating codons, independently of the reading frame imposed by the slippery motif. The presence of this motif in New World Leporids might allow verifying this scenario. The importance of CCL8-CCR5 signaling in parasite-host interaction would suggest that the CCL8 knock-out in Old World populations might be related to changes in pathogenic environment.
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Tsuji K, Hori M, Phyu MH, Liang H, Sota T. Colorful patterns indicate common ancestry in diverged tiger beetle taxa: Molecular phylogeny, biogeography, and evolution of elytral coloration of the genus Cicindela subgenus Sophiodela and its allies. Mol Phylogenet Evol 2015; 95:1-10. [PMID: 26578441 DOI: 10.1016/j.ympev.2015.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 11/26/2022]
Abstract
We investigated the phylogenetic relationships among tiger beetles of the subtribe Cicindelina (=Cicindela s. lat.; Coleoptera: Cicindelidae) mainly from the Oriental and Sino-Japanese zoogeographic regions using one mitochondrial and three nuclear gene sequences to examine the position of the subgenus Sophiodela, currently classified in the genus Cicindela s. str., their biogeography, and the evolution of their brilliant coloration. The subgenus Sophiodela was not related to the other subgenera of Cicindela s. str. but was closely related to the genus Cosmodela. In addition, the Oriental genus Calochroa was polyphyletic with three lineages, one of which was closely related to Sophiodela and Cosmodela. The clade comprising Sophiodela, Cosmodela and two Calochroa species, referred to here as the Sophiodela group, was strongly supported, and most species in this clade had similar brilliant coloration. The Sophiodela group was related to the genera Calomera, Cicindela (excluding Sophiodela) and Cicindelidia, and these were related to Lophyra, Hipparidium and Calochroa, except species in the Sophiodela group. Divergence time estimation suggested that these worldwide Cicindelina groups diverged in the early Oligocene, and the Sophiodela group, which is found in the Oriental and Sino-Japanese zoogeographic regions, in the mid Miocene. Some components of the elytral pattern related to maculation and coloration in the Cicindelina taxa studied contained weak, but significant, phylogenetic signals and were partly associated with habitat types. Therefore, the brilliant coloration of the Sophiodela was related to both phylogeny and habitat adaptation, although the function of coloration needs to be studied.
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Affiliation(s)
- Kaoru Tsuji
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Michio Hori
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Moe Hnin Phyu
- Department of Entomology and Zoology, Yezin Agricultural University, Yezin, Myanmar
| | - Hongbin Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Science, Beijing 100101, China
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
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12
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Kinoshita G, Sato JJ, Meschersky IG, Pishchulina SL, Simakin LV, Rozhnov VV, Malyarchuk BA, Derenko MV, Denisova GA, Frisman LV, Kryukov AP, Hosoda T, Suzuki H. Colonization history of the sableMartes zibellina(Mammalia, Carnivora) on the marginal peninsula and islands of northeastern Eurasia. J Mammal 2015. [DOI: 10.1093/jmammal/gyu021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Ishikawa N, Ikeda H, Yi TS, Takabe-Ito E, Okada H, Tsukaya H. Lineage diversification and hybridization in the Cayratia japonica–Cayratia tenuifolia species complex. Mol Phylogenet Evol 2014; 75:227-38. [DOI: 10.1016/j.ympev.2014.01.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/15/2014] [Accepted: 01/28/2014] [Indexed: 11/27/2022]
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14
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Nunome M, Kinoshita G, Tomozawa M, Torii H, Matsuki R, Yamada F, Matsuda Y, Suzuki H. Lack of association between winter coat colour and genetic population structure in the Japanese hare,Lepus brachyurus(Lagomorpha: Leporidae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mitsuo Nunome
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Gohta Kinoshita
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
| | | | - Harumi Torii
- Center for Natural Environment Education; Nara University of Education; Takabatake-cho Nara 630-8528 Japan
| | - Rikyu Matsuki
- Environmental Science Research Laboratory; Central Research Institute of Electric Power Industry; 1646 Abiko Chiba 270-1194 Japan
| | - Fumio Yamada
- Forestry and Forest Products Research Institute; PO Box 16 Tsukuba Norin Ibaraki 305-8687 Japan
| | - Yoichi Matsuda
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
