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Kuo HC, Schoneman T, Gao LM, Gruezo WS, Amoroso VB, Yang Y, Yang KC, Chien CT, Möller M, Wang CN. A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular Taxus in Taiwan and the Philippines. Front Genet 2024; 15:1372309. [PMID: 38756448 PMCID: PMC11096487 DOI: 10.3389/fgene.2024.1372309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/15/2024] [Indexed: 05/18/2024] Open
Abstract
The cool temperate origin of gymnosperm Taxus species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as T. phytonii, have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 Taxus individuals from Taiwan and the Philippines. Using four cpDNA and one nuclear marker, we showed in population genetic and genealogical analyses that the two insular lineages were genetically distinct from each other and also from other continental Taxus and that they represented each other's closest relative. Estimated with the coalescent-based multi-type tree (MTT) analyses, we inferred an origin of Taiwanese T. phytonii more ancient than 2.49 Mya and that of Philippine T. phytonii more ancient than 1.08 Mya. In addition, the divergence demographic history revealed by both MTT and isolation with migration (IM) analyses indicated the presence of recent post-split migrations from a continental taxon, T. mairei, to Taiwanese T. phytonii, as well as from Taiwanese T. phytonii to Philippine T. phytonii. Overall, this study suggests Taiwan as a stepping stone through which the temperate-origin yew trees can extend their distributions to tropical regions such as the Philippines.
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Affiliation(s)
- Hao-Chih Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Travis Schoneman
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - William Sm. Gruezo
- Plant Biology Division, College of Arts and Sciences, Institute of Biological Sciences, University of the Philippines at Los Baños, Laguna, Philippines
| | - Victor B. Amoroso
- Center for Biodiversity Research and Extension in Mindanao (CEBREM), Central Mindanao University, Mindanao, Philippines
| | - Yang Yang
- Tainan District Agricultural Research and Extension Station, Ministry of Agriculture, Tainan, Taiwan
| | - Kuo-Cheng Yang
- General Education Center, Providence University, Taichung, Taiwan
| | - Ching-Te Chien
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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Tsunenari K, Ito T, Yokota M, Shibabayashi M, Endo C, Chung KF, Suyama Y, Matsuo A, Abe A, Naiki A, Setoguchi H, Makino T, Isagi Y. Double migration of the endangered Tricyrtis formosana (Liliaceae) in Japan. Sci Rep 2024; 14:957. [PMID: 38200076 PMCID: PMC10781951 DOI: 10.1038/s41598-024-51431-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
The Ryukyu Islands of Japan are a biodiversity hotspot due to geographical and historical factors. Tricyrtis formosana is a perennial herbaceous plant that commonly found in Taiwan. But only a few populations have been identified in a limited habitat on Iriomote Island, while populations of unknown origin occur near human settlements in an area on the main island of Okinawa. To better understand these populations of the phylogenetic uniqueness and intrinsic vulnerability, we conducted comparative analyses including (1) phylogeny and population structure with MIG-seq data, (2) photosynthesis-related traits of plants grown under common conditions and (3) transcriptome analysis to detect deleterious variations. Results revealed that T. formosana was split into two clades by the congeners and that Iriomote and Okinawa populations independently derived from ancestral Taiwanese populations in each clade. Photosynthetic efficiency was lowest in the Iriomote population, followed by Okinawa and Taiwan. Transcriptome analysis showed that the Iriomote population accumulated more deleterious variations, suggesting intrinsic vulnerability. These results indicate that each T. formosana population in Japan is phylogenetically unique and has been independently dispersed from Taiwan, and that the Iriomote population presents a high conservation difficulty with a unique photosynthesis-related characteristic and a larger amount of deleterious variations.
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Affiliation(s)
- Kaori Tsunenari
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
- Japan Broadcasting Cooporation, Tokyo, Japan.
| | - Takuro Ito
- The Center for Academic Resources and Archives, Tohoku University, Sendai, Japan
| | | | | | - Chiharu Endo
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kuo-Fang Chung
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Ayumi Matsuo
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Atsushi Abe
- Okinawa Churashima Foundation Research Institute, Botanical Laboratory, Okinawa, Japan
| | - Akiyo Naiki
- Tropical Biosphere Research Center, University of the Ryukyus, Taketomi, Okinawa, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Takashi Makino
- Graduate School of Life Science, Tohoku University, Sendai, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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Kwak ML, Jones MD, Harman MEA, Smith SN, D'souza A, Knierim T, Barnes CH, Waengsothorn S, Amarga AKS, Kuo CC, Nakao R. The East Indies reptile tick Amblyomma helvolum Koch, 1844 (Acari: Ixodidae), taxonomy, biology and new host records, including the first record of human infestation. Ticks Tick Borne Dis 2023; 14:102224. [PMID: 37422945 DOI: 10.1016/j.ttbdis.2023.102224] [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: 01/13/2023] [Revised: 06/05/2023] [Accepted: 06/25/2023] [Indexed: 07/11/2023]
Abstract
Amblyomma helvolum is a widespread, generalist ectoparasite of reptiles in the oriental region, and has the potential to become highly invasive should it be inadvertently introduced outside its native range through the exotic pet trade. All life stages of A. helvolum are re-characterised morphologically and the first examples of nanism (dwarfism) and gynandromorphy (male and female tissue in one animal) for the species are described. Eighteen new hosts records are presented for A. helvolum, including the first case of human infestation. The taxonomy, distribution, ecology, phenology, disease associations, and invasion biology of the species are also discussed.
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Affiliation(s)
- Mackenzie L Kwak
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, 9 Chome Kita 18 Jonishi, Kita Ward, Sapporo, Hokkaido 060-0818, Japan
| | - Max D Jones
- Department of Fish and Wildlife Conservation, Virginia Tech, VA, United States
| | - Madison E A Harman
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, United States
| | - Samantha N Smith
- Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL, United States
| | - Anji D'souza
- Sakaerat Enviromental Research Station, Thailand Institute of Scientific and Technological Research, Nakhon Ratchasima, Thailand
| | - Tyler Knierim
- Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL, United States
| | - Curt H Barnes
- Center of Excellence for Ecoinformatics, School of Science, Walailak University, Thai Buri, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand
| | - Surachit Waengsothorn
- Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL, United States
| | - Ace Kevin S Amarga
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chi-Chien Kuo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, 9 Chome Kita 18 Jonishi, Kita Ward, Sapporo, Hokkaido 060-0818, Japan
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Harigai W, Saito A, Zemmoto C, Karasawa S, Yokoi T, Nagano AJ, Suzuki H, Yamamoto M. History of the terrestrial isopod genus Ligidium in Japan based on phylogeographic analysis. BMC Ecol Evol 2023; 23:38. [PMID: 37550609 PMCID: PMC10405464 DOI: 10.1186/s12862-023-02144-8] [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: 08/18/2022] [Accepted: 07/26/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Phylogeographical approaches explain the genetic diversity of local organisms in the context of their geological and geographic environments. Thus, genetic diversity can be a proxy for geological history. Here we propose a genus of woodland isopod, Ligidium, as a marker of geological history in relation to orogeny and the Quaternary glacial cycle. RESULTS Mitochondrial analysis of 721 individuals from 97 sites across Japan revealed phylogenetic divergence between the northeastern and southwestern Japan arcs. It also showed repeated population expansions in northeastern Japan in response to Quaternary glacial and interglacial cycles. Genome-wide analysis of 83 selected individuals revealed multiple genetic nuclear clusters. The genomic groupings were consistent with the local geographic distribution, indicating that the Ligidium phylogeny reflects its regional history. CONCLUSION Ligidium DNA sequence analysis can provide insight into the geological, geographical, and paleoenvironmental history of the studied region.
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Affiliation(s)
- Wakana Harigai
- Graduate School of Environmental Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan.
- Present address: Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan.
| | - Aya Saito
- Department of Earth and Planetary Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
| | - Chika Zemmoto
- Department of Earth and Planetary Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
| | - Shigenori Karasawa
- Faculty of Agriculture, Tottori University, 4-101, Koyama-Cho Minami, Tottori, 680-8553, Japan
| | - Touta Yokoi
- Faculty of Agriculture, Tottori University, 4-101, Koyama-Cho Minami, Tottori, 680-8553, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
- Faculty of Environmental Earth Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
| | - Masanobu Yamamoto
- Graduate School of Environmental Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
- Faculty of Environmental Earth Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
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Lyu R, Xiao J, Li M, Luo Y, He J, Cheng J, Xie L. Phylogeny and Historical Biogeography of the East Asian Clematis Group, Sect. Tubulosae, Inferred from Phylogenomic Data. Int J Mol Sci 2023; 24:3056. [PMID: 36769378 PMCID: PMC9917980 DOI: 10.3390/ijms24033056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/29/2023] [Indexed: 02/09/2023] Open
Abstract
The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae.
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Affiliation(s)
- Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Mingyang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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6
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Allopatric Lineage Divergence of the East Asian Endemic Herb Conandron ramondioides Inferred from Low-Copy Nuclear and Plastid Markers. Int J Mol Sci 2022; 23:ijms232314932. [PMID: 36499259 PMCID: PMC9740071 DOI: 10.3390/ijms232314932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
The evolutionary histories of ornamental plants have been receiving only limited attention. We examined the origin and divergence processes of an East Asian endemic ornamental plant, Conandron ramondioides. C. ramondioides is an understory herb occurring in primary forests, which has been grouped into two varieties. We reconstructed the evolutionary and population demography history of C. ramondioides to infer its divergence process. Nuclear and chloroplast DNA sequences were obtained from 21 Conandron populations on both sides of the East China Sea (ECS) to explore its genetic diversity, structure, and population differentiation. Interestingly, the reconstructed phylogeny indicated that the populations should be classified into three clades corresponding to geographical regions: the Japan (Honshu+Shikoku) clade, the Taiwan-Iriomote clade, and the Southeast China clade. Lineage divergence between the Japan clade and the Taiwan-Iriomote and Southeast China clades occured 1.14 MYA (95% HPD: 0.82-3.86), followed by divergence between the Taiwan-Iriomote and Southeast China clades approximately 0.75 MYA (95% HPD: 0.45-1.3). Furthermore, corolla traits (floral lobe length to tube length ratios) correlated with geographical distributions. Moreover, restricted gene flow was detected among clades. Lastly, the lack of potential dispersal routes across an exposed ECS seafloor during the last glacial maximum suggests that migration among the Conandron clades was unlikely. In summary, the extant Conandron exhibits a disjunct distribution pattern as a result of vicariance rather than long-distance dispersal. We propose that allopatric divergence has occurred in C. ramondioides since the Pleistocene. Our findings highlight the critical influence of species' biological characteristics on shaping lineage diversification of East Asian relic herb species during climate oscillations since the Quaternary.
