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Tapanainen R, Aasumets K, Fekete Z, Goffart S, Dufour E, L O Pohjoismäki J. Species-specific variation in mitochondrial genome tandem repeat polymorphisms in hares (Lepus spp., Lagomorpha, Leporidae) provides insight into their evolution. Gene 2024; 926:148644. [PMID: 38851366 DOI: 10.1016/j.gene.2024.148644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/23/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
The non-coding regions of the mitochondrial DNAs (mtDNAs) of hares, rabbits, and pikas (Lagomorpha) contain short (∼20 bp) and long (130-160 bp) tandem repeats, absent in related mammalian orders. In the presented study, we provide in-depth analysis for mountain hare (Lepus timidus) and brown hare (L. europaeus) mtDNA non-coding regions, together with a species- and population-level analysis of tandem repeat variation. Mountain hare short tandem repeats (SRs) as well as other analyzed hare species consist of two conserved 10 bp motifs, with only brown hares exhibiting a single, more variable motif. Long tandem repeats (LRs) also differ in sequence and copy number between species. Mountain hares have four to seven LRs, median value five, while brown hares exhibit five to nine LRs, median value six. Interestingly, introgressed mountain hare mtDNA in brown hares obtained an intermediate LR length distribution, with median copy number being the same as with conspecific brown hare mtDNA. In contrast, transfer of brown hare mtDNA into cultured mtDNA-less mountain hare cells maintained the original LR number, whereas the reciprocal transfer caused copy number instability, suggesting that cellular environment rather than the nuclear genomic background plays a role in the LR maintenance. Due to their dynamic nature and separation from other known conserved sequence elements on the non-coding region of hare mitochondrial genomes, the tandem repeat elements likely to represent signatures of ancient genetic rearrangements. clarifying the nature and dynamics of these rearrangements may shed light on the possible role of NCR repeated elements in mitochondria and in species evolution.
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Affiliation(s)
- Riikka Tapanainen
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Koit Aasumets
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Zsófia Fekete
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland; Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Steffi Goffart
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
| | - Jaakko L O Pohjoismäki
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland.
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2
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Tukhbatullin A, Ermakov O, Kapustina S, Starikov V, Tambovtseva V, Titov S, Brandler O. Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time. BIOLOGY 2023; 12:880. [PMID: 37372163 DOI: 10.3390/biology12060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species.
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Affiliation(s)
- Andrey Tukhbatullin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Oleg Ermakov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Svetlana Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Vladimir Starikov
- Department of Biology and Biotechnology, Institute of Natural and Technical Sciences, Surgut State University, Lenin Avenue 1, Surgut 628412, Russia
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Sergey Titov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Oleg Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
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Chen B, Bai Y, Wang J, Ke Q, Zhou Z, Zhou T, Pan Y, Wu R, Wu X, Zheng W, Xu P. Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:141-154. [PMID: 37275538 PMCID: PMC10232709 DOI: 10.1007/s42995-023-00165-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/25/2023] [Indexed: 06/07/2023]
Abstract
The large yellow croaker (Larimichthys crocea) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00165-2.
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Affiliation(s)
- Baohua Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
| | - Yulin Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Jiaying Wang
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Qiaozhen Ke
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
| | - Zhixiong Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Ying Pan
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, 350000 China
| | - Renxie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088 China
| | - Xiongfei Wu
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315012 China
| | - Weiqiang Zheng
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
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Gaertner K, Michell C, Tapanainen R, Goffart S, Saari S, Soininmäki M, Dufour E, Pohjoismäki JLO. Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares (
Lepus
spp., Lagomorpha: Leporidae). Mol Ecol 2022. [PMID: 36320183 DOI: 10.1111/mec.16755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/16/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
Abstract
Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological and behavioural differences. Each species has travelled its own evolutionary trajectory, influenced by random drift and driven by various types of natural selection, making the association of genetic differences between the species with the phenotypic differences extremely complex to dissect. In the present study, we have used an in vitro model to analyse in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare (Lepus timidus Linnaeus) and the temperate steppe-climate adapted brown hare (Lepus europaeus Pallas). We discovered the existence of a species-specific expression pattern of 1623 genes, manifesting in differences in cell growth, cell cycle control, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest that speciation acts on fundamental cellular processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on a cellular level, which could contribute to the maintenance of the species boundary.
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Affiliation(s)
- Kateryna Gaertner
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Craig Michell
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Riikka Tapanainen
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Sina Saari
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Manu Soininmäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
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Michell CT, Pohjoismäki JLO, Spong G, Thulin CG. Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831). Sci Data 2022; 9:667. [PMID: 36329035 PMCID: PMC9633808 DOI: 10.1038/s41597-022-01794-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
We provide the first whole genome sequences from three specimens of the mountain hare subspecies the heath hare (Lepus timidus sylvaticus), along with samples from two mountain hares (Lepus timidus timidus) and two brown hares (Lepus europaeus) from Sweden. The heath hare has a unique grey winter pelage as compared to other mountain hares (white) and brown hares (mostly brown), and face regional extinction, likely due to competitive exclusion from the non-native brown hare. Whole genome resequencing from the seven hare specimens were mapped to the Lepus timidus pseudoreference genome and used for detection of 11,363,883 polymorphic nucleotide positions. The data presented here could be useful for addressing local adaptations and conservation status of mountain hares and brown hares in Sweden, including unique subspecies. Measurement(s) | whole genome sequencing | Technology Type(s) | Illumina HiSeq X | Factor Type(s) | Species | Sample Characteristic - Organism | Lepus timidus • Lepus europaeus • Lepus timidus sylvaticus | Sample Characteristic - Location | Sweden |
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Affiliation(s)
- Craig T Michell
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland. .,Red Sea Research Center, King Abdullah University of Science and Technology, Box 4700, 23955-6900, Thuwal, Kingdom of Saudi Arabia.