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Watari Y, Nishijima S, Fukasawa M, Yamada F, Abe S, Miyashita T. Evaluating the "recovery level" of endangered species without prior information before alien invasion. Ecol Evol 2013; 3:4711-21. [PMID: 24363899 PMCID: PMC3867906 DOI: 10.1002/ece3.863] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/17/2013] [Accepted: 10/01/2013] [Indexed: 12/02/2022] Open
Abstract
For maintaining social and financial support for eradication programs of invasive species, quantitative assessment of recovery of native species or ecosystems is important because it provides a measurable parameter of success. However, setting a concrete goal for recovery is often difficult owing to lack of information prior to the introduction of invaders. Here, we present a novel approach to evaluate the achievement level of invasive predator management based on the carrying capacity of endangered species estimated using long-term monitoring data. In Amami-Oshima Island, Japan, where the eradication project of introduced small Indian mongoose is ongoing since 2000, we surveyed the population densities of four endangered species threatened by the mongoose (Amami rabbit, the Otton frog, Amami tip-nosed frog, and Amami Ishikawa's frog) at four time points ranging from 2003 to 2011. We estimated the carrying capacities of these species using the logistic growth model combined with the effects of mongoose predation and environmental heterogeneity. All species showed clear tendencies toward increasing their density in line with decreased mongoose density, and they exhibited density-dependent population growth. The estimated carrying capacities of three endangered species had small confidence intervals enough to measure recovery levels by the mongoose management. The population density of each endangered species has recovered to the level of the carrying capacity at about 20–40% of all sites, whereas no individuals were observed at more than 25% of all sites. We propose that the present approach involving appropriate monitoring data of native organism populations will be widely applicable to various eradication projects and provide unambiguous goals for management of invasive species.
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Affiliation(s)
- Yuya Watari
- Japan Forest Technology Association Rokuban-cho 7, Chiyoda, Tokyo, 102-0085, Japan
| | - Shota Nishijima
- Laboratory of Biodiversity Science, School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo, Tokyo, 113-0032, Japan
| | - Marina Fukasawa
- Laboratory of Biodiversity Science, School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo, Tokyo, 113-0032, Japan
| | - Fumio Yamada
- Department of Wildlife Biology, Forestry and Forest Products Research Institute Matsunosato 1, Tsukuba, Ibaraki, 305-8687, Japan
| | - Shintaro Abe
- Naha Nature Conservation Office, Ministry of the Environment Okinawa Tsukansha Building 4F, 5-21 Yamashita-cho, Naha, Okinawa, 900-0027, Japan
| | - Tadashi Miyashita
- Laboratory of Biodiversity Science, School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo, Tokyo, 113-0032, Japan
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Kinoshita G, Nunome M, Han SH, Hirakawa H, Suzuki H. Ancient colonization and within-island vicariance revealed by mitochondrial DNA phylogeography of the mountain hare (Lepus timidus) in Hokkaido, Japan. Zoolog Sci 2013; 29:776-85. [PMID: 23106564 DOI: 10.2108/zsj.29.776] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We examined the phylogenetic status and history of the mountain hare Lepus timidus in and around Hokkaido using mitochondrial cytochrome b (cyt b) sequences from 158 samples from Hokkaido and 14 from Sakhalin, as well as four samples from the Korean hare, L. coreanus. The phylogenetic analysis of the cyt b sequences generated in this study and obtained from DNA databases showed the clear genetic specificity of the Hokkaido lineage as a clade. The Hokkaido lineage was estimated to have diverged from the other conspecific and L. coreanus lineages 0.46 and 0.30 million years ago (Mya), respectively. These results suggest that the common ancestor of the mitochondrial lineage in Hokkaido and Korea inhabited Far East Asia before colonization by the present continental lineages of L. timidus, including the Sakhalin population. We estimated the time of the most recent common ancestor of the Hokkaido population to be 0.17 Mya, and found two distinct haplogroups within the island. One group had greater genetic diversity (mean number of pairwise differences: π = 0.0188 ± 0.0108) and appears to have expanded from the west to the entire island of Hokkaido. The other had lower genetic diversity (π = 0.0038 ± 0.0037) and its distribution was concentrated in the east. These contrasting west/east trends indicate that the Hokkaido population was fragmented in the past, and then subsequently expanded. Our study suggests that Hokkaido was an important refugium for boreal species in the far eastern region, and allowed the formation of various population genetic structures within the island.
