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Mamat M, Shan W, Dong P, Zhou S, Liu P, Meng Y, Nie W, Teng P, Zhang Y. Population genetics analysis of Tolai hares (Lepus tolai) in Xinjiang, China using genome-wide SNPs from SLAF-seq and mitochondrial markers. Front Genet 2022; 13:1018632. [PMID: 37006991 PMCID: PMC10064446 DOI: 10.3389/fgene.2022.1018632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
The main topic of population genetics and evolutionary biology is the influence of the ecological environment, geographical isolation, and climatic factors on population structure and history. Here, we estimated the genetic diversity, genetic structure, and population history of two subspecies of Tolai hares (Lepus tolai Pallas, 1778), L. t. lehmanni inhabiting Northern and Northwest Xinjiang and L. t. centrasiaticus inhabiting Central and Eastern Xinjiang using SNP of specific-length amplified fragment sequencing (SLAF-seq) and four mitochondrial DNA (mtDNA). Our results showed a relatively high degree of genetic diversity for Tolai hares, and the diversity of L. t. lehmanni was slightly higher than that of L. t. centrasiaticus, likely due to the more favorable ecological environment, such as woodlands and plains. Phylogenetic analysis from SNP and mtDNA indicated a rough phylogeographical distribution pattern among Tolai hares. Strong differentiation was found between the two subspecies and the two geographical groups in L. t. centrasiaticus, possibly due to the geographical isolation of mountains, basins, and deserts. However, gene flow was also detected between the two subspecies, which might be attributed to the Tianshan Corridor and the strong migration ability of hares. Tolai hare population differentiation occurred at approximately 1.2377 MYA. Population history analysis based on SNP and mtDNA showed that the Tolai hare population has a complex history and L. t. lehmanni was less affected by the glacial event, possibly because its geographic location and terrain conditions weaken the drastic climate fluctuations. In conclusion, our results indicated that the joint effect of ecological environment, geographic events, and climatic factors might play important roles in the evolutionary process of L. t. lehmanni and L. t. centrasiaticus, thus resulting in differentiation, gene exchange, and different population history.
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López-Cuamatzi IL, Ortega J, Baeza JA. The complete mitochondrial genome of the 'Zacatuche' Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico. Mol Biol Rep 2021; 49:1141-1149. [PMID: 34783988 DOI: 10.1007/s11033-021-06940-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/23/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND The 'Zacatuche', 'Teporingo', or Volcano rabbit (Romerolagus diazi) belongs to the family Leporidae, is an endemic species restricted to the Central part of the Trans-Mexican Volcanic Belt, and is considered 'endangered' by the IUCN Red List of Threatened Species. METHODS AND RESULTS This study reports, for the first time, the complete mitochondrial genome of R. diazi and examined the phylogenetic position of R. diazi among other closely related co-familiar species using mitochondrial protein-coding genes (PCGs). The mitogenome of R. diazi was assembled from short Illumina 150 bp pair-end reads with a coverage of 189x. The AT-rich mitochondrial genome of R. diazi is 17,400 bp in length and is comprised of 13 PCGs, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order observed in the mitochondrial genome of R. diazi is identical to that reported for other leporids. Phylogenetic analyses based on PCGs support the basal position of Romerolagus within the Leporidae, at least when compared to the genera Oryctolagus and Lepus. Nonetheless, additional mitochondrial genomes from species belonging to the genera Bunolagus, Sylvilagus, and Pronolagus, among others, are needed before a more robust conclusion about the derived vs basal placement of Romerolagus within the family Leporidae can be reached based on mitochondrial PCGs. CONCLUSIONS This is the first genomic resource developed for R. diazi and it represents a tool to improve our understanding about the ecology and evolutionary biology of this iconic and endangered species.
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Affiliation(s)
- Issachar Leonardo López-Cuamatzi
- Posgrado en Ecología Tropical, Centro de Investigaciones Tropicales, Universidad Veracruzana, José María Morelos 44, Zona Centro, Centro, 91000, Xalapa-Enríquez, Mexico.
