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Chen X, Feng Y, Chen S, Yang K, Wen X, Sun Y. Species Delimitation and Genetic Relationship of Castanopsis hainanensis and Castanopsis wenchangensis (Fagaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:3544. [PMID: 37896008 PMCID: PMC10609670 DOI: 10.3390/plants12203544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Castanopsis is one of the most common genus of trees in subtropical evergreen broad-leaved forests and tropical monsoon rainforests in China. Castanopsis hainanensis and Castanopsis wenchangensis are endemic to Hainan Island, but they were once confused as the same species due to very similar morphologies. In this study, nuclear microsatellite markers and chloroplast genomes were used to delimit C. hainanensis and C. wenchangensis. The allelic variations of nuclear microsatellites revealed that C. hainanensis and C. wenchangensis were highly genetically differentiated with very limited gene admixture. Both showed higher genetic diversity within populations and lower genetic diversity among populations, and neither had further population genetic structure. Furthermore, C. wenchangensis and C. hainanensis had very different chloroplast genomes. The independent genetic units, very limited gene admixture, different distribution ranges, and distinct habitats all suggest that C. wenchangensis and C. hainanensis are independent species, thus they should be treated as distinct conservation units.
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Affiliation(s)
- Xing Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Yi Feng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Shuang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Kai Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Xiangying Wen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
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Fujiwara T, Egashira T, Gutiérrez-Ortega JS, Hori K, Ebihara A, Watano Y. Establishment of an allotetraploid fern species, Lepisorus yamaokae Seriz., between two highly niche-differentiated parental species. AMERICAN JOURNAL OF BOTANY 2022; 109:1456-1471. [PMID: 35938973 DOI: 10.1002/ajb2.16043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The successful establishment of polyploid species is hypothesized to be promoted by niche differentiation from the parental species or by range shifts during climate oscillations. However, few studies have considered both of these factors simultaneously. We resolved the origin of a tetraploid fern, Lepisorus yamaokae, and explored a pattern of niche differentiation among the allotetraploid and parental species in past and current climates. METHODS We reconstructed phylogenetic trees based on plastid marker and single-copy nuclear genes to resolve the allopolyploid origin of L. yamaokae. We also evaluated climatic niche differentiation among L. yamaokae and its two parental species using species distribution models in geographic space and principal component analysis. RESULTS We infer that L. yamaokae had a single allotetraploid origin from L. annuifrons and L. uchiyamae. Climatic niche analyses show that the parental species currently occupy different niche spaces. The predicted distribution of the parental species at the Last Glacial Maximum (LGM) suggests more opportunities for hybridization during the LGM or during other recent temporary range shifts. Lepisorus yamaokae has a narrower niche than the additive niche of the parental species. We also observed niche conservatism in L. yamaokae. CONCLUSIONS Range shifts of the parental species during climatic oscillations in the Quaternary likely facilitated the formation and establishment of L. yamaokae. Further, the genetic intermediacy of L. yamaokae may have enabled a niche shift in its microenvironment, resulting in its successful establishment without a macroclimatic niche shift in L. yamaokae.
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Affiliation(s)
- Tao Fujiwara
- Makino Herbarium, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji, Tokyo, 192-0397, Japan
| | - Tsubasa Egashira
- Department of Biology, Faculty of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan
| | | | - Kiyotaka Hori
- The Kochi Prefectural Makino Botanical Garden, 4200-6 Godaisan, Kochi, 781-8125, Japan
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan
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Niwa K, Tran DV, Nishikawa K. Differentiated historical demography and ecological niche forming present distribution and genetic structure in coexisting two salamanders (Amphibia, Urodela, Hynobiidae) in a small island, Japan. PeerJ 2022; 10:e13202. [PMID: 35505683 PMCID: PMC9057287 DOI: 10.7717/peerj.13202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/09/2022] [Indexed: 01/12/2023] Open
Abstract
Background The climatic oscillations in the Quaternary period considerably shaped the distribution and population genetic structure of organisms. Studies on the historical dynamics of distribution and demography not only reflect the current geographic distribution but also allow us to understand the adaption and genetic differentiation of species. However, the process and factors affecting the present distribution and genetic structure of many taxa are still poorly understood, especially for endemic organisms to small islands. Methods Here, we integrated population genetic and ecological niche modelling approaches to investigate the historical distribution and demographic dynamics of two co-existing salamanders on Tsushima Island, Japan: the true H. tsuensis (Group A), and Hynobius sp. (Group B). We also examined the hypothesis on the equivalency and similarity of niches of these groups by identity and background tests for ecological niche space. Results Our result showed that Group A is considered to have undergone a recent population expansion after the Last Glacial Maximum while it is unlikely to have occurred in Group B. The highest suitability was predicted for Group A in southern Tsushima Island, whereas the northern part of Tsushima Island was the potential distribution of Group B. The results also suggested a restricted range of both salamanders during the Last Interglacial and Last Glacial Maximum, and recent expansion in Mid-Holocene. The genetic landscape-shape interpolation analysis and historical suitable area of ecological niche modelling were consistent, and suggested refugia used during glacial ages in southern part for Group A, and in northern part of Tsushima Island for Group B. Additionally, we found evidence of nonequivalence for the ecological niche of the two groups of the salamanders, although our test could not show either niche divergence or conservatism based on the background tests. The environmental predictors affecting the potential distribution of each group also showed distinctiveness, leading to differences in selecting suitable areas. Finally, the combination of population genetics and ecological modeling has revealed the differential demographic/historical response between coexisting two salamanders on a small island.