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Affiliation(s)
- Gohta Kinoshita
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo, Japan.
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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
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18
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Sato JJ, Hosoda T, Kryukov AP, Kartavtseva IV, Suzuki H. Genetic Diversity of the Sable (Martes zibellina, Mustelidae) in Russian Far East and Hokkaido Inferred from Mitochondrial NADH Dehydrogenase Subunit 2 Gene Sequences. MAMMAL STUDY 2011. [DOI: 10.3106/041.036.0404] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Nunome M, Torii H, Matsuki R, Kinoshita G, Suzuki H. The Influence of Pleistocene Refugia on the Evolutionary History of the Japanese Hare, Lepus brachyurus. Zoolog Sci 2010; 27:746-54. [DOI: 10.2108/zsj.27.746] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Mitsuo Nunome
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Harumi Torii
- Center for Natural Environment Education, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan
| | - Rikyu Matsuki
- Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, 1646 Abiko, Chiba 270-1194, JAPAN
| | - Gohta Kinoshita
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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20
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Abrantes J, Carmo CR, Matthee CA, Yamada F, van der Loo W, Esteves PJ. A shared unusual genetic change at the chemokine receptor type 5 between Oryctolagus, Bunolagus and Pentalagus. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9990-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Shinohara A, Kawada SI, Harada M, Koyasu K, Oda SI, Suzuki H. Phylogenetic relationships of the short-faced mole, Scaptochirus moschatus (Mammalia: Eulipotyphla), among Eurasian fossorial moles, as inferred from mitochondrial and nuclear gene sequences. MAMMAL STUDY 2008. [DOI: 10.3106/1348-6160(2008)33[77:protsm]2.0.co;2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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22
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Phylogenetic analysis of mtCR-1 sequences of Tunisian and Egyptian hares (Lepus sp. or spp., Lagomorpha) with different coat colours. Mamm Biol 2007. [DOI: 10.1016/j.mambio.2006.03.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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25
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Esteves PJ, Carmo C, Godinho R, van der Loo W. Genetic diversity at the hinge region of the unique immunoglobulin heavy gamma (IGHG) gene in leporids (Oryctolagus, Sylvilagus and Lepus). Int J Immunogenet 2006; 33:171-7. [PMID: 16712647 DOI: 10.1111/j.1744-313x.2006.00588.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unlike other species, European rabbit (Oryctolagus cuniculus) possesses only one immunoglobulin gamma class. Allelic diversity at the Ig (immunoglobulin) gamma constant region encoded by the unique IGHG (immunoglobulin heavy gamma) gene is moreover much reduced. In the European rabbit, the genetic variation at IGGH hinge region is limited to a single nucleotide substitution, which causes a Met-Thr interchange at amino acid position 9 (IMGT hinge numbering). We have analysed the diversity at this region more in-depth by, (1) analysing the allelic variation in 11 breeds of domestic European rabbit (Oryctolagus cuniculus cuniculus), and (2) sequencing the gamma hinge exon in wild specimens of six species of rabbit (Oryctolagus and Sylvilagus) and hares (Lepus), including the two Oryctolagus subspecies (O. cuniculus cuniculus and O. cuniculus algirus). It appeared that among leporid species, amino acid changes occur exclusively at positions 8 and 9. However, while position 8 is occupied by either Pro or Ser residues, four different residues can occur at position 9 (Met, Thr, Pro and Leu). This variation concerns sites of potential O-glycosylation and/or proteolytic cleavage, suggesting that the underlying genetic diversity could be the outcome of selection. Preservation of the gamma hinge polymorphism in domestic stocks could therefore be important. We report here a polymerase chain reaction/restriction fragment length polymorphism protocol that has allowed the monitoring of the heterozygosity levels at the gamma hinge in 11 breeds of domestic European rabbit.