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland
| | - Göran Spong
- Department of Wildlife, Fish, and Environmental Studies, Molecular Ecology Group, Swedish University of Agricultural Sciences, Skogmarksgränd, 901 83, Umeå, Sweden
| | - Carl-Gustaf Thulin
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, 750 07, Uppsala, Sweden.
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Reid N, Hughes MF, Hynes RA, Montgomery WI, Prodöhl PA. Bidirectional hybridisation and introgression between introduced European brown hare, Lepus europaeus and the endemic Irish hare, L. timidus hibernicus. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01471-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractIntroduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus, and the endemic Irish hare, L. timidus hibernicus. Roadkill hares (n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin (Tf) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus. Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus, 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.
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Visscher DR, Wood JR. Decadal trends in a population of urban white-tailed jackrabbits at the northern edge of its range. MAMMAL RES 2022. [DOI: 10.1007/s13364-022-00641-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Hybridization with mountain hares increases the functional allelic repertoire in brown hares. Sci Rep 2021; 11:15771. [PMID: 34349207 PMCID: PMC8338973 DOI: 10.1038/s41598-021-95357-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.
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Sirén APK, Morelli TL. Interactive range-limit theory (iRLT): An extension for predicting range shifts. J Anim Ecol 2020; 89:940-954. [PMID: 31758805 PMCID: PMC7187220 DOI: 10.1111/1365-2656.13150] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/20/2019] [Indexed: 11/28/2022]
Abstract
A central theme of range-limit theory (RLT) posits that abiotic factors form high-latitude/altitude limits, whereas biotic interactions create lower limits. This hypothesis, often credited to Charles Darwin, is a pattern widely assumed to occur in nature. However, abiotic factors can impose constraints on both limits and there is scant evidence to support the latter prediction. Deviations from these predictions may arise from correlations between abiotic factors and biotic interactions, as a lack of data to evaluate the hypothesis, or be an artifact of scale. Combining two tenets of ecology-niche theory and predator-prey theory-provides an opportunity to understand how biotic interactions influence range limits and how this varies by trophic level. We propose an expansion of RLT, interactive RLT (iRLT), to understand the causes of range limits and predict range shifts. Incorporating the main predictions of Darwin's hypothesis, iRLT hypothesizes that abiotic and biotic factors can interact to impact both limits of a species' range. We summarize current thinking on range limits and perform an integrative review to evaluate support for iRLT and trophic differences along range margins, surveying the mammal community along the boreal-temperate and forest-tundra ecotones of North America. Our review suggests that range-limit dynamics are more nuanced and interactive than classically predicted by RLT. Many (57 of 70) studies indicate that biotic factors can ameliorate harsh climatic conditions along high-latitude/altitude limits. Conversely, abiotic factors can also mediate biotic interactions along low-latitude/altitude limits (44 of 68 studies). Both scenarios facilitate range expansion, contraction or stability depending on the strength and the direction of the abiotic or biotic factors. As predicted, biotic interactions most often occurred along lower limits, yet there were trophic differences. Carnivores were only limited by competitive interactions (n = 25), whereas herbivores were more influenced by predation and parasitism (77%; 55 of 71 studies). We highlight how these differences may create divergent range patterns along lower limits. We conclude by (a) summarizing iRLT; (b) contrasting how our model system and others fit this hypothesis and (c) suggesting future directions for evaluating iRLT.
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Affiliation(s)
- Alexej P. K. Sirén
- Department of Interior Northeast Climate Adaptation Science CenterU.S. Geological SurveyAmherstMAUSA
- Department of Environmental ConservationUniversity of MassachusettsAmherstMAUSA
| | - Toni Lyn Morelli
- Department of Interior Northeast Climate Adaptation Science CenterU.S. Geological SurveyAmherstMAUSA
- Department of Environmental ConservationUniversity of MassachusettsAmherstMAUSA
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10
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Levänen R, Pohjoismäki JLO, Kunnasranta M. Home Ranges of Semi-Urban Brown Hares (Lepus europaeus) and Mountain Hares (Lepus timidus) at Northern Latitudes. ANN ZOOL FENN 2019. [DOI: 10.5735/086.056.0110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Rikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
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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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12
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Levänen R, Thulin CG, Spong G, Pohjoismäki JLO. Widespread introgression of mountain hare genes into Fennoscandian brown hare populations. PLoS One 2018; 13:e0191790. [PMID: 29370301 PMCID: PMC5784980 DOI: 10.1371/journal.pone.0191790] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/11/2018] [Indexed: 11/29/2022] Open
Abstract
In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.
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Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Carl-Gustaf Thulin
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Spong
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
- * E-mail:
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