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Kang B, Hsu K, Wu J, Chiu Y, Lin H, Ju Y. Population genetic diversity and structure of Rhinogobius candidianus (Gobiidae) in Taiwan: Translocation and release. Ecol Evol 2022; 12:e9154. [PMID: 35979520 PMCID: PMC9366559 DOI: 10.1002/ece3.9154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 06/17/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022] Open
Abstract
Rhinogobius candidianus is a freshwater goby distributed in north, northwest, west, and south Taiwan, but this species has been introduced to east Taiwan and became dominant. To investigate its native population genetic diversity and structure and evaluate the sources and diversity of translocated populations, the mitochondrial DNA control region and cytochrome b gene (1981 bp) from 220 specimens were analyzed. These results indicated that (1) the east populations originated from two sources in west Taiwan; (2) translocated populations exist in east Taiwan and south Taiwan; (3) many populations have likely been moved secondarily by human intervention; (4) the effective size of the populations had declined greatly; (5) within the native populations, the ancestral populations colonized Taiwan during the land bridge phase in the Pleistocene through north Taiwan; (6) the landform changes in Taiwan shaped the population structure; and (7) the landforms of the coastline during glaciation also shaped the native range. The low-level genetic diversity, high population differentiation, and population decline greatly suggest the need for resource management and conservation interventions. Four clades (α-δ) should be managed as four distinct evolutionarily significant units, while the translocated populations should be managed as separate management units. Moreover, the translocated populations in east Taiwan should be evaluated and monitored carefully.
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Affiliation(s)
- Bin Kang
- The Key Laboratory of Mariculture (Ocean University of China)Ministry of EducationQingdaoChina
| | - Kui‐Ching Hsu
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
| | - Jui‐Hsien Wu
- Eastern Marine Biology Research Center of Fisheries Research InstituteCouncil of AgricultureTaitungTaiwan
| | - Yuh‐Wen Chiu
- Department of Biological ResourcesNational Chiayi UniversityChiayiTaiwan
| | - Hung‐Du Lin
- The Affiliated School of National Tainan First Senior High SchoolTainanTaiwan
| | - Yu‐Min Ju
- National Museum of Marine Biology and AquariumPingtungTaiwan
- Department of Marine Biotechnology and ResourcesNational Sun Yat‐sen UniversityKaohsiungTaiwan
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Xia M, Cai M, Comes HP, Zheng L, Ohi-Toma T, Lee J, Qi Z, Konowalik K, Li P, Cameron KM, Fu C. An overlooked dispersal route of Cardueae (Asteraceae) from the Mediterranean to East Asia revealed by phylogenomic and biogeographical analyses of Atractylodes. ANNALS OF BOTANY 2022; 130:53-64. [PMID: 35533344 PMCID: PMC9295924 DOI: 10.1093/aob/mcac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/06/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS The East Asian-Tethyan disjunction pattern and its mechanisms of formation have long been of interest to researchers. Here, we studied the biogeographical history of Asteraceae tribe Cardueae, with a particular focus on the temperate East Asian genus Atractylodes DC., to understand the role of tectonic and climatic events in driving the diversification and disjunctions of the genus. METHODS A total of 76 samples of Atractylodes from 36 locations were collected for RAD-sequencing. Three single nucleotide polymorphism (SNP) datasets based on different filtering strategies were used for phylogenetic analyses. Molecular dating and ancestral distribution reconstruction were performed using both chloroplast DNA sequences (127 Cardueae samples) and SNP (36 Atractylodes samples) datasets. KEY RESULTS Six species of Atractylodes were well resolved as individually monophyletic, although some introgression was identified among accessions of A. chinensis, A. lancea and A. koreana. Dispersal of the subtribe Carlininae from the Mediterranean to East Asia occurred after divergence between Atractylodes and Carlina L. + Atractylis L. + Thevenotia DC. at ~31.57 Ma, resulting in an East Asian-Tethyan disjunction. Diversification of Atractylodes in East Asia mainly occurred from the Late Miocene to the Early Pleistocene. CONCLUSIONS Aridification of Asia and the closure of the Turgai Strait in the Late Oligocene promoted the dispersal of Cardueae from the Mediterranean to East China. Subsequent uplift of the Qinghai-Tibet Plateau as well as changes in Asian monsoon systems resulted in an East Asian-Tethyan disjunction between Atractylodes and Carlina + Atractylis + Thevenotia. In addition, Late Miocene to Quaternary climates and sea level fluctuations played major roles in the diversification of Atractylodes. Through this study of different taxonomic levels using genomic data, we have revealed an overlooked dispersal route between the Mediterranean and far East Asia (Japan/Korea) via Central Asia and East China.
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Affiliation(s)
| | | | - Hans Peter Comes
- Department of Biosciences, Salzburg University, Salzburg, Austria
| | - Li Zheng
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Jiaxing Second Hospital, Jiaxing, Zhejiang, China
| | - Tetsuo Ohi-Toma
- Nature Fieldwork Center, Okayama University of Science, Okayama, Japan
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, South Korea
| | - Zhechen Qi
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Kamil Konowalik
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631, Wroclaw, Poland
| | - Pan Li
- For correspondence. E-email
| | | | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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Resolving species-level diversity of Beringiana and Sinanodonta mussels (Bivalvia: Unionidae) in the Japanese archipelago using genome-wide data. Mol Phylogenet Evol 2022; 175:107563. [PMID: 35809852 DOI: 10.1016/j.ympev.2022.107563] [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: 11/07/2021] [Revised: 06/04/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
Abstract
Accurate species identification is of primary importance in ecology and evolutionary biology. For a long time, the unionid mussels Beringiana and Sinanodonta have puzzled researchers trying to unravel their diversity because of their poorly discernible morphologies. A recent study conducted species delineation of unionid mussels based on mitochondrial DNA variation, opening up a new avenue to grasp species diversity of the mussels. However, mtDNA-based classification may not align with species boundaries because mtDNA is prone to introgression and incomplete lineage sorting that cause discordance between species affiliation and gene phylogeny. In this study, we evaluated the validity of the mtDNA-based classification of unionid mussels Beringiana and Sinanodonta in Japan using mitochondrial sequence data, double digest restriction site-associated DNA library (ddRAD) sequencing, and morphological data. We found significant inconsistencies in the mitochondrial and nuclear DNA phylogenies, casting doubt on the reliability of the mtDNA-based classification in this group. In addition, nuclear DNA phylogeny revealed that there are at least two unionid lineages hidden in the mtDNA phylogeny. Although molecular dating technique indicates that Beringiana and Sinanodonta diverged >35 million years ago, their shell morphologies are often indistinguishable. Specifically, morphological analyses exhibited the parallel appearance of nearly identical ball-like shell forms in the two genera in Lake Biwa, which further complicates species identification and the morphological evolution of unionid mussels. Our study adds to a growing body of literature that accurate species identification of unionid mussels is difficult when using morphological characters alone. Although mtDNA-based classification is a simple and convenient way to classify unionid mussels, considerable caution is warranted for its application in ecological and evolutionary studies.
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10
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Suzuki Y, Hiramatsu T, Tatsuta H. Two new species and a new genus of ray spiders (Araneae, Theridiosomatidae) from the Ryukyu Islands, southwest Japan, with notes on their natural history. Zookeys 2022; 1109:67-101. [PMID: 36762341 PMCID: PMC9848742 DOI: 10.3897/zookeys.1109.83807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/16/2022] [Indexed: 11/12/2022] Open
Abstract
This paper provides descriptions of two new theridiosomatid species, Theridiosomanigrivirgatum sp. nov. and Sennintanikawai gen. nov., sp. nov. from the Ryukyu Islands, southwest Japan, with photographs and illustrations of both sexes. Sennin gen. nov. is a troglophilic genus composed of two species, S.tanikawai sp. nov. (Iriomote Island, Japan) and S.coddingtoni (Zhu, Zhang & Chen, 2001), comb. nov. (southern China). Zomadibaiyin Miller, Griswold & Yin, 2009, which recently joined the Japanese fauna, was morphologically reexamined based on specimens from the Ryukyus, and taxonomic features of Zoma males were reassessed. A distributional map of theridiosomatid spiders in the Ryukyus is also provided, including T.dissimulatum Suzuki, Serita & Hiramatsu, 2020, and T.alboannulatum Suzuki, Serita & Hiramatsu, 2020 with their habitat types, web morphology, and web-building behavior in detail.