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Sto. Tomas, 11340, Ciudad de México, México
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA.,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA.,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
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Ababaikeri B, Zhang Y, Dai H, Shan W. Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing. Front Zool 2021; 18:50. [PMID: 34565397 PMCID: PMC8474959 DOI: 10.1186/s12983-021-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 09/07/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Yarkand hare (Lepus yarkandensis Günther, 1875) is endemic to oasis and desert areas around the Tarim Basin in the Xinjiang Uyghur Autonomous Region of northwest China; however, genome-wide information for this species remains limited. Moreover, the genetic variation, genetic structure, and phylogenetic relationships of Yarkand hare from the plateau mountain regions have not been reported. Thus, we used specific-length amplified fragment sequencing (SLAF-seq) technology to evaluate the genetic diversity of 76 Yarkand hares from seven geographic populations in the northern and southwestern parts of the Tarim Basin to investigate single-nucleotide polymorphism (SNP) marker-based population differentiation and evolutionary processes. Selective sweep analysis was conducted to identify genetic differences between populations. RESULTS Using SLAF-seq, a total of 1,835,504 SNPs were initially obtained, of which 308,942 high-confidence SNPs were selected for further analysis. Yarkand hares exhibited a relatively high degree of genetic diversity at the SNP level. Based on pairwise FST estimates, the north and southwest groups showed a moderate level of genetic differentiation. Phylogenetic tree and population structure analyses demonstrated evident systematic phylogeographical structure patterns consistent with the geographical distribution of the hares. Hierarchical analysis of molecular variation further indicated that genetic variation was mainly observed within populations. Low to moderate genetic differentiation also occurred among populations despite a common genomic background, likely due to geographical barriers, genetic drift, and differential selection pressure of distinct environments. Nevertheless, the observed lineage-mixing pattern, as indicated by the evolutionary tree, principal component analysis, population structure, and TreeMix analyses, suggests a certain degree of gene flow between the north and southwest groups. This may be related to the migration of hares to high-altitude water sources southwest of the basin during glacial climatic oscillations, as well as river re-diffusion and oasis restoration in the basin following the glacial period. We also identified candidate genes, and their associated gene ontology terms and pathways, related to the adaptation of Yarkand hares to different environmental habitats. CONCLUSIONS The identified genome-wide SNPs, genetic diversity, and population structure of Yarkand hares expand our understanding of the genetic background of this endemic species and provide valuable insights into its environmental adaptation, allowing for further exploration of the underlying mechanisms.
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Affiliation(s)
- Buweihailiqiemu Ababaikeri
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
- College of Xinjiang Uyghur Medicine, Hoten, 848000, Xinjiang, China
| | - Yucong Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Huiying Dai
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China.
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Kraatz B, Belabbas R, Fostowicz-Frelik Ł, Ge DY, Kuznetsov AN, Lang MM, López-Torres S, Mohammadi Z, Racicot RA, Ravosa MJ, Sharp AC, Sherratt E, Silcox MT, Słowiak J, Winkler AJ, Ruf I. Lagomorpha as a Model Morphological System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.636402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.
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Buglione M, Petrelli S, de Filippo G, Troiano C, Rivieccio E, Notomista T, Maselli V, di Martino L, Carafa M, Gregorio R, Latini R, Fortebraccio M, Romeo G, Biliotti C, Fulgione D. Contribution to the ecology of the Italian hare (Lepus corsicanus). Sci Rep 2020; 10:13071. [PMID: 32753640 PMCID: PMC7403147 DOI: 10.1038/s41598-020-70013-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/06/2020] [Indexed: 11/09/2022] Open
Abstract
The Italian hare (Lepus corsicanus) is endemic to Central-Southern Italy and Sicily, classified as vulnerable due to habitat alterations, low density and fragmented populations and ecological competition with the sympatric European hare (Lepus europaeus). Despite this status, only few and local studies have explored its ecological features. We provided some key traits of the ecological niche of the Italian hare as well as its potential distribution in the Italian peninsula. All data derived from genetically validated presences. We generated a habitat suitability model using maximum entropy distribution model for the Italian hare and its main competitor, the European hare. The dietary habits were obtained for the Italian hare with DNA metabarcoding and High-Throughput Sequencing on faecal pellets. The most relevant environmental variables affecting the potential distribution of the Italian hare are shared with the European hare, suggesting a potential competition. The variation in the observed altitudinal distribution is statistically significant between the two species.The diet of the Italian hare all year around includes 344 plant taxa accounted by 62 families. The Fagaceae, Fabaceae, Poaceae, Rosaceae and Solanaceae (counts > 20,000) represented the 90.22% of the total diet. Fabaceae (60.70%) and Fagaceae (67.47%) were the most abundant plant items occurring in the Spring/Summer and Autumn/Winter diets, respectively. The Spring/Summer diet showed richness (N = 266) and diversity index values (Shannon: 2.329, Evenness: 0.03858, Equitability: 0.4169) higher than the Autumn/Winter diet (N = 199, Shannon: 1.818, Evenness: 0.03096, Equitability: 0.3435). Our contribution adds important information to broaden the knowledge on the environmental (spatial and trophic) requirements of the Italian hare, representing effective support for fitting management actions in conservation planning.
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Affiliation(s)
- Maria Buglione
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Simona Petrelli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Claudia Troiano
- Department of Humanities, University of Naples Federico II, Napoli, Italy
| | | | - Tommaso Notomista
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | | | - Romano Gregorio
- Cilento, Vallo di Diano e Alburni National Park, Salerno, Italy
| | - Roberta Latini
- Abruzzo, Lazio and Molise National Park, Pescasseroli, Aquila, Italy
| | | | - Giorgia Romeo
- Wildlife Section, Tuscan Regional Council, Grosseto, Italy
| | - Claudia Biliotti
- SOS Animali Onlus, Wildlife Rescue Center, Semproniano, Grosseto, Italy
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Naples, Italy.