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Affiliation(s)
- Keita Niwa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Akita Prefectural Office, Akita, Japan
| | - Dung Van Tran
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan,Wildlife Department, Faculty of Forest Resources and Environmental Management, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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Late Pleistocene pottery production and exchange: Provenance studies of hunter-gatherer wares from southern Kyushu, Japan by neutron activation analysis. PLoS One 2022; 17:e0265329. [PMID: 35294491 PMCID: PMC8926207 DOI: 10.1371/journal.pone.0265329] [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: 11/05/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
Late Pleistocene hunter-gatherers in East Asia adopted pottery, yet the ability to reconstruct circulation, mobility, and exchange has been hampered, in part, due to problematic regional geochronology. The driving forces behind pottery adoption is unclear. The purpose of this study is to test our results of the first systematic petrographic pottery sourcing from the pre-Younger Dryas by utilizing neutron activation analysis. We examine samples from the Sankauyama I site on Tanegashima Island, southern Japan, dating to the Incipient Jomon, ca. 14,000/13,500–12,800 cal BP, with a well-defined geochronology. Our NAA results corroborate with the petrographic study suggesting that pottery was mainly produced in-situ, but some vessels were transported long distances from another island. Changing from high mobility, sedentary Incipient Jomon foragers made pottery, occasionally investing in long-distance ceramic vessel transportation and exchange likely involving ocean crossing. This may be associated with a risk-buffering strategy in the context of rising sea levels and isolation of Tanegashima.
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Li Y, Zhang X, Wang L, Sork VL, Mao L, Fang Y. Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China. ANNALS OF BOTANY 2022; 129:231-245. [PMID: 34893791 PMCID: PMC8796672 DOI: 10.1093/aob/mcab140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/31/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. METHODS We analyse genetic variation at seven nuclear microsatellites (1111 individuals) and three chloroplast intergenic spacers (576 individuals) to determine the present admixture pattern and ancient hybridization history. We apply an information-theoretic model selection approach to explore the associations of genetic admixture degree with past climatic niche suitability at multiple spatial scales. KEY RESULTS More than 70 % of the hybrids determined by Bayesian clustering analysis and more than 90 % of the individuals with locally shared chloroplast haplotypes are concentrated within a mid-Pliocene contact zone between ~30°N and 35°N. Climatic niche suitabilities for Q. chenii during the mid-Pliocene Warm Period [mPWP, ~3.264-3.025 million years ago (mya)] and during the Last Glacial Maximum (LGM, ~0.022 mya) best explain the admixture patterns across all Q. acutissima populations and across those within the ancient contact zone, respectively. CONCLUSIONS Our results highlight that palaeoclimate change shapes present admixture patterns by influencing the extent of historical range overlap. Specifically, the mid-Pliocene warm climate promoted ancient contact, allowing widespread hybridization throughout central China. In contrast, the Pleistocene cool climate caused the local extinction of Q. chenii, reducing the probability of interspecific gene flow in most areas except those sites having a high level of ecological stability.