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Affiliation(s)
- Yuya Suzuki
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Korimoto, Kagoshima-shi, Kagoshima, 890-0065, JapanKagoshima UniversityKagoshimaJapan,Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395 JapanKyushu UniversityMotookaJapan
| | - Takehisa Hiramatsu
- Fregrance-Uwado 203, Uwado, Kawagoe-shi, Saitama, 350-0816, JapanUnaffiliatedSaitamaJapan
| | - Haruki Tatsuta
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395 JapanKyushu UniversityMotookaJapan
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11
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Cultural transmission of traditional songs in the Ryukyu Archipelago. PLoS One 2022; 17:e0270354. [PMID: 35749479 PMCID: PMC9231793 DOI: 10.1371/journal.pone.0270354] [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: 10/08/2021] [Accepted: 06/08/2022] [Indexed: 11/19/2022] Open
Abstract
Geographic patterns of cultural variations are affected by how cultural traits are transmitted within and between populations. It has been argued that cultural traits are transmitted in different manners depending on their characteristics; for example, words for basic concepts are less liable to horizontal transmission between populations (i.e., borrowing) than other words. Here we examine the geographic variation of traditional songs in the Ryukyu Archipelago, southwestern islands of Japan, to explore cultural evolution of music with a focus on different social contexts in which songs are sung. Published scores of 1,342 traditional songs are coded using the CantoCore song classification scheme and distances between the songs are calculated from the codings. Neighbor-Net graphs of regions/islands are generated on the basis of the musical distances, and delta scores are obtained to examine the treelikeness of the networks. We also perform analysis of molecular variance (AMOVA) to evaluate the extent of musical diversification among regions/islands. Our results suggest that horizontal transmission between populations has played a greater role in the formation of musical diversity than that of linguistic diversity in the Ryukyu Archipelago and that the social context in which songs are sung has an effect on how they are transmitted within and between populations. In addition, we compare the observed patterns of song diversity among regions/islands with those of lexical and mitochondrial-DNA (mtDNA) diversity, showing that the variation of songs sung in the "work" context are associated with the linguistic variation, whereas no association is found between the musical and genetic variation.
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Chang JT, Chao CT, Nakamura K, Liu HL, Luo MX, Liao PC. Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data. FRONTIERS IN PLANT SCIENCE 2022; 13:824158. [PMID: 35615129 PMCID: PMC9125193 DOI: 10.3389/fpls.2022.824158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The divergence process of incipient species is fascinating but elusive by incomplete lineage sorting or gene flow. Species delimitation is also challenging among those morphologically similar allopatric species, especially when lacking comprehensive data. Cycas sect. Asiorientales, comprised of C. taitungensis and C. revoluta in the Ryukyu Archipelago and Taiwan, diverged recently with continuous gene flow, resulting in a reciprocal paraphyletic relationship. Their previous evolutionary inferences are questioned from few genetic markers, incomplete sampling, and incomprehensive morphological comparison by a long-term taxonomic misconception. By whole range sampling, this study tests the geographic mode of speciation in the two species of Asiorientales by approximate Bayesian computation (ABC) using genome-wide single nucleotide polymorphisms (SNPs). The individual tree was reconstructed to delimit the species and track the gene-flow trajectory. With the comparison of diagnostic morphological traits and genetic data, the allopatric speciation was rejected. Alternatively, continuous but spatially heterogeneous gene flow driven by transoceanic vegetative dispersal and pollen flow with contrasting population sizes blurred their species boundary. On the basis of morphological, genetic, and evolutionary evidence, we synonymized these two Cycas species. This study highlights not only the importance of the Kuroshio Current to species evolution but also the disadvantage of using species with geographically structured genealogies as conservation units.
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Affiliation(s)
- Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Hsiao-Lei Liu
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
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13
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Kim C, Kim DK, Sun H, Kim JH. Phylogenetic relationship, biogeography, and conservation genetics of endangered Fraxinus chiisanensis (Oleaceae), endemic to South Korea. PLANT DIVERSITY 2022; 44:170-180. [PMID: 35505990 PMCID: PMC9043305 DOI: 10.1016/j.pld.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/03/2021] [Accepted: 06/13/2021] [Indexed: 06/14/2023]
Abstract
Endemic plants are important for understanding phylogenetic relationships, biogeographical history, and genetic variation because of their restricted distribution and their role in conserving biodiversity. Here, we investigated the phylogenetic relationships of the Korean endemic Fraxinus chiisanensis by reconstructing the molecular phylogeny of Fraxinus based on two nuclear DNA (nrITS and phantastica) and two chloroplast DNA (psbA-trnH and rpl32-trnL) regions. Within our fossil-calibrated phylogenetic framework, we also inferred the biogeographical history of F. chiisanensis. To provide a scientific basis for the conservation of F. chiisanensis, we determined the levels of genetic diversity and genetic differentiation in this species. Combining information from nuclear and chloroplast DNA sequence data, our molecular phylogenetic analyses identified F. chiisanensis as a genetically distinct unit from its sister group, Fraxinus platypoda from Japan. Our molecular dating analyses using nuclear and chloroplast DNA data sets show F. chiisanensis diverged from its sister F. platypoda in the Early or Middle Miocene and differentiated in the Late Miocene on the Korean Peninsula. Our results suggest that the divergence of F. chiisanensis was associated with the submergence of the East China Sea land bridge and enhanced monsoons in East Asia. When compared to F. platypoda, F. chiisanensis exhibits low genetic diversity within populations and high genetic differentiation among populations. These results help us to understand the evolutionary history of F. chiisanensis and to develop a conservation strategy for this species.
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Affiliation(s)
- Changkyun Kim
- Plant Research Division, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
| | - Dong-Kap Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon 11186, Republic of Korea
| | - Hang Sun
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, Yunnan, PR China
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam 13120, Republic of Korea
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14
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Liu H, Tong Y, Zheng Y, Li S, Hou Z. Sea–land transition drove terrestrial amphipod diversification in East Asia, with a description of a new species. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Sea–land transition caused by marine incursion and regression is hypothesized to be a major driving force in terrestrial biodiversity, providing opportunities for marine ancestors to colonize terrestrial habitats and driving vicariant speciation in distinct geographical regions. Here, we test this hypothesis in East Asia using amphipods of the Morinoia japonica complex. We constructed a dataset from 269 individuals covering all known ranges of this species complex. Phylogenetic and biogeographic analyses revealed that sea–land transition during the Miocene drove the coastal ancestor to invade terrestrial habitats in East Asia and subsequently split into eight biogeographic lineages in eastern China, Korea, Japan and some Pacific islands. Stepping-stone dispersal resulted in a relatively wide distribution of M. japonica, and long-term geographical isolation led to the diversification of the M. japonica complex. Species delimitation analysis suggests that this complex contains eight species. We describe the geographical group from eastern China as a new species, Morinoia aosen sp. nov., based on genetic and morphological comparisons with other geographical groups. Type specimens are deposited in the Institute of Zoology, Chinese Academy of Sciences (IZCAS) in Beijing, China.
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Affiliation(s)
- Hongguang Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Tong
- College of Life Science, Anhui Normal University, Wuhu 241000, China
| | - Yami Zheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhonge Hou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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15
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Hirano T, Saito T, Viktor von Oheimb P, C M von Oheimb K, Van Do T, Yamazaki D, Kameda Y, Chiba S. Patterns of diversification of the operculate land snail genus Cyclophorus (Caenogastropoda: Cyclophoridae) on the Ryukyu Islands, Japan. Mol Phylogenet Evol 2022; 169:107407. [PMID: 35031464 DOI: 10.1016/j.ympev.2022.107407] [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: 05/03/2021] [Revised: 12/14/2021] [Accepted: 01/06/2022] [Indexed: 11/24/2022]
Abstract
The Ryukyu Islands, an island chain in southwestern Japan, originated from land masses that separated from the Eurasian continent due to the formation of sea barriers about 1.55 million years ago. In this study, we investigated the phylogenetic relationships of the operculate land snail genus Cyclophorus (Caenogastropoda: Cyclophoridae) in the Ryukyu Archipelago and surrounding regions based on DNA sequence data. According to our results, all studied Cyclophorus specimens from Japan form a monophyletic group containing eight subclades. Six of these subclades were found only on the Ryukyu Islands. On most islands of the Ryukyu Archipelago, no more than one Cyclophorus subclade was recorded, which may be due to limited ecological niche space and competition. No subclade was found to occur on both sides of the Watase Line, a regional zoogeographical boundary. Divergence times were estimated based on a time-calibrated phylogeny. We found that multiple splits among the Japanese Cyclophorus subclades predate the emergence of major sea barriers in the Ryukyu Archipelago. Vicariance due to sea barrier formation, as assumed for many other taxa from the region, was thus likely not the main driver for subclade divergence in these snails. Instead, certain geographical features might have shaped the diversification of subclades prior to sea barrier formation. Given that Cyclophorus populations were also present on islands that have never been connected to other land masses, the snails must have colonized them via oversea dispersal. As not all nominal taxa corresponded to monophyletic groups, our molecular phylogenetic approach revealed that a taxonomic revision of the Japanese Cyclophorus fauna is necessary. The eight subclades may be regarded as potential species-level groups based on COI p-distances. A canonical discriminant analysis using shell morphological data revealed slight differences among the subclades.