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Zhang X, Fu L, Guo S. The sequence and characterization of mitochondrial of Lepus oiostolus (Lagomorpha: Leporidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2135-2136. [PMID: 33366947 PMCID: PMC7510751 DOI: 10.1080/23802359.2020.1768930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 05/09/2020] [Indexed: 10/28/2022]
Abstract
Lepus oiostolus is widely inhabited in the Qinghai-Tibet Plateau. So far, little mitochondrial genome information of this genus has been described. To grasp a better comprehension on the molecular basis of L. oiostolus, we obtained the complete mitochondrial DNA genome sequences of this species. The mitogenome was 17,320 bp in length, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 noncoding regions. The complete mitochondrial genome of L. oiostolus would be of great utility in the phylogenetic analysis of the Lagomorpha and also provide meritorious insights into the deeper problems of the phylogenic analysis.
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Affiliation(s)
- Xuze Zhang
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Lin Fu
- Center of life science, School of life sciences, Yunnan University, Kunming
| | - Songchang Guo
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
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Pinheiro A, de Sousa-Pereira P, Almeida T, Ferreira CC, Otis JA, Boudreau MR, Seguin JL, Lanning DK, Esteves PJ. Sequencing of VDJ genes in Lepus americanus confirms a correlation between VHn expression and the leporid species continent of origin. Mol Immunol 2019; 112:182-187. [PMID: 31174011 DOI: 10.1016/j.molimm.2019.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/12/2019] [Accepted: 05/27/2019] [Indexed: 10/26/2022]
Abstract
Leporid VH genes used in the generation of their primary antibody repertoire exhibit highly divergent lineages. For the European rabbit (Oryctolagus cuniculus) four VHa lineages have been described, the a1, a2, a3 and a4. Hares (Lepus spp.) and cottontail (Sylvilagus floridanus) express one VHa lineage each, the a2L and the a5, respectively, along with a more ancient lineage, the Lepus spp. sL and S. floridanus sS. Both the European rabbit and the Lepus europaeus use a third lineage, VHn, in a low proportion of their VDJ rearrangements. The VHn genes are a conserved ancestral polymorphism that is being maintained in the leporid genome.Their usage in a low proportion of VDJ rearrangements by both European rabbit and L. europaeus but not S. floridanus has been argued to be a remnant of an ancient European leporid immunologic response to pathogens. To address this hypothesis, in this study we sequenced VDJ rearranged genes for another North American leporid, L. americanus. Our results show that L. americanus expressed these genes less frequently and in a highly modified fashion compared to the European Lepus species. Our results suggest that the American leporid species use a different VH repertoire than the European species which may be related with an immune adaptation to different environmental conditions, such as different pathogenic agents.
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Affiliation(s)
- Ana Pinheiro
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Patricia de Sousa-Pereira
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal; Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tereza Almeida
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Catarina C Ferreira
- Department of Biology, Trent University, Peterborough, Ontario, Canada; UFZ - Helmholtz Centre for Environmental Research, Department of Conservation Biology, Leipzig, Germany
| | - Josée-Anne Otis
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | | | - Jacob L Seguin
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | - Dennis K Lanning
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States
| | - Pedro J Esteves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal; Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, 4585-116, Gandra, Portugal
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Kumar B, Cheng J, Ge D, Xia L, Yang Q. Phylogeography and ecological niche modeling unravel the evolutionary history of the Yarkand hare, Lepus yarkandensis (Mammalia: Leporidae), through the Quaternary. BMC Evol Biol 2019; 19:113. [PMID: 31153378 PMCID: PMC6545225 DOI: 10.1186/s12862-019-1426-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/22/2019] [Indexed: 01/29/2023] Open
Abstract
Background The Taklimakan Desert in China is characterized by unique geological and historical dynamics and endemic flora and fauna, but the influence of historical climate oscillations on the evolutionary history of endemic animals is poorly understood. Lepus yarkandensis is an oases-dependent Near Threatened species that lives in fragmented oasis habitats in the Taklimakan Desert, China. We investigated the geological and climatic impacts on its geographical differentiation, demographic history and influence of Pleistocene glacial-interglacial cycles on the evolutionary history of L. yarkandensis. Further, studied the impact of climatic oscillation based modification on phylogeography, distribution and diversification pattern of Yarkand hare by using Cytb (1140 bp), MGF (592 bp) and SPTBN1 (619 bp) markers. Ecological niche modeling (ENM) revealed the evolutionary history of this species in response to climate change during the Quaternary. Paleodistribution modeling was used to identify putative refugia and estimate their historical distributions. Results Both historical demographic analyses and climatic niche modeling revealed strong effects of glacial climate changes, suggesting recurrent range contractions and expansions. The EBSP results indicated clear population expansion of L. yarkandensis since the Pleistocene. In the “early Pleistocene”, the demographic expansion continued from 0.83 MYA to the last glacial period. The ENM analysis supported a wide distribution of Lepus yarkandensis at high altitudes during the last interglacial (LIG) period. During the last glacial maximum (LGM), the suitable climate was reduced and restricted to the western part of the Taklimakan Desert. Conclusions Inland