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Affiliation(s)
- Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xingwang Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
| | - Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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Development of the first microsatellite markers using high-throughput sequencing for a hexaploid coastal species, Tournefortia argentea L. f. (Boraginaceae). Mol Biol Rep 2021; 48:7049-7055. [PMID: 34462831 DOI: 10.1007/s11033-021-06668-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUD Tournefortia argentea L. f. is a hexaploid shrub or tree species with ecological and evolutionary significances, which forms the fringe of vegetation closest to the sea on tropical coral islands. Previous studies have never addressed on genetic information, and thus genomic resources remain scarce. METHODS AND RESULTS We used nine individuals from different islands to identify polymorphic microsatellites of T. argentea by Illumina high-throughput sequencing. Thirty-five polymorphic microsatellite markers were developed. Characteristics of each locus were tested using 48 individuals collected from three populations of T. argentea. A total of 320 alleles were found across the 35 microsatellite loci. The number of alleles per locus ranged from 5 to 15, with an average of 9.1. Observed and expected heterozygosities in each locus per population varied from 0.000 to 1.000 and from 0.000 to 0.893, respectively. CONCLUSIONS In this study, we report the development of 35 polymorphic microsatellite markers based on Illumina high-throughput sequencing. These markers will facilitate the investigations of genetic diversity, population structures and evolutionary history of T. argentea.
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Ohta M, Endo Y, Fujinaga A, Kawasaki T, Watanabe K, Matsuda T, Nakanuma H, Kawamura M, Hirashita T, Masaki T, Inomata M. Predictors of early withdrawal from follow-up visits after laparoscopic sleeve gastrectomy in a Japanese institution. Surg Today 2021; 52:46-51. [PMID: 34101018 DOI: 10.1007/s00595-021-02318-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/28/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE Postoperative weight loss is related to postoperative adherence to follow-up after bariatric/metabolic surgery, but many patients stop attending follow-up visits early. The aim of this study was to clarify predictors of early withdrawal from follow-up after laparoscopic sleeve gastrectomy (LSG) in a Japanese institution. METHODS One hundred and fifty-three patients who underwent LSG were retrospectively included in this study. Multivariate analysis was performed to evaluate independent predictors of withdrawal from follow-up visits within 12 months after LSG among significant or nearly significant factors in the univariate analyses. The discrimination power of significant factors was estimated using area under the receiver operating characteristic curve (AUC). RESULTS Within 12 months after LSG, 25 of the 153 patients withdrew from follow-up visits. The multivariate analysis showed that age was the only significant predictor of withdrawal. The AUC for age was 0.685, and the cut-off value was < 40 years. The younger patients (< 40 years old) had a significantly higher rate of withdrawal compared with the older patients (≥ 40 years) (27.0% vs. 8.9%). CONCLUSION Older Japanese patients (≥ 40 years old) may be better candidates for LSG. We consider it significant to continue to emphasize the importance of follow-up visits in younger patients after LSG.
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Affiliation(s)
- Masayuki Ohta
- Global Oita Medical Advanced Research Center for Health, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan. .,Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan.
| | - Yuichi Endo
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan
| | - Atsuro Fujinaga
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan
| | - Takahide Kawasaki
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan
| | - Kiminori Watanabe
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan
| | - Takashi Matsuda
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan
| | - Hiroaki Nakanuma
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan
| | - Masahiro Kawamura
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan
| | - Teijiro Hirashita
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan
| | - Takayuki Masaki
- Department of Endocrinology, Metabolism, Rheumatology and Nephrology, Oita University Faculty of Medicine, Oita, Japan
| | - Masafumi Inomata
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Oita, Japan
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Sakaguchi S, Asaoka Y, Takahashi D, Isagi Y, Imai R, Nagano AJ, Qiu YX, Li P, Lu R, Setoguchi H. Inferring historical survivals of climate relicts: the effects of climate changes, geography, and population-specific factors on herbaceous hydrangeas. Heredity (Edinb) 2021; 126:615-629. [PMID: 33510468 PMCID: PMC8115046 DOI: 10.1038/s41437-020-00396-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/25/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
Climate relicts hold considerable importance because they have resulted from numerous historical changes. However, there are major interspecific variations among the ways by which they survived climate changes. Therefore, investigating the factors and timing that affected population demographics can expand our understanding of how climate relicts responded to historical environmental changes. Here, we examined herbaceous hydrangeas of genus Deinanthe in East Asia, which show limited distributions and a remarkable disjunction between Japan and central China. Chloroplast genome and restriction site-associated DNA sequencing revealed that speciation event occurred in the late Miocene (ca. 7-9 Mya) in response to global climate change. Two lineages apparently remained not branched until the middle Quaternary, and afterwards started to diverge to regional population groups. The narrow endemic species in central China showed lower genetic diversity (He = 0.082), as its population size rapidly decreased during the Holocene due to isolation in montane refugia. Insular populations in the three Japanese islands (He = 0.137-0.160) showed a genetic structure that was inconsistent with sea barriers, indicating that it was shaped in the glacial period when its range retreated to coastal refugia on the exposed sea floor. Demographic modelling by stairway-plot analysis reconstructed variable responses of Japanese populations: some experienced glacial bottlenecks in refugial isolation, while post-glacial range expansion seemingly exerted founder effects on other populations. Overall, this study demonstrated the involvement of not just one, but multiple factors, such as the interplay between climate changes, geography, and other population-specific factors, that determine the demographics of climate relicts.