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Affiliation(s)
- P J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Portugal
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26
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Carmo CR, Esteves PJ, Ferrand N, van der Loo W. Genetic variation at chemokine receptor CCR5 in leporids: alteration at the 2nd extracellular domain by gene conversion with CCR2 in Oryctolagus, but not in Sylvilagus and Lepus species. Immunogenetics 2006; 58:494-501. [PMID: 16596402 DOI: 10.1007/s00251-006-0095-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Accepted: 01/24/2006] [Indexed: 10/24/2022]
Abstract
Whereas in its natural host (Sylvilagus sps.) the effects of myxoma virus infections are benign, in European rabbit (Oryctolagus cuniculus), it causes a highly infectious disease with very high mortality rate, known as myxomatosis. There is evidence that, as with HIV-1 virus in human, myxoma virus may use chemokine receptors such as CCR5 of the host target cell for entry and activation of pathways of immune avoidance. We have characterized and compared CCR5 genes of leporid species with different susceptibility levels to myxomatosis. The CCR5 protein of O. cuniculus differs markedly from all those known from other species. The most striking was the replacement of a specific peptide motif of the second extracellular loop (ECL2) by a motif, which in other species characterizes the CCR2 molecules. While absent in Sylvilagus and Lepus species, this CCR2 imposed CCR5-ECL2 alteration was observed in all genomes of 25 European rabbits, representing the subspecies O. cuniculus algirus and O. cuniculus cuniculus. Allelic variation at the rabbit CCR5 locus confirmed that the gene conversion predates the subspecies split (1-2 Ma).
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Affiliation(s)
- C R Carmo
- Departamento de Zoologia e Antropologia-, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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27
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Seki SI. The origin of the East Asian Erithacus robin, Erithacus komadori, inferred from cytochrome b sequence data. Mol Phylogenet Evol 2006; 39:899-905. [PMID: 16529957 DOI: 10.1016/j.ympev.2006.01.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Revised: 01/27/2006] [Accepted: 01/27/2006] [Indexed: 11/27/2022]
Affiliation(s)
- Shin-Ichi Seki
- Kyushu Research Center, Forestry and Forest Products Research Institute, 4-11-16 Kurokami, Kumamoto 860-0862, Japan.