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Affiliation(s)
- Takahiro Hirano
- Centre of Northeast Asian Studies, Tohoku University, Sendai, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
| | - Takumi Saito
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Parm Viktor von Oheimb
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Katharina C M von Oheimb
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Tu Van Do
- Department of Aquatic Ecology and Water Environment, Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Vietnam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Daishi Yamazaki
- Centre of Northeast Asian Studies, Tohoku University, Sendai, Miyagi, Japan
| | - Yuichi Kameda
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tokyo, Tsukuba, Ibaraki, Japan
| | - Satoshi Chiba
- Centre of Northeast Asian Studies, Tohoku University, Sendai, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
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16
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Sata N, Nakano T. Insights into the phylogenetic position and phylogeography of the monospecific skink-parasite genus. INVERTEBR SYST 2022. [DOI: 10.1071/is21026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Neoentomelas asatoi Hasegawa, 1989 is a parasitic nematode that infests only the scincid lizard Ateuchosaurus pellopleurus (Hallowell, 1861) that inhabits the forest floor in the Northern and Central Ryukyu Archipelago, Japan. As a member of Rhabdiasidae, the reproductive mode of N. asatoi is characterised by the alternation of the protandrous hermaphroditic mode and gonochoristic mode throughout the life cycle. The intrafamily phylogenetic position and intraspecific diversity of this nematode species were inferred by molecular phylogenetic analyses. The results revealed the phylogenetic distinctiveness of Neoentomelas Hasegawa, 1989 in Rhabdiasidae that supports the unique generic status of Neoentomelas within the family. The intraspecific phylogenetic analyses of N. asatoi revealed a minor concordant phylogenetic pattern with the host and mosaic geographic arrangement of the major clades that was discordant with the host. The analyses and distribution pattern of subclades suggested that this geographic arrangement can be explained by at least three dispersal events and subsequent switching to indigenous host populations. Colonisation events might be promoted by the high establishment rate of new populations stemming from the parthenogenesis-like reproduction mode of N. asatoi. This study demonstrated that reproductive modes can affect the intraspecific genetic diversity of parasites.
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17
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Dufresnes C, Litvinchuk SN. Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abstract
Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology & Environment, Nanjing Forestry University, Nanjing, China
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Biology, Dagestan State University, Makhachkala, Russia
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18
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Tsai TS, Wang YM, Tsai IH. Sequence determination and bioinformatic comparison of ten venom serine proteases of Trimeresurus gracilis, a Taiwanese endemic pitviper with controversial taxonomy. Toxicon 2021; 206:28-37. [PMID: 34929211 DOI: 10.1016/j.toxicon.2021.12.014] [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: 09/25/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022]
Abstract
Trimeresurus gracilis (Tgc) is endemic to Taiwan and shown to be closely related with Ovophis okinavensis by previous phylogenetic analyses, but their taxonomic status remain controversial. Here, we cloned and sequenced ten of its venom serine-proteases (designated as Tgc-vSPs). All the Tgc-vSPs conserve the catalytic triads, six appear to be kallikrein-like (KNs) and four are plasminogen-activator homologs (PAHs and PAs). They are studied under four structural categories: (1) highly similar Tgc-KN1, Tgc-KN2 and Tgc-KN3, with four predicted N-glycosylation sites; (2) Tgc-KN4, with a single N -glycosylation site; (3) Tgc-KN5 and Tgc-KN6, with two distinct N-glycosylation sites; (4) Tgc-PAH1/PAH2, TgcPA3, and Tgc-PA4, with two conserved N-glycosylation sites. Additionally, Tgc-KN1, Tgc-KN4 and Tgc-PAH1 were purified by reversed-phase HPLC and identified by peptide-mass-fingerprinting. Results of BLAST and sequence alignments reveal that Tgc-KN1∼3 and Tgc-KN6 are most like the vSPs of rattlesnakes, while the sequences of Tgc-KN4, KN5 and Tgc-PAH1/PAH2 match closely to the partial sequences of three O. okinavensis vSPs. Thus, our results reveal non-overlapping similarities of Tgc-vSPs to the O. okinavensis vSPs and vSPs of the New World pitvipers. In addition, molecular phylogenetic analyses of the plasminogen-activator like vSPs reveal separate evolution of two clusters of the enzymes with distinct functions.
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Affiliation(s)
- Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Ying-Ming Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Inn-Ho Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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19
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Smart U, Ingrasci MJ, Sarker GC, Lalremsanga H, Murphy RW, Ota H, Tu MC, Shouche Y, Orlov NL, Smith EN. A comprehensive appraisal of evolutionary diversity in venomous Asian coralsnakes of the genus
Sinomicrurus
(Serpentes: Elapidae) using Bayesian coalescent inference and supervised machine learning. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Utpal Smart
- Center for Human Identification University of North Texas Health Science Center Fort Worth Texas USA
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
| | - Matthew J. Ingrasci
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
| | - Goutam C. Sarker
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
| | | | - Robert W. Murphy
- Royal Ontario Museum Centre for Biodiversity and Conservation Biology Toronto ON Canada
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Kunming China
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences Museum of Nature and Human Activities University of Hyogo Sanda Japan
| | - Ming Chung Tu
- Department of Life Sciences National Taiwan Normal University Taipei City Taiwan
| | - Yogesh Shouche
- National Centre for Microbial ResourceNational Center for Cell Science Pune India
| | - Nikolai L. Orlov
- Zoological Institute Russian Academy of SciencesSaint Petersburg Russia
| | - Eric N. Smith
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
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Miyake T, Nakajima J, Umemura K, Onikura N, Ueda T, Smith C, Kawamura K. Genetic diversification of the Kanehira bitterling Acheilognathus rhombeus inferred from mitochondrial DNA, with comments on the phylogenetic relationship with its sister species Acheilognathus barbatulus. JOURNAL OF FISH BIOLOGY 2021; 99:1677-1695. [PMID: 34498257 DOI: 10.1111/jfb.14876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 07/23/2021] [Accepted: 08/08/2021] [Indexed: 06/13/2023]
Abstract
The Kanehira bitterling, Acheilognathus rhombeus, is a freshwater fish, discontinuously distributed in western Japan and the Korean Peninsula. Unusually among bitterling it is an autumn-spawning species and shows developmental diapause. Consequently, the characterization of its evolutionary history is significant not only in the context of the fish assemblage of East Asia, but also for understanding life-history evolution. This study aimed to investigate the phylogeography of A. rhombeus and its sister species Acheilognathus barbatulus, distributed in China, using a mitochondrial analysis of the ND1 gene from 311 samples collected from 50 localities in Japan and continental Asia. Phylogenetic analysis revealed that A. barbatulus is included in A. rhombeus and genetically closer to Japanese A. rhombeus than to Korean A. rhombeus. Divergence of Korean A. rhombeus and A. barbatulus from Japanese A. rhombeus was estimated to be from the late Pliocene (3.44 Mya) and the early Pleistocene (1.98 Mya), respectively. Each event closely coincided with the time of the Japan Sea opening. Japanese A. rhombeus comprised seven lineages: three in Honshu and four in Kyushu. One lineage in central Kyushu was genetically closer to the Honshu lineages than to other lineages in northern Kyushu. Divergence of Japanese lineages was estimated to be from the early to middle Pleistocene (0.55-0.93 Mya), during a period of geological and paleoclimatic change, including volcanic activity. Population expansion in the late Pleistocene (<0.10 Ma) was suggested in many of the lineages, which accords with other freshwater fishes. Biogeographically the ancestral A. rhombeus/A. barbatulus was likely to have repeatedly colonized Japan from the continent through land bridges in the late Pliocene and the early Pleistocene. However, the close genetic relationship between Japanese A. rhombeus and A. barbatulus suggests another possibility, with the second colonization occurring in reverse, from Japan to China. The small genetic distance between them indicates that the colonization occurred later than colonization events of other freshwater fishes, including other bitterling species.
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Affiliation(s)
| | - Jun Nakajima
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Keitaro Umemura
- Fishery Research Laboratory, Kyushu University, Fukuoka, Japan
| | - Norio Onikura
- Fishery Research Laboratory, Kyushu University, Fukuoka, Japan
| | | | - Carl Smith
- Department of Ecology & Vertebrate Zoology, University of Łódź, Łódź, Poland
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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21
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The biogeographical history of giant earthworms of the Metaphire formosae species group (Clitellata: Megascolecidae) in Taiwan and the Ryukyu Archipelago, with the description of a new species from Yonagunijima, Southern Ryukyus. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00529-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Kanke E, Suzuki K, Sekiné K, Suzuki T, Hatta K, Yang MM, Tojo K. Unexpected population genetic structure in two closely related euphaeid damselflies from the Yaeyama and Taiwan Islands (Odonata: Euphaeidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
In general, population genetics theory predicts that a fragmented smaller population will contain relatively less genetic diversity than a larger population, and so will have a higher rate of genetic fixation due to random genetic drift or inbreeding. However, in this study, having analysed the genetic structure of the mitochondrial DNA COI region between two closely related euphaeid damselflies, we obtained unexpected results which contradict the theoretically expected patterns. Despite their geographical proximity, Euphaea yayeyamana was clearly genetically isolated on Ishigaki and Iriomote Islands, and no haplotype crossovers were observed. Even within each island, several diverse haplotypes were observed, indicating a significantly high haplotype intra-island diversity. However, the genetic diversity within Taiwan’s population of Euphaea formosa was significantly lower than that within either Ishigaki or Iriomote Island, even though Taiwan is significantly larger, with high mountain ranges that reach c. 4000 m a.s.l. and an abundance of habitats, all factors that should contribute to high genetic diversity. The current low diversity status for Taiwan’s population may be due to genetic bottleneck effects. In contrast, despite the very small population sizes of Ishigaki and Iriomote Islands coupled with the effects of glacial and interglacial geological events, they have maintained markedly high genetic diversity.
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Affiliation(s)
- Emi Kanke
- Department of Biology, Faculty of Science, Shinshu University, Asahi, Matsumoto, Nagano, Japan
| | - Kohei Suzuki
- Department of Biology, Faculty of Science, Shinshu University, Asahi, Matsumoto, Nagano, Japan
| | - Kazuki Sekiné
- Department of Biology, Faculty of Science, Shinshu University, Asahi, Matsumoto, Nagano, Japan
- Faculty of Geo-environmental Science, Rissho University, Magechi, Kumagaya, Saitama, Japan
| | - Tomoya Suzuki
- Department of Biology, Faculty of Science, Shinshu University, Asahi, Matsumoto, Nagano, Japan
| | - Kokichi Hatta
- Nagoya Women’s University, Shinji-cho, Mizuho Ward, Nagoya, Aichi, Japan
- Department of Entomology, National Chug Hsing University, South District, Taichung, Taiwan
| | - Man-Miao Yang
- Department of Entomology, National Chug Hsing University, South District, Taichung, Taiwan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Asahi, Matsumoto, Nagano, Japan
- Institute of Mountain Science, Shinshu University, Asahi, Matsumoto, Nagano, Japan
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Diversification of mandarin citrus by hybrid speciation and apomixis. Nat Commun 2021; 12:4377. [PMID: 34312382 PMCID: PMC8313541 DOI: 10.1038/s41467-021-24653-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.