aridification, oasis evolution and river flow played major roles in the population differentiation and demographic history of Yarkand hares. Historically, the large, continuous oases in the Taklimakan Desert contained a viable and unique population of L. yarkandensis. The fragmented desert environment might have caused low gene flow between individuals or groups, thus leading to predominant genetic differentiation. The Pleistocene climatic cycles triggered the diversification and expansion of this species during cold and warm periods, respectively, leading to multiple colonization events within the Taklimakan Desert. These events might be due to the expansion of the Taklimakan Desert during the Middle Pleistocene. Yarkand hare previously occupied vast areas at low and intermediate altitudes in Xinjiang, Gansu, Shanxi, Henan and Shaanxi Provinces in China. The past aridification, climate change-induced oasis modifications, changes in river volumes and flow directions, and human activities all affected the population demography and phylogeography of the Yarkand hare. Electronic supplementary material The online version of this article (10.1186/s12862-019-1426-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brawin Kumar
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.,International College, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
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9
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The evolutionary history of the Cape hare (Lepus capensis sensu lato): insights for systematics and biogeography. Heredity (Edinb) 2019; 123:634-646. [PMID: 31073237 DOI: 10.1038/s41437-019-0229-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/11/2019] [Accepted: 04/19/2019] [Indexed: 12/27/2022] Open
Abstract
Inferring the phylogeography of species with large distributions helps deciphering major diversification patterns that may occur in parallel across taxa. Here, we infer the evolutionary history of the Cape hare, Lepus capensis sensu lato, a species distributed from southern Africa to Asia, by analyzing variation at 18 microsatellites and 9 DNA (1 mitochondrial and 8 nuclear) sequenced loci, from field and museum-collected samples. Using a combination of assignment and coalescent-based methods, we show that the Cape hare is composed of five evolutionary lineages, distributed in distinct biogeographic regions-north-western Africa, eastern Africa, southern Africa, the Near East and the Arabian Peninsula. A deep phylogenetic break possibly dating to the Early Pleistocene was inferred between the African and Asian L. capensis groups, and the latter appear more closely related to other Eurasian hare species than to African Cape hares. The inferred phylogeographic structure is shared by numerous taxa distributed across the studied range, suggesting that environmental changes, such as the progressive aridification of the Saharo-Arabian desert and the fluctuations of savannah habitats in Sub-Saharan Africa, had comparable impacts across species. Fine-scale analyses of the western Sahara-Sahel populations showed rich fragmentation patterns for mitochondrial DNA but not for microsatellites, compatible with the environmental heterogeneity of the region and female philopatry. The complex evolutionary history of L. capensis sensu lato, which possibly includes interspecific gene flow, is not reflected by taxonomy. Integrating evolutionary inference contributes to an improved characterization of biodiversity, which is fundamental to foster the conservation of relevant evolutionary units.
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10
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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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Tolesa Z, Bekele E, Tesfaye K, Ben Slimen H, Valqui J, Getahun A, Hartl GB, Suchentrunk F. Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia. PLoS One 2017; 12:e0180137. [PMID: 28767659 PMCID: PMC5540492 DOI: 10.1371/journal.pone.0180137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/10/2017] [Indexed: 11/28/2022] Open
Abstract
For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals. For the hares from Ethiopia, genotype composition at twelve microsatellite loci (n = 107) was used to explore both interspecific gene pool separation and levels of current hybridization, as has been observed in some other Lepus species. For phylogenetic analyses ATP6 and TF sequences of Lepus species from South and North Africa (L. capensis, L. saxatilis), the Anatolian peninsula and Europe (L. europaeus, L. timidus) were also produced and additional TF sequences of 18 Lepus species retrieved from GenBank were included as well. Median joining networks, neighbour joining, maximum likelihood analyses, as well as Bayesian inference resulted in similar models of evolution of the three species from Ethiopia for the ATP6 and TF sequences, respectively. The Ethiopian species are, however, not monophyletic, with signatures of contemporary uni- and bidirectional mitochondrial introgression and/ or shared ancestral polymorphism. Lepus habessinicus carries mtDNA distinct from South African L. capensis and North African L. capensis sensu lato; that finding is not in line with earlier suggestions of its conspecificity with L. capensis. Lepus starcki has mtDNA distinct from L. capensis and L. europaeus, which is not in line with earlier suggestions to include it either in L. capensis or L. europaeus. Lepus fagani shares mitochondrial haplotypes with the other two species from Ethiopia, despite its distinct phenotypic and microsatellite differences; moreover, it is not represented by a species-specific mitochondrial haplogroup, suggesting considerable mitochondrial capture by the other species from Ethiopia or species from other parts of Africa. Both mitochondrial and nuclear sequences indicate close phylogenetic relationships among all three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. TF sequences suggest close evolutionary relationships between the three Ethiopian species and Cape hares from South and North Africa; they further suggest that hares from Ethiopia hold a position ancestral to many Eurasian and North American species.