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28
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Esteves PJ, Lanning D, Ferrand N, Knight KL, Zhai SK, van der Loo W. The evolution of the immunoglobulin heavy chain variable region (IgV H ) in Leporids: an unusual case of transspecies polymorphism. Immunogenetics 2005; 57:874-82. [PMID: 16247606 DOI: 10.1007/s00251-005-0022-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Accepted: 07/06/2005] [Indexed: 10/25/2022]
Abstract
In domestic rabbit (Oryctolagus cuniculus), three serological types have been distinguished at the variable domain of the antibody H chain, the so-called V(H) a allotypes a1, a2, and a3. They correspond to highly divergent allelic lineages of the V(H) 1 gene, which is the gene rabbit utilizes in more than 80% of VDJ rearrangements. The sharing of serological V(H) a markers between rabbit and snowshoe hare (Lepus americanus) has suggested that the large genetic distances between rabbit V(H) 1 alleles (9-14% nucleotide differences) can be explained by unusually long lineage persistence times (transspecies polymorphism). Because this interpretation of the serological data is uncertain, we have determined the nucleotide sequences of V(H) genes expressed in specimens of Lepus species. Two sequence groups were distinguished, one of which occurred only in hare specimen displaying serological motifs of the rabbit V(H) a-a2 allotype. Sequences of this group are part of a monophyletic cluster containing the V(H) 1 sequences of the rabbit a2 allotype. The fact that this "transspecies a2 cluster" did not include genes of other rabbit V(H) a allotypes (a1, a3, and a4) is incompatible with the existence of a common V(H) a ancestor gene within the species, and suggests that the divergence of the V(H) a lineages preceded the Lepus vs Oryctolagus split. The sequence data are furthermore compatible with the hypothesis that the V(H)a polymorphism can be two times older than the divergence time between the Lepus and Oryctolagus lineages, which was estimated at 16-24 million years.
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Affiliation(s)
- P J Esteves
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), ICETA-UP, Campus Agrário de Vairão Rua Padre Armando Quintas, Portugal
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30
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Wu C, Wu J, Bunch TD, Li Q, Wang Y, Zhang YP. Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences. Mol Phylogenet Evol 2005; 37:45-61. [PMID: 15990340 DOI: 10.1016/j.ympev.2005.05.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Revised: 04/29/2005] [Accepted: 05/12/2005] [Indexed: 11/18/2022]
Abstract
In spite of several classification attempts among taxa of the genus Lepus, phylogenetic relationships still remain poorly understood. Here, we present molecular genetic evidence that may resolve some of the current incongruities in the phylogeny of the leporids. The complete mitochondrial cytb, 12S genes, and parts of ND4 and control region fragments were sequenced to examine phylogenetic relationships among Chinese hare taxa and other leporids throughout the World using maximum parsimony, maximum likelihood, and Bayesian phylogenetic reconstruction approaches. Using reconstructed phylogenies, we observed that the Chinese hare is not a single monophyletic group as originally thought. Instead, the data infers that the genus Lepus is monophyletic with three unique species groups: North American, Eurasian, and African. Ancestral area analysis indicated that ancestral Lepus arose in North America and then dispersed into Eurasia via the Bering Land Bridge eventually extending to Africa. Brooks Parsimony analysis showed that dispersal events followed by subsequent speciation have occurred in other geographic areas as well and resulted in the rapid radiation and speciation of Lepus. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches estimated the divergence time between the three major groups within Lepus. The genus appears to have arisen approximately 10.76 MYA (+/-0.86 MYA), with most speciation events occurring during the Pliocene epoch (5.65+/-1.15 MYA approximately 1.12 +/- 0.47 MYA).