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24
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Distribution and Genetic Diversity of the Amphibian Chytrid in Japan. J Fungi (Basel) 2021; 7:jof7070522. [PMID: 34210103 PMCID: PMC8307550 DOI: 10.3390/jof7070522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/28/2022] Open
Abstract
While research on frog chytrid fungus Batrachochytrium dendrobatidis (Bd), an infectious disease that threatens amphibian diversity, continues to advance worldwide, little progress has been made in Japan since around 2010. The reason for this is, which we pointed out in 2009, that the origin of frog chytrid fungus may be in the East Asian region, including Japan based on the Bd ITS-DNA variation, and as few cases of mass mortality caused by this fungus have been observed in wild amphibian populations in Japan, the interest of the Japanese government and the general public in Bd has waned. However, we believe that organizing the data obtained so far in Japan and distributing the status of frog chytrid fungus in Japan to the world will provide useful insight for future risk management of this pathogen. We collected more than 5500 swab samples from wild amphibians throughout Japan from 2009 to 2010. Then, we investigated the infection status using the Nested-PCR method. We sequenced the obtained DNA samples and constructed a maximum-parsimony (MP) tree to clarify the phylogenetic diversity of Bd. We detected Bd infection in 11 (nine native and two alien) amphibian species in Japan and obtained 44 haplotypes of Bd ITS-DNA. The MP tree showed a high diversity of Bd strains in Japan, suggesting that some strains belong to Bd-GPL and Bd-Brazil. Except for local populations of the Japanese giant salamanders Andrias japonicus in Honshu Island and the sword tail newts Cynops ensicauda in Okinawa Island, the Bd infection prevalence in native amphibian species was very low. The alien bullfrog Aquarana catesbeiana had high Bd infection rates in all areas where they were sampled. No Bd infection was detected in other native amphibians in the areas where giant salamanders, sword tail newts, and bullfrogs were collected, suggesting that many native amphibians are resistant to Bd infection. The sword tail newt of Okinawa Island had both the highest infectious incidence and greatest number of haplotypes. The giant salamanders also showed relatively high infection prevalence, but the infected strains were limited to those specific to this species. These two Caudata species are endemic to a limited area of Japan, and it was thought that they may have been refugia for Bd, which had been distributed in Japan Islands for a long time.
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Aoki D, Sakamoto H, Kitazawa M, Kryukov AP, Takagi M. Migration-tracking integrated phylogeography supports long-distance dispersal-driven divergence for a migratory bird species in the Japanese archipelago. Ecol Evol 2021; 11:6066-6079. [PMID: 34141203 PMCID: PMC8207368 DOI: 10.1002/ece3.7387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/02/2021] [Accepted: 02/20/2021] [Indexed: 11/10/2022] Open
Abstract
Long-distance dispersal (LDD) outside a species' breeding range contributes to genetic divergence. Previous phylogeographic studies of migratory bird species have not discriminated LDD from vicariant speciation in their diversification process. We conducted an integrative phylogeographic approach to test the LDD hypothesis, which predicts that a Japanese migratory bird subspecies diverged from a population in the coastal region of the East China Sea (CRECS) via LDD over the East China Sea (ECS). Haplotype networks of both mitochondrial and nuclear genes of its three subspecies were reconstructed to examine whether the Japanese subspecies of the Brown Shrike (Lanius cristatus superciliosus) diverged from an ancestral CRECS population. A species distribution model (SDM) for the Japanese subspecies was constructed using bioclimatic variables under the maximum entropy algorithm. It was projected backwards to the climate of the last glacial maximum (LGM) to infer the candidate source area of colonization. A migratory route of L. c. superciliosus, which possibly reflects a candidate past colonization route, was tracked by light-level geolocators. Molecular phylogenetic networks suggest that the Japanese subspecies diverged from a population in the CRECS and maintained anciently diverged haplotypes. The SDM inferred that the emerged continental shelf of the ECS and the present CRECS were suitable breeding areas for the Japanese subspecies during the LGM. A major migratory route for L. c. superciliosus was inferred between the CRECS and the Japanese archipelago across the ECS. Our integrative approach supported the LDD hypothesis for divergence of the Japanese subspecies of the Brown Shrike. Shrinkage of the ECS may have been responsible for successful population establishment, due to a sufficient number of migrants overshooting to the Japanese archipelago from the CRECS. Our framework provides a new phylogeographic scenario for this region. Discriminating LDD and vicariance models helps improve our understanding of the phylogeographic histories of migratory species.
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Affiliation(s)
- Daisuke Aoki
- Department of Natural History SciencesGraduate School of ScienceHokkaido UniversitySapporoJapan
| | - Haruna Sakamoto
- Department of Natural History SciencesGraduate School of ScienceHokkaido UniversitySapporoJapan
| | - Munehiro Kitazawa
- Frontiers in Environmental SciencesGraduate School of AgricultureHokkaido UniversitySapporoJapan
| | - Alexey P. Kryukov
- Laboratory of Evolutionary Zoology and GeneticsFederal Scientific Center of the East Asia Terrestrial BiodiversityFar Eastern Branch of the Russian Academy of SciencesVladivostokRussia
| | - Masaoki Takagi
- Department of Natural History SciencesFaculty of ScienceHokkaido UniversitySapporoJapan
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Pfingstl T, Wagner M, Hiruta SF, Bardel‐Kahr I, Hagino W, Shimano S. Geological and paleoclimatic events reflected in phylogeographic patterns of intertidal arthropods (Acari, Oribatida, Selenoribatidae) from southern Japanese islands. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - Shimpei F. Hiruta
- Center for Molecular Biodiversity Research National Museum of Nature and Science Tsukuba Japan
| | | | - Wataru Hagino
- Department of Bioresources Engineering National Institute of Technology Okinawa College Nago‐City Japan
| | - Satoshi Shimano
- Science Research Center Hosei University Tokyo Japan
- International Center for Island Studies Amami Station Kagoshima University Kagoshima Japan
- Graduate School of Science Tokyo Metropolitan University Tokyo Japan
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Kuraishi N, Matsui M, Ota H, Eto K. Unique Evolution of Hyla hallowellii Among Amphibians of the Central Ryukyus, Japan (Anura: Hylidae). Zoolog Sci 2021; 38:112-121. [PMID: 33812351 DOI: 10.2108/zs200105] [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: 07/22/2020] [Accepted: 09/21/2020] [Indexed: 11/17/2022]
Abstract
Fauna of the Central Ryukyus includes a high percentage of endemic species, and Hallowell's tree frog Hyla hallowellii Thompson, 1912 is one of such elements, occurring in a total of eight islands in the Amami and Okinawa Island groups. Using samples representing all of these eight island populations, we studied variations in morphology, karyotype, allozyme, and mtDNA, to clarify the pattern of geographic differentiation of H. hallowellii and consider factors for its formation. We could not clearly discriminate one population from another in morphology, nor could we find any interpopulation difference in karyotype. From genetic analyses, using allozymes and cyt b, we found low overall differentiations among populations. However, the southern populations from Okinawajima and Yoronjima were genetically nearly identical with the northern Amamioshima population. From that group the geographically intermediate Tokunoshima and Kakeromajima populations showed prominent differentiations. These patterns of geographical differentiation greatly differ from those known in other amphibian species of the Central Ryukyus, and suggest that H. hallowellii has evolutionary history unique to the species.
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Affiliation(s)
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan,
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences, University of Hyogo, Museum of Nature and Human Activities, Sanda, Hyogo 669-1546, Japan
| | - Koshiro Eto
- Kitakyushu Museum of Natural History & Human History, Yahatahigashi, Kitakyushu, Fukuoka 805-0071, Japan
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Jin DP, Park JS, Choi BH. Historical migration and taxonomic entity of Korean endemic shrub Lespedeza maritima (Fabaceae) based on microsatellite loci. AOB PLANTS 2021; 13:plab009. [PMID: 33767807 PMCID: PMC7983312 DOI: 10.1093/aobpla/plab009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/11/2021] [Indexed: 07/06/2023]
Abstract
Various plant species are endemic to the Korean Peninsula, but their evolutionary divergence and establishment are poorly understood. One of these, Lespedeza maritima, has been proposed as either a hybrid (L. cyrtobotrya × L. maximowiczii) or a synonym of L. thunbergii. A distinct taxon, L. uekii, has been proposed for inland populations. We investigated genetic diversity and structure in L. maritima and related taxa to resolve this. Genotypes of L. maritima (n = 244, including L. uekii) were determined using 12 microsatellite loci, then compared with those of related species. Genetic diversity within L. maritima was estimated, and Bayesian clustering analysis was used to represent its genetic structure and that of related taxa. Its distribution during the last glacial maximum (LGM) was predicted using ecological niche modelling (ENM). Neighbour-joining (NJ) analysis and principal coordinate analysis (PCoA) were used to investigate relationships among species. Bayesian tree based on nuclear ribosomal internal transcribed spacers (nrITS) was also reconstructed to show relationships and divergence time among species. Morphological features were examined using flower characteristics. In result, expected heterozygosity (H E) and allelic richness (A R) within L. maritima were higher in southern than northern populations. Bayesian clustering analysis largely assigned populations to two clusters (K = 2) (south vs. north). The ENM showed that L. maritima occurred around the East China Sea and Korean Strait land bridge during the LGM. Compared with other Lespedeza species, L. maritima was assigned to an independent cluster (K = 2-5), supported by the NJ, PCoA, Bayesian tree and morphological examination results. Lespedeza maritima and L. uekii were clustered to one clade on Bayesian tree. Given results, current L. maritima populations derive from post-LGM colonization away from southern refugia. The type L. uekii, which grows inland, is thought synonym of L. maritima. In addition, L. maritima is considered a distinct species, compared with related taxa.