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Affiliation(s)
- Zelalem Tolesa
- Department of Biology, Hawassa University, Hawassa, Ethiopia
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Endashaw Bekele
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Centre of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hichem Ben Slimen
- Institut Supérieur de Biotechnologie de Béja, Avenue Habib Bourguiba, Béja, Tunisia
| | - Juan Valqui
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Abebe Getahun
- Department of Zoological Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Günther B. Hartl
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
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12
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Beugin MP, Letty J, Kaerle C, Guitton JS, Muselet L, Queney G, Pontier D. A single multiplex of twelve microsatellite markers for the simultaneous study of the brown hare (Lepus europaeus) and the mountain hare (Lepus timidus). Ecol Evol 2017. [DOI: 10.1002/ece3.2943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Marie-Pauline Beugin
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
- Univ Lyon; Université Lyon 1; CNRS; Laboratoire de Biométrie et Biologie Evolutive UMR5558; F-69622 Villeurbanne France
| | - Jérôme Letty
- Research Department; National Hunting and Wildlife Agency (ONCFS); Juvignac Nantes France
| | - Cécile Kaerle
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
| | - Jean-Sébastien Guitton
- Research Department; National Hunting and Wildlife Agency (ONCFS); Juvignac Nantes France
| | - Lina Muselet
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
| | - Guillaume Queney
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
| | - Dominique Pontier
- Univ Lyon; Université Lyon 1; CNRS; Laboratoire de Biométrie et Biologie Evolutive UMR5558; F-69622 Villeurbanne France
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13
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Niche overlap of mountain hare subspecies and the vulnerability of their ranges to invasion by the European hare; the (bad) luck of the Irish. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1330-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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14
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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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15
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Ding L, Chen C, Wang H, Zhang B. Complete mitochondrial DNA sequence of Lepus tolai (Leporidae: Lepus). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2085-6. [PMID: 25391036 DOI: 10.3109/19401736.2014.982568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, we determined the complete nucleotide sequence of the mitochondrial (mt) genome of tolai hare, Lepus tolai (Leporidae: Lepus) by using polymerase chain reaction (PCR) technique. The entire mtDNA sequence is 17,472 bp long and contains 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA gens and one long non-coding region known as the control region.
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Affiliation(s)
- Ling Ding
- a School of Life Sciences, Anhui University , Hefei , Anhui , China
| | - Changmao Chen
- a School of Life Sciences, Anhui University , Hefei , Anhui , China
| | - Hui Wang
- a School of Life Sciences, Anhui University , Hefei , Anhui , China
| | - Baowei Zhang
- a School of Life Sciences, Anhui University , Hefei , Anhui , China
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16
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Mengoni C, Mucci N, Randi E. Genetic diversity and no evidences of recent hybridization in the endemic Italian hare (Lepus corsicanus). CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0674-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Melo-Ferreira J, Seixas FA, Cheng E, Mills LS, Alves PC. The hidden history of the snowshoe hare,Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation. Mol Ecol 2014; 23:4617-30. [DOI: 10.1111/mec.12886] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 01/09/2023]
Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Fernando A. Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; 4099-002 Porto Portugal
| | - Ellen Cheng
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
- Ugyen Wangchuck Institute for Conservation and Environment; Lamai Goempa Bumthang Bhutan
| | - L. Scott Mills
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
- Fisheries, Wildlife and Conservation Biology Program; North Carolina State University; Raleigh NC 27695-7617 USA
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; 4099-002 Porto Portugal
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
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18
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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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19
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Kong L, Wang W, Cong H, Son Nguyen T, Yang Q, Wu Y, Li Y. Molecular evidence revealed Lepus hainanus and L. peguensis have a conspecific relationship. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:265-9. [PMID: 24548010 DOI: 10.3109/19401736.2014.888550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Accurate species delimitation in Lepus was often hindered by highly conserved morphology and frequent introgression. In this study, we used rigorous molecular species delimitation methods to evaluate the taxonomic status of Hainan hare (Lepus hainanus) which has been traditionally identified as a distinct species, or a subspecies of Burmese hare (L. peguensis). The genetic distance and phylogenetic network support L. hainanus and L. peguensis are conspecific. However, the phylogenetic species concept and Bayesian species delimitation analysis based on combined mtDNA supported they are different species. The discordance between different methods can be explained by different species criterion. By taking into account our conflict results, we hold the opinion that adoption of the phylogenetic species concept and Bayesian species delimitation analysis would increase the risk of taxonomic inflation of island biota or otherwise spatially isolated population. Conservatively, we suggest that L. hainanus and L. peguensis are conspecific based on the results of our genetic divergence and phylogenetic network exclusively.