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Affiliation(s)
- Chunhua Wu
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
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31
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ROBINSON TJ, MATTHEE CA. Phylogeny and evolutionary origins of the Leporidae: a review of cytogenetics, molecular analyses and a supermatrix analysis. Mamm Rev 2005. [DOI: 10.1111/j.1365-2907.2005.00073.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Shinohara A, Suzuki H, Tsuchiya K, Zhang YP, Luo J, Jiang XL, Wang YX, Campbell KL. Evolution and biogeography of talpid moles from continental East Asia and the Japanese islands inferred from mitochondrial and nuclear gene sequences. Zoolog Sci 2005; 21:1177-85. [PMID: 15613798 DOI: 10.2108/zsj.21.1177] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We sequenced the cytochrome b gene from two little-studied mammal species from the highlands of Southwest China, the long-tailed mole Scaptonyx fusicaudus and the gracile shrew-like mole Uropsilus gracilis. This data was used to examine the phylogenetic relationships among 19 talpid species within the family Talpidae (Mammalia: Eulipotyphla). Cytochrome b gene trees supported a basal placement of shrew-like moles (Uropsilus) within the Talpidae, and suggested that fossorial specializations arose twice during talpid evolution. To assess the evolutionary relationships of moles endemic to this region, we additionally sequenced the 12S rRNA gene and the nuclear recombination-activating gene-1 from eight and ten East Asian taxa, respectively. Analyses of these single and concatenated data sets suggested that East Asian shrew moles diverged prior to the evolution of fossorial Eurasian moles. However, we were unable to determine whether semi-fossorial shrew moles are monophyletic. In contrast, fossorial Eurasian genera (Talpa, Mogera and Euroscaptor) were consistently found to form a monophyletic clade, with Mogera and Euroscaptor representing sister taxa. Furthermore, this fossorial clade grouped with the semi-aquatic Desmana, although with fairly low (35-62%) bootstrap support. Mogera imaizumii was found to be more closely related to M. wogura than to M. tokudae. This implies that the ancestors of these three species entered Japan from the Asian continent in this order via a series of migration events, suggesting that the Japanese Islands have played an important role in preserving mole lineages from ancient to recent times.
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Affiliation(s)
- Akio Shinohara
- Department of Bio-resources, Division of Biotechnology, Frontier Science Research Center, University of Miyazaki, Kiyotake, Japan
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33
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Matthee CA, van Vuuren BJ, Bell D, Robinson TJ. A molecular supermatrix of the rabbits and hares (Leporidae) allows for the identification of five intercontinental exchanges during the Miocene. Syst Biol 2004; 53:433-47. [PMID: 15503672 DOI: 10.1080/10635150490445715] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The hares and rabbits belonging to the family Leporidae have a nearly worldwide distribution and approximately 72% of the genera have geographically restricted distributions. Despite several attempts using morphological, cytogenetic, and mitochondrial DNA evidence, a robust phylogeny for the Leporidae remains elusive. To provide phylogenetic resolution within this group, a molecular supermatrix was constructed for 27 taxa representing all 11 leporid genera. Five nuclear (SPTBN1, PRKCI, THY, TG, and MGF) and two mitochondrial (cytochrome b and 12S rRNA) gene fragments were analyzed singly and in combination using parsimony, maximum likelihood, and Bayesian inference. The analysis of each gene fragment separately as well as the combined mtDNA data almost invariably failed to provide strong statistical support for intergeneric relationships. In contrast, the combined nuclear DNA topology based on 3601 characters greatly increased phylogenetic resolution among leporid genera, as was evidenced by the number of topologies in the 95% confidence interval and the number of significantly supported nodes. The final molecular supermatrix contained 5483 genetic characters and analysis thereof consistently recovered the same topology across a range of six arbitrarily chosen model specifications. Twelve unique insertion-deletions were scored and all could be mapped to the tree to provide additional support without introducing any homoplasy. Dispersal-vicariance analyses suggest that the most parsimonious solution explaining the current geographic distribution of the group involves an Asian or North American origin for the Leporids followed by at least nine dispersals and five vicariance events. Of these dispersals, at least three intercontinental exchanges occurred between North America and Asia via the Bering Strait and an additional three independent dispersals into Africa could be identified. A relaxed Bayesian molecular clock applied to the seven loci used in this study indicated that most of the intercontinental exchanges occurred between 14 and 9 million years ago and this period is broadly coincidental with the onset of major Antarctic expansions causing land bridges to be exposed.
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Affiliation(s)
- Conrad A Matthee
- Evolutionary Genomics Group, Department of Zoology, University of Stellenbosch, Stellenbosch, 7602, South Africa.