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Affiliation(s)
- Dong-Pil Jin
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jong-Soo Park
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Byoung-Hee Choi
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
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Lin KP, Chaw SM, Lo YH, Kinjo T, Tung CY, Cheng HC, Liu Q, Satta Y, Izawa M, Chen SF, Ko WY. Genetic Differentiation and Demographic Trajectory of the Insular Formosan and Orii's Flying Foxes. J Hered 2021; 112:192-203. [PMID: 33675222 PMCID: PMC8006818 DOI: 10.1093/jhered/esab007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/24/2021] [Indexed: 12/04/2022] Open
Abstract
Insular flying foxes are keystone species in island ecosystems due to their critical roles in plant pollination and seed dispersal. These species are vulnerable to population decline because of their small populations and low reproductive rates. The Formosan flying fox (Pteropus dasymallus formosus) is one of the 5 subspecies of the Ryukyu flying fox. Pteropus dasymallus formosus has suffered from a severe decline and is currently recognized as a critically endangered population in Taiwan. On the contrary, the Orii's flying fox (Pteropus dasymallus inopinatus) is a relatively stable population inhabiting Okinawa Island. Here, we applied a genomic approach called double digest restriction-site associated DNA sequencing to study these 2 subspecies for a total of 7 individuals. We detected significant genetic structure between the 2 populations. Despite their contrasting contemporary population sizes, both populations harbor very low degrees of genetic diversity. We further inferred their demographic history based on the joint folded site frequency spectrum and revealed that both P. d. formosus and P. d. inopinatus had maintained small population sizes for a long period of time after their divergence. Recently, these populations experienced distinct trajectories of demographic changes. While P. d. formosus suffered from a drastic ~10-fold population decline not long ago, P. d. inopinatus underwent a ~4.5-fold population expansion. Our results suggest separate conservation management for the 2 populations-population recovery is urgently needed for P. d. formosus while long-term monitoring for adverse genetic effects should be considered for P. d. inopinatus.
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Affiliation(s)
- Kung-Ping Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yun-Hwa Lo
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | - Chien-Yi Tung
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | - Quintin Liu
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Masako Izawa
- Kitakyushu Museum of Natural History and Human History, Fukuoka, Japan
| | - Shiang-Fan Chen
- Center for General Education, National Taipei University, New Taipei City, Taiwan
| | - Wen-Ya Ko
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
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30
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Chen S, Juan C, Rossiter SJ, Kinjo T, Fukui D, Kawai K, Tsang SM, Veluz MJ, Sakurai H, Lin H, Jang‐Liaw N, Osawa K, Ko W, Izawa M. Population genetic structure of the insular Ryukyu flying fox
Pteropus dasymallus. Biotropica 2021. [DOI: 10.1111/btp.12897] [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]
Affiliation(s)
- Shiang‐Fan Chen
- Center for General Education National Taipei University New Taipei City Taiwan
| | - Chung‐Hao Juan
- Center for General Education National Taipei University New Taipei City Taiwan
| | | | | | - Dai Fukui
- The University of Tokyo Hokkaido Forest The University of Tokyo Hokkaido Japan
| | - Kuniko Kawai
- Department of Biology Tokai University Hokkaido Japan
| | - Susan M. Tsang
- Department of Mammalogy American Museum of Natural History New York NY USA
- Mammalogy Section National Museum of Natural History Manila Philippines
| | | | | | - Hua‐Ching Lin
- Forestry Bureau Council of Agriculture Taipei Taiwan
| | | | | | - Wen‐Ya Ko
- Department of Life Sciences and Institute of Genome Sciences National Yang‐Ming University Taipei Taiwan
| | - Masako Izawa
- Biology Program Faculty of Science University of the Ryukyus Okinawa Japan
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Sato Y, Tsurui‐Sato K, Katoh M, Kimura R, Tatsuta H, Tsuji K. Population genetic structure and evolution of Batesian mimicry in Papilio polytes from the Ryukyu Islands, Japan, analyzed by genotyping-by-sequencing. Ecol Evol 2021; 11:872-886. [PMID: 33520172 PMCID: PMC7820160 DOI: 10.1002/ece3.7092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 01/03/2023] Open
Abstract
Batesian mimicry is a striking example of Darwinian evolution, in which a mimetic species resembles toxic or unpalatable model species, thereby receiving protection from predators. In some species exhibiting Batesian mimicry, nonmimetic individuals coexist as polymorphism in the same population despite the benefits of mimicry. In a previous study, we proposed that the abundance of mimics is limited by that of the models, leading to polymorphic Batesian mimicry in the swallowtail butterfly, Papilio polytes, on the Ryukyu Islands in Japan. We found that their mimic ratios (MRs), which varied among the Islands, were explained by the model abundance of each habitat, rather than isolation by distance or phylogenetic constraint based on the mitochondrial DNA (mtDNA) analysis. In the present study, this possibility was reexamined based on hundreds of nuclear single nucleotide polymorphisms (SNPs) of 93 P. polytes individuals from five Islands of the Ryukyus. We found that the population genetic and phylogenetic structures of P. polytes largely corresponded to the geographic arrangement of the habitat Islands, and the genetic distances among island populations show significant correlation with the geographic distances, which was not evident by the mtDNA-based analysis. A partial Mantel test controlling for the present SNP-based genetic distances revealed that the MRs of P. polytes were strongly correlated with the model abundance of each island, implying that negative frequency-dependent selection interacting with model species shaped and maintained the mimetic polymorphism. Taken together, our results support the possibility that predation pressure, not isolation by distance or other neutral factors, is a major driving force of evolution of the Batesian mimicry in P. polytes from the Ryukyus.
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Affiliation(s)
- Yukuto Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Kaori Tsurui‐Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Mitsuho Katoh
- Department of Agro‐Environmental SciencesFaculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Ryosuke Kimura
- Department of Human Biology and AnatomyGraduate School of MedicineUniversity of the RyukyusOkinawaJapan
| | - Haruki Tatsuta
- Department of Agro‐Environmental SciencesFaculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Kazuki Tsuji
- Department of Agro‐Environmental SciencesFaculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
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Ihara Y, Koike N, Nakano T. Integrative taxonomy reveals multiple lineages of the spider genus Cybaeus endemic to the Ryukyu Islands, Japan (Arachnida : Araneae : Cybaeidae). INVERTEBR SYST 2021. [DOI: 10.1071/is20070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The epigean spiders of the genus Cybaeus L. Koch, 1868 are known to have diversified in western North America and the Japanese Archipelago. To date, ~80 species of Cybaeus are known from Japan, but they have not previously been recorded from the Ryukyu Islands that harbour a diversity of endemic species. Here we describe eight new species of Cybaeus from the Ryukyu Islands, extending the range of Cybaeus southward to the central Ryukyus. Both sexes of each of the new species are described, and their phylogenetic relationships are estimated using nuclear and mitochondrial gene markers. Although Cybaeus okumurai, sp. nov. and C. kumadori, sp. nov. possess genital features that are common in the other Japanese congeners, the other six species (C. yakushimensis, sp. nov., C. kodama, sp. nov., C. amamiensis, sp. nov., C. aikana, sp. nov., C. tokunoshimensis, sp. nov., and C. hikidai, sp. nov.) are characterised by an elongated embolus and tubular spermathecae. These unique genital characteristics and the phylogeny recovered here suggest that these features evolved independently among the Japanese and Ryukyu Cybaeus species. Phylogenetic analyses highlight an unusual biogeographical pattern in which C. yakushimensis and C. kodama endemic to Yakushima Island in the northern Ryukyus are related to species distributed in the central Ryukyus. In contrast, our phylogeny suggests that C. okumurai from Tanegashima Island in the northern Ryukyus is sister to C. ashikitaensis (Komatsu, 1968), distributed in Kyushu of the Japanese Archipelago. The retreat constructs and sympatric distribution of Cybaeus found among the Ryukyus are also briefly discussed.
ZooBank: urn:lsid:zoobank.org:pub:640D15AA-17F4-48EE-88B4-485CFF8FCD60
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Xu X, Su YC, Ho SYW, Kuntner M, Ono H, Liu F, Chang CC, Warrit N, Sivayyapram V, Aung KPP, Pham DS, Norma-Rashid Y, Li D. Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders. Syst Biol 2020; 70:1110-1122. [PMID: 33367903 DOI: 10.1093/sysbio/syaa098] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/24/2023] Open
Abstract
The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2,765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show that the crown group of Liphistiidae appeared in the mid-Cretaceous at 102 Ma (95% credibility interval 92-113 Ma), but it was not until the Neogene that much of the diversification within the family occurred in mainland Southeast and East Asia. This diversification was coincident with tectonic events such as the extension of the East Asian continental margin, as well as geological upheavals in Indochina induced by the collision between India and Asia. Our study highlights the important role of major tectonic events in shaping the evolutionary history, present-day diversity, and geographical distribution of mesothele and liphistiid spiders.