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Affiliation(s)
- Lingming Kong
- a Marine College, Shandong University , Weihai , China
| | - Wenquan Wang
- b Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , Haikou , China
| | - Haiyan Cong
- a Marine College, Shandong University , Weihai , China
| | - Truong Son Nguyen
- c Department of Zoology , Institute of Ecology and Biological Resources , Hanoi , Vietnam
| | - Qisen Yang
- d Institute of Zoology, Chinese Academy of Sciences , Beijing , China , and
| | - Yi Wu
- e College of Life Science, Guangzhou University , Guangzhou , China
| | - Yuchun Li
- a Marine College, Shandong University , Weihai , China
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20
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Yacoub HA, Fathi MM, Sadek MA. Using cytochrome b gene of mtDNA as a DNA barcoding marker in chicken strains. ACTA ACUST UNITED AC 2013; 26:217-23. [PMID: 24020964 DOI: 10.3109/19401736.2013.825771] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This was the second study to apply using of a cytochrome b gene as barcoding tool in distinguishing among chicken strains. We performed polymerase chain reaction (PCR) amplification using universal primer to amplify around 415 bp fragment of cytochrome b gene of mtDNA. The tree reported that both Saudi chicken strains (black and dark brown) are closely related and it might be separated from same origin rather than bronze ones. The phylogenetic tree also, exploited that native chicken strains were closely related to cluster of Ceylon jungle fowl, black Minorca egg chicken and Fayoumi egg chicken. The genetic divergence between these populations or types of chickens in Saudi Arabia was low (0.02) and it was very low (0.011), when compared to other species of Gallus. We confirmed that short fragment of cyt-b gene as a universal DNA barcode region. It was much more accurate and efficient tool to discriminate inter-species than intra-species. Applying cyt-b of mtDNA was successfully distinguished among native strains and other species of Gallus as in a previous study. However, applying this thought on different species of farm animal species is recommended.
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Affiliation(s)
- Haitham A Yacoub
- Biological Sciences Department, Faculty of Sciences, King Abdul Aziz University , P.O. Box 80203, Jeddah , Kingdom of Saudi Arabia
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21
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Yu JN, Chung CU, Kwak M. The complete mitochondrial genome sequence of the Korean hare (Lepus coreanus). ACTA ACUST UNITED AC 2013; 26:129-30. [PMID: 23883283 DOI: 10.3109/19401736.2013.815170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitogenome of the Korean hare (Lepus coreanus) was determined by the long and accurate polymerase chain reaction and primer-walking methods. The mitogenome of the Korean hare is 17,472 bp in length and contains sequences that encode 13 protein genes, 22 tRNAs, 2 rRNAs and a noncoding control region. The mitogenome is arranged in an identical order to that found in most other vertebrates. All mitochondrial genes are encoded on the heavy strand, except for eight tRNA genes and the ND6 gene. The control region contains putative termination associated elements, conserved sequence blocks and short and long tandem repeats motifs.
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Affiliation(s)
- Jeong-Nam Yu
- National Institute of Biological Resources , Incheon , Korea and
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22
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Kirihara T, Shinohara A, Tsuchiya K, Harada M, Kryukov AP, Suzuki H. Spatial and temporal aspects of occurrence of Mogera species in the Japanese islands inferred from mitochondrial and nuclear gene sequences. Zoolog Sci 2013; 30:267-81. [PMID: 23537237 DOI: 10.2108/zsj.30.267] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We assessed dispersal and vicariant events in four species of Japanese moles in the genera Mogera and Euroscaptor to better understand the factors shaping intra- and interspecific differentiation in Japanese moles. We used the combined viewpoints of molecular phylogeny and historical geology using nucleotide sequences of mitochondrial (cytochrome b; Cytb) and nuclear (A2ab, Bmp4, Tcf25, vWf) genes. The divergence times estimated from the molecular data were verified with available geological data on the chronology of fluctuations in sea level in the Korea Strait, assuming sequential migration and speciation events. This produced possible migration times of 5.6, 3.5, 2.4, and 1.3 million years ago for four species of Japanese moles, Euroscaptor mizura, Mogera tokudae, M. imaizumii, and M. wogura, respectively. For the western Japanese mole M. wogura, Cytb sequences revealed four major phylogroups with strong geographic affinities in southwestern Central Honshu (I), western Honshu/Shikoku (II), Kyushu/westernmost Honshu (III), and Korea/Russian Primorye (IV). The nuclear gene sequences supported the distinctiveness of phylogroups I and IV, indicating long, independent evolutionary histories. In contrast, phylogroups II and III were merged into a single geographic group based on the nuclear gene data. Intraspecific divergences in M. imaizumii and M. tokudae were rather apparent in Cytb but not in nuclear gene sequences. The results suggest that repeated dispersal events have occurred between the Asian continent and the Japanese Islands, and intensive vicariant events associated with abiotic and biotic factors have created higher levels of species and genetic diversities in moles occurring on the Japanese Islands.