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan.
| | - Yui Asaoka
- Faculty of Integrated Human Studies, Kyoto University, Kyoto, 606-8501, Japan
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuji Isagi
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryosuke Imai
- Iriomote Station, Tropical Biosphere Research Centre, University of the Ryukyus, Okinawa, 907-1541, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
| | - Ying-Xiong Qiu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ruisen Lu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan
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Shi M, Wang Y, Duan T, Qian X, Zeng T, Zhang D. In situ glacial survival maintains high genetic diversity of Mussaenda kwangtungensis on continental islands in subtropical China. Ecol Evol 2020; 10:11304-11321. [PMID: 33144966 PMCID: PMC7593160 DOI: 10.1002/ece3.6768] [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: 11/18/2019] [Revised: 07/06/2020] [Accepted: 08/18/2020] [Indexed: 11/23/2022] Open
Abstract
Generally, island populations are predicted to have less genetic variation than their mainland relatives. However, a growing number of studies have nevertheless reported exceptions, indicating that the relationships were impacted by several factors, for example, historical processes. In the present study, we chose a group of subtropical islands located in South China as the study system, which are quite younger and much closer to the mainland than most of the previous studied island systems, to test the hypothesis that in situ glacial survival contributes to high levels of genetic diversity in island populations. We conducted a comparison of genetic variation between 12 island and 11 nearby mainland populations of Mussaenda kwangtungensis using eleven nuclear microsatellite and three chloroplast markers, evaluated effects of the island area and distance to mainland on genetic diversity of island populations, and simulated the potential distribution over the past by ecological niche modeling, together with the genetic data to detect the role of islands during the glacial periods. The island populations displayed comparable levels of genetic diversity and differentiation with mainland populations, overall high levels of unique polymorphisms, and the greatest values of specific within-population genetic diversity. No significant correlation was detected between genetic diversity of island populations and distance to mainland, as well as area of islands, except that allelic richness was significantly positively correlated with the area of islands. Nuclear microsatellites revealed two main clusters, largely corresponding to islands and inland populations, which divergence dated to a time of island formation by ABC analysis. Ecological niche modeling predicted a highly climatic suitability on islands during the last glacial maximum (LGM). Our results suggest that the islands have acted as refugia during the LGM and highlight the role of in situ glacial survival in maintaining high levels of genetic diversity of M. kwangtungensis in continental islands of subtropical China.
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Affiliation(s)
- Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Yuyuan Wang
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Xin Qian
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Tong Zeng
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
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Han EK, Cho WB, Park JS, Choi IS, Kwak M, Kim BY, Lee JH. A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak ( Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization. Genes (Basel) 2020; 11:E1114. [PMID: 32977695 PMCID: PMC7598624 DOI: 10.3390/genes11101114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022] Open
Abstract
Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. To test this hypothesis, we examined the levels of genetic diversity of marginal-edge populations of Quercus gilva, restricted to a few habitats on Jeju Island, and compared them with the southern Kyushu populations. We also evaluated their evolutionary potential and conservation value. The genetic diversity and structure were analyzed using 40 polymorphic microsatellite markers developed in this study. Ecological Niche Modeling (ENM) has been employed to develop our insights, which can be inferred from historical distribution changes. Contrary to our expectations, we detected a similar level of genetic diversity in the Jeju populations, comparable to that of the southern Kyushu populations, which have been regarded as long-term glacial refugia with a high genetic variability of East Asian evergreen trees. We found no signatures of recent bottlenecks in the Jeju populations. The results of STRUCTURE, neighbor-joining phylogeny, and Principal Coordinate Analysis (PCoA) with a significant barrier clearly demonstrated that the Jeju and Kyushu regions are genetically distinct. However, ENM showed that the probability value for the distribution of the trees on Jeju Island during the Last Glacial Maximum (LGM) converge was zero. In consideration of these results, we hypothesize that independent massive postglacial colonization from a separate large genetic source, other than Kyushu, could have led to the current genetic diversity of Jeju Island. Therefore, we suggest that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU). These findings improve our understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks.