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Suzuki H, Shimada T, Terashima M, Tsuchiya K, Aplin K. Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences. Mol Phylogenet Evol 2004; 33:626-46. [PMID: 15522792 DOI: 10.1016/j.ympev.2004.08.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2004] [Revised: 07/09/2004] [Indexed: 11/17/2022]
Abstract
We sequenced mitochondrial (cytochrome b, 12S rRNA) and nuclear (IRBP, RAG1) genes for 17 species of the Old World murine genus Mus, drawn primarily from the Eurasian subgenus Mus. Phylogenetic analysis of the newly and previously available sequences support recognition of four subgenera within Mus (Mus, Coelomys, Nannomys, and Pyromys), with an unresolved basal polytomy. Our data further indicate that the subgenus Mus contains three distinct 'species groups': (1) a Mus booduga Species Group, also including Mus terricolor and Mus fragilicauda (probably also Mus famulus); (2) a Mus cervicolor Species Group, also including Mus caroli and Mus cookii; and (3) a Mus musculus Species Group, also including Mus macedonicus, Mus spicilegus, and Mus spretus. Species diversity in Eurasian Mus is probably explicable in terms of several phases of range expansion and vicariance, and by a propensity within the group to undergo biotope transitions. IRBP and RAG1 molecular clocks for Mus date the origin of subgenera to around 5-6 mya and the origin of Species Groups within subgenus Mus to around 2-3 mya. The temporal pattern of evolution among Eurasian Mus is more complex than that within the Eurasian temperate genus Apodemus.
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Affiliation(s)
- Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan.
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35
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Lovegrove BG. Locomotor Mode, Maximum Running Speed, and Basal Metabolic Rate in Placental Mammals. Physiol Biochem Zool 2004; 77:916-28. [PMID: 15674766 DOI: 10.1086/425189] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2004] [Indexed: 11/03/2022]
Abstract
The locomotor performance (absolute maximum running speed [MRS]) of 120 mammals was analyzed for four different locomotor modes (plantigrade, digitigrade, unguligrade, and lagomorph-like) in terms of body size and basal metabolic rate (BMR). Analyses of conventional species data showed that the MRS of plantigrade and digitigrade mammals and lagomorphs increases with body mass, whereas that of unguligrade mammals decreases with body mass. These trends were confirmed in plantigrade mammals and lagomorphs using phylogenetically independent contrasts. Multiple regression analyses of MRS contrasts (dependent variable) as a function of body mass and BMR contrasts (predictor variables) revealed that BMR was a significant predictor of MRS in the complete data set, as well as in plantigrade and nonplantigrade mammals. However, there was severe multicollinearity in the nonplantigrade model that may influence the interpretation of these models. Although these data show mass-independent correlation between BMR and MRS, they are not necessarily indicative of a cause-effect relationship. However, the analyses do identify a negligible role of body size associated with MRS once phylogenetic and BMR effects are controlled, suggesting that the body size increase in large mammals over time (i.e., Cope's rule) can probably rule out MRS as a driving variable.
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Affiliation(s)
- Barry G Lovegrove
- School of Biological and Conservation Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, South Africa.
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Shinohara A, Kawada SI, Yasuda M, Liat LB. Phylogenetic position of the Malaysian mole, Euroscaptor micrura (Mammalia: Eulipotyphla), inferred from three gene sequences. MAMMAL STUDY 2004. [DOI: 10.3106/mammalstudy.29.185] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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SUZUKI HITOSHI, SATO JUNJ, TSUCHIYA KIMIYUKI, LUO JING, ZHANG YAPING, WANG YINGXIANG, Jiang XL. Molecular phylogeny of wood mice (Apodemus, Muridae) in East Asia. Biol J Linn Soc Lond 2003. [DOI: 10.1046/j.1095-8312.2003.00253.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Terashima M, Suyanto A, Tsuchiya K, Moriwaki K, Jin ML, Suzuki H. Geographic variation of Mus caroli from East and Southeast Asia based on mitochondrial cytochrome b gene sequences. MAMMAL STUDY 2003. [DOI: 10.3106/mammalstudy.28.67] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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