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Affiliation(s)
- Xin Xu
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, and Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei Province, China.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Yong-Chao Su
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Matjaž Kuntner
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei Province, China.,Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia.,Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA
| | - Hirotsugu Ono
- Department of Zoology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba-shi, Ibaraki-ken, Japan
| | - Fengxiang Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei Province, China
| | - Chia-Chen Chang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore
| | - Natapot Warrit
- Center of Excellence in Entomology and Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Varat Sivayyapram
- Center of Excellence in Entomology and Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Khin Pyae Pyae Aung
- Department of Zoology, University of Yangon, Kamayut Township, Pyay Road, Yangon, Myanmar.,Department of Biology, Taungoo Education College, Taungoo, Myanmar
| | - Dinh Sac Pham
- Department of Experimental Taxonomy and Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Y Norma-Rashid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Daiqin Li
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore
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Kolcsár LP, Kato D, Gamboa M, Watanabe K. Revision of Japanese species of Nipponomyia Alexander, 1924 (Diptera, Pediciidae). Zookeys 2020; 1000:71-105. [PMID: 33354136 PMCID: PMC7728730 DOI: 10.3897/zookeys.1000.55021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/15/2020] [Indexed: 12/02/2022] Open
Abstract
Japanese species of the genus Nipponomyia Alexander, 1924 are revised. Two new species, Nipponomyiaokinawensis Kolcsár & Kato, sp. nov. and N.yakushimensis Kolcsár & Kato, sp. nov. are described from the Ryukyu Islands. Images of habitus and wings, illustrations of male and female terminalia, and distribution maps are provided for the Japanese species. A key to the world species of Nipponomyia is added. DNA barcodes of three Japanese Nipponomyia are provided, representing the first barcodes from the genus.
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Affiliation(s)
- Levente-Péter Kolcsár
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Daichi Kato
- Echigo-Matsunoyama Museum of Natural Sciences, 'Kyororo', 1712-2 Matsunoyama, Tôkamachi, 942-1411, Japan
| | - Maribet Gamboa
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime 790-8577, Japan
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35
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Richmond JQ, Ota H, Grismer LL, Fisher RN. Influence of niche breadth and position on the historical biogeography of seafaring scincid lizards. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Niche breadth and position can influence diversification among closely related species or populations, yet limited empirical data exist concerning the predictability of the outcomes. We explored the effects of these factors on the evolution of the Emoia atrocostata species group, an insular radiation of lizards in the western Pacific Ocean and Indo-Australasia composed of both endemic and widespread species that differ in niche occupancy. We used molecular data and phylogeographical diffusion models to estimate the timing and patterns of range expansion, and ancestral reconstruction methods to infer shifts in ecology. We show evidence of multidirectional spread from a centre of origin in western Micronesia, and that the phyletic diversity of the group is derived from a putative habitat specialist that survives in the littoral zone. This species is composed of paraphyletic lineages that represent stages or possible endpoints in the continuum toward speciation. Several descendant species have transitioned to either strand or interior forest habitat, but only on remote islands with depauperate terrestrial faunas. Our results suggest that the atrocostata group might be in the early phases of a Wilsonian taxon cycle and that the capacity to tolerate salt stress has promoted dispersal and colonization of remote oceanic islands. Divergence itself, however, is largely driven by geographical isolation rather than shifts in ecology.
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Affiliation(s)
| | - Hidetoshi Ota
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - L Lee Grismer
- Department of Biology, La Sierra University, Riverside, CA, USA
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Lee Y, Ni G, Shin J, Kim T, Kern EMA, Kim Y, Kim SC, Chan B, Goto R, Nakano T, Park JK. Phylogeography of Mytilisepta virgata (Mytilidae: Bivalvia) in the northwestern Pacific: Cryptic mitochondrial lineages and mito-nuclear discordance. Mol Phylogenet Evol 2020; 157:107037. [PMID: 33278586 DOI: 10.1016/j.ympev.2020.107037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
The purplish bifurcate mussel Mytilisepta virgata is widely distributed and represents one of the major components of the intertidal community in the northwestern Pacific (NWP). Here, we characterized population genetic structure of NWP populations throughout nearly their whole distribution range using both mitochondrial (mtDNA cox1) and nuclear (ITS1) markers. Population genetic analyses for mtDNA cox 1 sequences revealed two monophyletic lineages (i.e., southern and northern lineages) geographically distributed according to the two different surface water temperature zones in the NWP. The timing of the lineage split is estimated at the Pliocene- mid-Pleistocene (5.49-1.61 Mya), which is consistent with the timing of the historical isolation of the East Sea/Sea of Japan from the South and East China Seas due to sea level decline during glacial cycles. Historical sea level fluctuation during the Pliocene-Pleistocene and subsequent adaptation of mussels to different surface water temperature zones may have contributed to shaping the contemporary genetic diversity and deep divergence of the two mitochondrial lineages. In contrast to mtDNA sequences, a clear lineage split between the two mitochondrial lineages was not found in ITS1 sequences, which showed a star-like structure composed of a mixture of southern and northern mitochondrial lineages. Possible reasons for this type of mito-nuclear discordance include stochastic divergence in the coalescent processes of the two molecular markers, or balancing selection under different marine environments. Cryptic speciation cannot be ruled out from these results, and future work using genomic analyses is required to address whether the thermal physiology of these mussels corresponds to the deep divergence of their mitochondrial genes and to test for the existence of morphologically indistinguishable but genetically separate cryptic species.
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Affiliation(s)
- Yucheol Lee
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Gang Ni
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, Shandong, China
| | - Jinkyung Shin
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Taeho Kim
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Elizabeth M A Kern
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Yuseob Kim
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do 16419, South Korea
| | - Benny Chan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ryutaro Goto
- Seto Marine Biological Laboratory, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan
| | - Tomoyuki Nakano
- Seto Marine Biological Laboratory, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea.
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Origin and intraspecific diversification of the scincid lizard Ateuchosaurus pellopleurus with implications for historical island biogeography of the Central Ryukyus of Japan. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Matsui M, Tominaga A. Distinct Species Status of a Microhyla from the Yaeyama Group of the Southern Ryukyus, Japan (Amphibia, Anura, Microhylidae). CURRENT HERPETOLOGY 2020. [DOI: 10.5358/hsj.39.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Sakyo, Kyoto 606–8501, JAPAN
| | - Atsushi Tominaga
- Department of Natural Sciences, Faculty of Education, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903–0213, JAPAN
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Identification of the population source of free-ranging cats threatening endemic species on Tokunoshima Island, Japan. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00528-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractFree-ranging cats Felis silvestris catus are harmful to endemic species, especially on islands. Effective management practices require an understanding of their habitat use and population source at the landscape level. We aimed to identify the source of the free-ranging cat population on Tokunoshima Island, Japan, which harbors a variety of endemic organisms as well as human settlements. Trapping data for the whole island were provided by local governments, and landscape factors (residential, agricultural, and woodlot areas and cattle barn density) affecting cat density were explored. An analysis of live-capture data indicated that the density (per 1 km2) of free-ranging cats was positively correlated with the densities of cattle barns and woodlot areas and negatively correlated with residential areas. An interview survey revealed that nearly half of the cattle barns feed free-ranging cats. The source habitat of free-ranging cats appears to be areas with a high density of cattle barns and a high percentage of woodlots in human-dominated landscapes. Feeding cats in cattle barns may strengthen the bottom-up process of population growth on the island. To reduce the impact of cats on endemic species on Tokunoshima Island, efforts to stop feeding cats in cattle barns are important. Reaching a consensus with stakeholders will require further studies of the ecological risks posed by free-ranging cats.
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Gorin VA, Solovyeva EN, Hasan M, Okamiya H, Karunarathna DS, Pawangkhanant P, de Silva A, Juthong W, Milto KD, Nguyen LT, Suwannapoom C, Haas A, Bickford DP, Das I, Poyarkov NA. A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae). PeerJ 2020; 8:e9411. [PMID: 32685285 PMCID: PMC7337035 DOI: 10.7717/peerj.9411] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/03/2020] [Indexed: 11/22/2022] Open
Abstract
Frogs of the genus Microhyla include some of the world's smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genus Microhyla remains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorial Glyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genus Microhyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species. Within the largest major clade of Microhyla are seven well-supported subclades that we identify as the M. achatina, M. fissipes, M. berdmorei, M. superciliaris, M. ornata, M. butleri, and M. palmipes species groups. The phylogenetic position of 12 poorly known Microhyla species is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show the Microhyla-Glyphoglossus assemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. While Glyphoglossus and Microhyla II remained within their ancestral ranges, Microhyla I expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of five Microhyla species groups independently, starting with the end Oligocene-early Miocene that coincides with an onset of seasonally dry climates in South Asia. Body size evolution modeling suggests that four groups of Microhyla have independently achieved extreme miniaturization with adult body size below 15 mm. Three of the five smallest Microhyla species are obligate phytotelm-breeders and we argue that their peculiar reproductive biology may be a factor involved in miniaturization. Body size increases in Microhyla-Glyphoglossus seem to be associated with a burrowing adaptation to seasonally dry habitats. Species delimitation analyses suggest a vast underestimation of species richness and diversity in Microhyla and reveal 15-33 undescribed species. We revalidate M. nepenthicola, synonymize M. pulverata with M. marmorata, and provide insights on taxonomic statuses of a number of poorly known species. Further integrative studies, combining evidence from phylogeny, morphology, advertisement calls, and behavior will result in a better systematic understanding of this morphologically cryptic radiation of Asian frogs.