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Affiliation(s)
- Eun-Kyeong Han
- Department of Biological Sciences and Biotechnology, Chonnam National University, Gwangju 61186, Korea;
| | - Won-Bum Cho
- Department of Biology Education, Chonnam National University, Gwangju 61186, Korea;
| | - Jong-Soo Park
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Korea;
| | - In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Myounghai Kwak
- Biological and Genetic Resources Utilization Division, National Institute of Biological Resources, Incheon 22689, Korea;
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Korea;
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju 61186, Korea;
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Ye B, Saito T, Hirano T, Dong Z, Do VT, Chiba S. Human-geographic effects on variations in the population genetics of Sinotaia quadrata (Gastropoda: Viviparidae) that historically migrated from continental East Asia to Japan. Ecol Evol 2020; 10:8055-8072. [PMID: 32788961 PMCID: PMC7417235 DOI: 10.1002/ece3.6456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Anthropogenic factors potentially affect observed biogeographical patterns in population genetics, but the effects of ancient human activities on the original patterns created by natural processes are unknown. Sinotaia quadrata, a widely distributed freshwater snail species in East Asia, was used to investigate this issue. It is unclear whether S. quadrata in Japan was introduced from China and how different human uses and varying geographic patterns affect the contemporary population genetics between the two regions. Thus, we investigated the demography of S. quadrata and detected its genetic structure in Japan and continental East Asia. RESULTS Sinotaia quadrata populations first naturally migrated from continental East Asia to Japan, which is associated with the ancient period in Japanese geohistory (about 70,000 years ago). They were then artificially introduced in association with agriculture expansion by human movements in two recent periods (about 8,000 and 1,200 years ago). Populations in different parts of Japan have their own sources. Natural migration in the ancient period and artificial introduction in the recent period suggest that the population distribution is affected by both the geohistory of East Asia and the history of human expansion. In the background of the historical migration and introduction, contemporary populations in the two regions show different genetic patterns. Population divergence levels were significantly correlated with geographical patterns in Japan and significantly correlated with human interventions variables in continental East Asia, suggesting that long-term geographical isolation is likely the major factor that shaped the contemporary population genetics in Japan, while modern human uses are likely the major factor in continental East Asia. CONCLUSIONS Our preliminary results show a complex demography and unusual genetic patterns in the contemporary populations for a common freshwater snail and are of significance to determine the historical formation and contemporary patterns of biogeography in Japan and continental East Asia.
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Affiliation(s)
- Bin Ye
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Takumi Saito
- Department of BiologyFaculty of ScienceToho UniversityFunabashiJapan
| | - Takahiro Hirano
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
- Center for Northeast Asian StudiesTohoku UniversitySendaiJapan
| | - Zhengzhong Dong
- Agricultural Experiment StationZhejiang UniversityHangzhouChina
| | - Van Tu Do
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHa NoiVietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and TechnologyHa NoiVietnam
| | - Satoshi Chiba
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
- Center for Northeast Asian StudiesTohoku UniversitySendaiJapan
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Takahashi D, Teramine T, Sakaguchi S, Setoguchi H. Genetic data reveals a complex history of multiple admixture events in presently allopatric wild gingers (Asarum spp.) showing intertaxonomic clinal variation in calyx lobe length. Mol Phylogenet Evol 2019; 137:146-155. [PMID: 31075504 DOI: 10.1016/j.ympev.2019.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 10/26/2022]
Abstract
Clinal variation is a major pattern of observed phenotypic diversity and identifying underlying demographic processes is a necessary step to understand the establishment of clinal variation. The wild ginger series Sakawanum (genus Asarum) comprises four taxa, which exhibit intertaxonomic clinal variation in calyx lobe length across two continental islands isolated by a sea strait. To test alternative hypotheses of the evolutionary history and to determine the implications for the formation of clinal variation, we conducted approximate Bayesian computation (ABC) analysis and ecological niche modeling (ENM). ABC analysis indicated that the scenario assuming multiple admixture events was strongly supported. This scenario assumed two admixture events occurred between morphologically distinct taxa, likely leading to the generation of intermediate taxa. One of the admixture events was estimated to have occurred during the last glacial maximum (LGM), during which the taxa were estimated to have formed a common refugia in southern areas by ENM analysis. Although four taxa are currently distributed allopatrically on different islands and trans-oceanic dispersal appears unlikely, the formation of a land bridge and the geographic range shift to refugia would have allowed secondary contact between previously isolated taxa. This study suggests that clinal variation can be shaped by demographic history including multiple admixtures due to climatic oscillations.
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Affiliation(s)
- Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu, Sakyo-ku, Kyoto 606-8501, Japan.
| | | | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu, Sakyo-ku, Kyoto 606-8501, Japan
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