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Affiliation(s)
- Takashi Kirihara
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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23
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Ge D, Wen Z, Xia L, Zhang Z, Erbajeva M, Huang C, Yang Q. Evolutionary history of lagomorphs in response to global environmental change. PLoS One 2013; 8:e59668. [PMID: 23573205 PMCID: PMC3616043 DOI: 10.1371/journal.pone.0059668] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 02/18/2013] [Indexed: 11/18/2022] Open
Abstract
Although species within Lagomorpha are derived from a common ancestor, the distribution range and body size of its two extant groups, ochotonids and leporids, are quite differentiated. It is unclear what has driven their disparate evolutionary history. In this study, we compile and update all fossil records of Lagomorpha for the first time, to trace the evolutionary processes and infer their evolutionary history using mitochondrial genes, body length and distribution of extant species. We also compare the forage selection of extant species, which offers an insight into their future prospects. The earliest lagomorphs originated in Asia and later diversified in different continents. Within ochotonids, more than 20 genera occupied the period from the early Miocene to middle Miocene, whereas most of them became extinct during the transition from the Miocene to Pliocene. The peak diversity of the leporids occurred during the Miocene to Pliocene transition, while their diversity dramatically decreased in the late Quaternary. Mantel tests identified a positive correlation between body length and phylogenetic distance of lagomorphs. The body length of extant ochotonids shows a normal distribution, while the body length of extant leporids displays a non-normal pattern. We also find that the forage selection of extant pikas features a strong preference for C3 plants, while for the diet of leporids, more than 16% of plant species are identified as C4 (31% species are from Poaceae). The ability of several leporid species to consume C4 plants is likely to result in their size increase and range expansion, most notably in Lepus. Expansion of C4 plants in the late Miocene, the so-called ‘nature’s green revolution’, induced by global environmental change, is suggested to be one of the major ‘ecological opportunities’, which probably drove large-scale extinction and range contraction of ochotonids, but inversely promoted diversification and range expansion of leporids.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhaoqun Zhang
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Margarita Erbajeva
- Geological Institute, Siberian Branch, Russian Academy of Sciences, Ulan-Ude, Russia
| | - Chengming Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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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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25
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Mu XD, Wang XJ, Song HM, Yang YX, Luo D, Gu DE, Xu M, Liu C, Luo JR, Hu YC. Mitochondrial DNA as effective molecular markers for the genetic variation and phylogeny of the family Osteoglossidae. Gene 2012; 511:320-5. [PMID: 23036711 DOI: 10.1016/j.gene.2012.09.087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 08/05/2012] [Accepted: 09/12/2012] [Indexed: 11/25/2022]
Abstract
The present study examined the genetic variation of the family Osteoglossidae from different geographical locations based on the mitochondrial NADH dehydrogenase subunit 2 (ND2) and ATPase subunit 6 (ATPase6) genes; we then re-constructed the phylogenetic relationships using the two sequences in combination. The results showed that the partial sequences of mitochondrial ND2 and ATPase6 of the family Osteoglossidae were 813 bp and 669 bp, respectively. A total of 42 species-specific nucleotide positions of the family Osteoglossidae were found to be useful for molecular identification. The sequence variation showed greater differences (8.3%~28.1% for the combined sequences, 8.3%~26.7% for the ND2 gene, and 9.3%~28.7% for the ATPase6 gene) among the different species of Osteoglossidae, and there was a significant association between the genetic difference and geographical location. Phylogenetic analyses using neighbor-joining, Bayesian inference, and maximum parsimony (MP) methods based on the combined sequences of the two genes were able to distinguish the different species and were in agreement with the existing taxonomy based on morphological characters and in association with the geographical distribution among seven species of the family Osteoglossidae.
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Affiliation(s)
- Xi-dong Mu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou 510380, China
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26
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Kim SI, An J, Choi SK, Lee YS, Park HC, Kimura J, Kim KS, Min MS, Lee H. Development and characterization of nine microsatellite loci from the Korean hare (Lepus coreanus) and genetic diversity in South Korea. Anim Cells Syst (Seoul) 2012. [DOI: 10.1080/19768354.2011.640351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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27
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Ge D, Lissovsky AA, Xia L, Cheng C, Smith AT, Yang Q. Reevaluation of several taxa of Chinese lagomorphs (Mammalia: Lagomorpha) described on the basis of pelage phenotype variation. Mamm Biol 2012. [DOI: 10.1016/j.mambio.2011.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Liu J, Yu L, Arnold ML, Wu CH, Wu SF, Lu X, Zhang YP. Reticulate evolution: frequent introgressive hybridization among Chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci. BMC Evol Biol 2011; 11:223. [PMID: 21794180 PMCID: PMC3155923 DOI: 10.1186/1471-2148-11-223] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/28/2011] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. RESULTS Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. CONCLUSION This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.
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Affiliation(s)
- Jiang Liu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Li Yu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Michael L Arnold
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Chun-Hua Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
- Utah State University Department of Animal, Dairy & Veterinary Sciences Old Main Hill 4700 Center for Integrated Biosystems Rm315 Logan, UT 84322-4700, USA
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Xin Lu
- Department of Zoology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ya-Ping Zhang
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
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Genetic consequences of postglacial colonization by the endemic Yarkand hare (Lepus yarkandensis) of the arid Tarim Basin. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4460-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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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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31
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Zachos FE, Ben Slimen H, Hackländer K, Giacometti M, Suchentrunk F. Regional genetic
in situ
differentiation despite phylogenetic heterogeneity in Alpine mountain hares. J Zool (1987) 2010. [DOI: 10.1111/j.1469-7998.2010.00710.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. E. Zachos
- Zoological Institute, Christian‐Albrechts‐University, Kiel, Germany
| | - H. Ben Slimen
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Campus Universitaire El Manar, Tunis, Tunisia
| | - K. Hackländer
- Department of Integrative Biology and Biodiversity Research, Institute of Wildlife Biology and Game Management, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | | | - F. Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
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32
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Koh HS, Jang KH. Genetic distinctness of the Korean hare, Lepus coreanus (Mammalia, Lagomorpha), revealed by nuclear thyroglobulin gene and mtDNA control region sequences. Biochem Genet 2010; 48:706-10. [PMID: 20526735 DOI: 10.1007/s10528-010-9353-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 03/29/2010] [Indexed: 11/27/2022]
Affiliation(s)
- Hung Sun Koh
- Department of Biology, Chungbuk University, Cheongju, Korea.
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33
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Estimated evolutionary tempo of East Asian gobionid fishes (Teleostei: Cyprinidae) from mitochondrial DNA sequence data. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-3159-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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35
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36
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Alves PC, Melo-Ferreira J, Freitas H, Boursot P. The ubiquitous mountain hare mitochondria: multiple introgressive hybridization in hares, genus Lepus. Philos Trans R Soc Lond B Biol Sci 2008; 363:2831-9. [PMID: 18508749 DOI: 10.1098/rstb.2008.0053] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Climatic oscillations during the glaciations forced dramatic changes in species distributions, such that some presently temperate regions were alternately occupied by temperate and arctic species. These species could have met and hybridized during climatic transitions. This phenomenon happened for three hare species present in Iberia (Lepus granatensis, Lepus europaeus and Lepus castroviejoi), which display high frequencies of mitochondrial DNA (mtDNA) from Lepus timidus, an arctic/boreal species presently extinct in Iberia. Here, we extend our previous geographical survey to determine whether the distribution of this mtDNA lineage extends beyond the northern half of the Iberian Peninsula, where it is found at high frequencies. We also review the taxonomy, distribution and molecular phylogeny of the genus Lepus. The phylogenetic inference reveals the presence of L. timidus-like mtDNA in several other hare species in Asia and North America, suggesting that the mitochondrial introgression observed in Iberia might be generalized. Comparison with the available nuclear gene phylogenies suggests that introgression could have happened repeatedly, possibly during different climatic transitions. We discuss demographic and adaptive scenarios that could account for the repetition in time and space of this spectacular phenomenon and suggest ways to improve our understanding of its determinants and consequences. Such high levels of introgressive hybridization should discourage attempts to revise hare taxonomy based solely on mtDNA.
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Affiliation(s)
- Paulo C Alves
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
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37
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On shortcomings of using mtDNA sequence divergence for the systematics of hares (genus Lepus): An example from cape hares. Mamm Biol 2008. [DOI: 10.1016/j.mambio.2007.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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38
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Alves PC, Melo-Ferreira J, Branco M, Suchentrunk F, Ferrand N, Harris DJ. Evidence for genetic similarity of two allopatric European hares (Lepus corsicanus and L. castroviejoi) inferred from nuclear DNA sequences. Mol Phylogenet Evol 2007; 46:1191-7. [PMID: 18178109 DOI: 10.1016/j.ympev.2007.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 11/02/2007] [Accepted: 11/15/2007] [Indexed: 11/17/2022]
Affiliation(s)
- P C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
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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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40
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Zhang YP, Ge S. Molecular evolution study in China: progress and future promise. Philos Trans R Soc Lond B Biol Sci 2007; 362:973-86. [PMID: 17317644 PMCID: PMC2435564 DOI: 10.1098/rstb.2007.2027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
China has a large land area with highly diverse topography, climate and vegetation, and animal resources and is ranked eighth in the world and first in the Northern Hemisphere on richness of biodiversity. Even though little work on molecular evolution had been reported a decade ago, studies on both the evolution of macromolecules and the molecular phylogeny have become active in China in recent years. This review highlights some of the interesting and important developments in molecular evolution study in China. Chinese scientists have made significant contribution on the methods inferring phylogeny and biogeography of animals and plants in East Asia using molecular data. Studies on population and conservation genetics of animals and plants, such as Golden monkey and Chinese sturgeon, provided useful information for conserving the endangered species. East and South Asia has been demonstrated to be one of the centres of domestication. Origin and evolution of genes and gene families have been explored, which shed new insight on the genetic mechanism of adaptation. In the genomic era, Chinese researchers also made a transition from single-gene to a genomic investigation approach. Considering the fact that amazing progress has been made in the past few years, and more and more talented young scientists are entering field, the future of molecular evolution study in China holds much promise.
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Affiliation(s)
- Ya-ping Zhang
- Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 JiaoChangDongLu, Kunming, Yunnan 650223, People's Republic of China.
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41
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Alves PC, Harris DJ, Melo-Ferreira J, Branco M, Ferrand N, Suchentrunk F, Melo-Ferreira J, Boursot P. Hares on thin ice: Introgression of mitochondrial DNA in hares and its implications for recent phylogenetic analyses. Mol Phylogenet Evol 2006; 40:640-1. [PMID: 16624594 DOI: 10.1016/j.ympev.2006.02.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 01/19/2006] [Accepted: 02/19/2006] [Indexed: 10/24/2022]
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