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Affiliation(s)
- Vladislav A. Gorin
- Faculty of Biology, Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Mahmudul Hasan
- Department of Fisheries, Bangamata Sheikh Fazilatunnesa Mujib Science & Technology University, Jamalpur, Bangladesh
| | - Hisanori Okamiya
- Department of Biological Science, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
| | | | | | - Anslem de Silva
- Amphibia and Reptile Research Organization of Sri Lanka, Gampola, Sri Lanka
| | | | | | | | | | - Alexander Haas
- Center for Natural History, Universität Hamburg, Hamburg, Germany
| | | | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | - Nikolay A. Poyarkov
- Faculty of Biology, Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
- Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam
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Yamasaki YY, Takeshima H, Kano Y, Oseko N, Suzuki T, Nishida M, Watanabe K. Ecosystem size predicts the probability of speciation in migratory freshwater fish. Mol Ecol 2020; 29:3071-3084. [DOI: 10.1111/mec.15415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 02/13/2020] [Accepted: 03/05/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Yo Y. Yamasaki
- Graduate School of Science Kyoto University Sakyo Kyoto Japan
- Ecological Genetics Laboratory Department of Genomics and Evolutionary Biology National Institute of Genetics Mishima Shizuoka Japan
| | - Hirohiko Takeshima
- Research Institute for Humanity and Nature Kita Kyoto Japan
- Department of Marine Biology Tokai University Shimizu Shizuoka Japan
| | - Yuichi Kano
- Graduate Education and Research Training Programme in Decision Science for a Sustainable Society Kyushu University Fukuoka Japan
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Kobayashi G. Small-scale population genetic structure of the sand bubbler crab Scopimera ryukyuensis in the Ryukyu Islands, Japan. Mol Biol Rep 2020; 47:2619-2626. [PMID: 32140958 DOI: 10.1007/s11033-020-05350-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/25/2020] [Indexed: 11/29/2022]
Abstract
Generally, the gene flow of marine organisms is well maintained, but some local populations of coastal species are genetically differentiated even on a small scale (genetic patchiness). Small-scale isolation can be crucial for understanding genetic diversity within a species. The present study examined the population genetic structure of the sand bubbler crab Scopimera ryukyuensis, which is endemic to the Ryukyu Islands in the northwestern Pacific. A total of 52 haplotypes of mitochondrial cytochrome c oxidase subunit I were recovered from 197 specimens collected from four islands. The haplotype and nucleotide diversities were relatively high in the central Ryukyus (Amami-Oshima and Okinawa Islands) with some exceptions but were low at the southern edge of the geographical distribution of the species, i.e., the southern Ryukyus (Ishigaki and Iriomote Islands). Pairwise FST analysis suggested that the gene flow of S. ryukyuensis was largely restricted. The local populations of the species are differentiated among islands, except for stations on Ishigaki Island and a station on Iriomote Island. Moreover, a clear intra-island population genetic structure was observed within Amami-Oshima and Iriomote Islands, e.g., only 20 km between stations. Small-scale isolation among local populations may be a common tendency for coastal species in the Ryukyu Islands, considering the results of previous studies on corals.
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Affiliation(s)
- Genki Kobayashi
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama, 649-2211, Japan.
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43
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Gobioecetes longibasais n. sp. (Monogenea: Dactylogyridae) from Rhinogobius similis Gill (Perciformes: Gobiidae) from Okinawa-jima Island, the Ryukyu Archipelago, southern Japan, with a new host record for Gobioecetes biwaensis Ogawa & Itoh, 2017. Syst Parasitol 2020; 97:193-200. [PMID: 32065369 DOI: 10.1007/s11230-020-09905-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/11/2020] [Indexed: 10/25/2022]
Abstract
Gobioecetes longibasis n. sp. (Monogenea: Dactylogyridae) from the gills of the freshwater goby Rhinogobius similis Gill (Perciformes: Gobiidae) in the River Teima, Okinawa-jima Island, the Ryukyu Archipelago, southern Japan, is described. The new species is distinguished from two congeneric species of Gobioecetes Ogawa & Itoh, 2017, G. rhinogobius (Ling, 1973) and G. biwaensis Ogawa & Itoh, 2017, by having longer ventral hamuli, longer and wider internal process of the dorsal hamuli, and the ratio of dorsal hamulus length to base length. This new species is host-specific to R. similis and considered to be endemic to Okinawa-jima Island or the Ryukyu Archipelago. We also report Rhinogobius sp. OM from a tributary of Lake Biwa, Shiga Prefecture, central Japan, as a new host of G. biwaensis.
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44
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Pfingstl T, Wagner M, Hiruta SF, Koblmüller S, Hagino W, Shimano S. Phylogeographic patterns of intertidal arthropods (Acari, Oribatida) from southern Japanese islands reflect paleoclimatic events. Sci Rep 2019; 9:19042. [PMID: 31836729 PMCID: PMC6911088 DOI: 10.1038/s41598-019-55270-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/25/2019] [Indexed: 11/17/2022] Open
Abstract
The Japanese islands represent one of the world's biodiversity hotspots. Their geological history and present geography resulted in a high number of endemic species in nearly all major metazoan clades. We investigated the phylogeography of three different intertidal mite species from the Ryukyu islands and southern mainland by means of morphometry and molecular genetics. None of the species represents an endemic, nearly all show distributions ranging over at least the southern and central Ryukyus. Two species, Fortuynia shibai and F. churaumi sp. n. clearly represent sister species that are derived from a common Eastern ancestor. Molecular genetic results indicate that these species separated approx. 3 Ma before the opening of the Okinawa trough, whereas F. shibai most likely showed an ancestral distribution stretching from the central Ryukyus across the Tokara strait to Japanese mainland, whereas F. churaumi probably evolved somewhere south of the Tokara strait. Phylogenetic data further indicates that long periods of isolation resulted in heterogeneous genetic structure but subsequent low sea level stands during Pleistocene allowed recent expansion and gene flow between island populations. Comparing these patterns with those of other animals, these tiny wingless mites apparently show better dispersal abilities than partially volant terrestrial organism groups.
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Affiliation(s)
- Tobias Pfingstl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
| | - Maximilian Wagner
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Shimpei F Hiruta
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki, 305-0005, Japan
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Wataru Hagino
- Department of Bioresource Engineering, National Institute of Technology, Okinawa College, Henoko 905, Nago-City, Okinawa, 905-2192, Japan
| | - Satoshi Shimano
- Science Research Center, Hosei University, Fujimi 2-17-1 Chiyoda-ku, Tokyo, 102-8160, Japan
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Sanchez G, Jolly J, Reid A, Sugimoto C, Azama C, Marlétaz F, Simakov O, Rokhsar DS. New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis. Commun Biol 2019; 2:465. [PMID: 31840110 PMCID: PMC6906322 DOI: 10.1038/s42003-019-0661-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 10/22/2019] [Indexed: 01/17/2023] Open
Abstract
Bobtail squid are emerging models for host-microbe interactions, behavior, and development, yet their species diversity and distribution remain poorly characterized. Here, we combine mitochondrial and transcriptome sequences with morphological analysis to describe three species of bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu archipelago, and compare them with related taxa. One Ryukyuan type was previously unknown, and is described here as Euprymna brenneri sp. nov. Another Ryukyuan type is morphologically indistinguishable from Sepiola parva Sasaki, 1913. Molecular analyses, however, place this taxon within the genus Euprymna Steenstrup, 1887, and additional morphological investigation led to formal rediagnosis of Euprymna and reassignment of this species as Euprymna parva comb. nov. While no adults from the third Ryukyuan type were found, sequences from hatchlings suggest a close relationship with E. pardalota Reid, 2011, known from Australia and East Timor. The broadly sampled transcriptomes reported here provide a foundation for future phylogenetic and comparative studies.
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Affiliation(s)
- Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi Hiroshima, Hiroshima, Japan
| | - Jeffrey Jolly
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Amanda Reid
- Australian Museum Research Institute, 1 William Street, Sydney, Australia 2010
| | - Chikatoshi Sugimoto
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Chika Azama
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Ferdinand Marlétaz
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Daniel S. Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
- Department of Molecular and Cell Biology, Life Sciences Addition #3200, Berkeley, CA 94720-3200 USA
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Shao CC, Shen TT, Jin WT, Mao HJ, Ran JH, Wang XQ. Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae). Mol Phylogenet Evol 2019; 141:106610. [DOI: 10.1016/j.ympev.2019.106610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 01/21/2023]
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Lu RS, Chen Y, Tamaki I, Sakaguchi S, Ding YQ, Takahashi D, Li P, Isaji Y, Chen J, Qiu YX. Pre-quaternary diversification and glacial demographic expansions of Cardiocrinum (Liliaceae) in temperate forest biomes of Sino-Japanese Floristic Region. Mol Phylogenet Evol 2019; 143:106693. [PMID: 31778814 DOI: 10.1016/j.ympev.2019.106693] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/11/2019] [Accepted: 11/22/2019] [Indexed: 11/27/2022]
Abstract
The Sino-Japanese Floristic Region (SJFR) in East Asia is one of the most diverse temperate floras in the world. However, the relative influence of Neogene palaeogeographical changes and Quaternary climatic fluctuations as causal mechanisms on species diversification remains largely controversial, because most divergence time estimates were inferred from single-locus data and have limited geographic or taxonomic sampling. To evaluate these influences, we use SNP markers from restriction site-associated DNA sequencing (RAD-Seq) loci and expressed sequence tags-simple sequence repeat (EST-SSR) markers to investigate the levels of genetic variation, speciation and demographic history of the temperate-deciduous forest (TDF) endemic Cardiocrinum (Endlicher) Lindley (Liliaceae), a genus comprising three species in China (C. giganteum, C. cathayanum) and Japan (C. cordatum). Phylogenomic and population genomic coalescent-based analyses demonstrated that Late Neogene tectonic/climatic events triggered speciation of Cardiocrinum, and Pleistocene climatic fluctuations had limited influence on its divergence history. Population demographic inference using Approximate Bayesian Computation from EST-SSRs and palaeoclimatic niche models both indicated that all three Cardiocrinum species experienced population expansions during the transition from the LIG to the LGM. We also discussed the implications of these results on the conservation of montane TDF species in the SJFR under ongoing environmental change. Our results improve our understanding of how the constituents of montane TDF across the SJFR responded to previous periods of rapid climate and environmental change in terms of speciation and population demographic processes.
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Affiliation(s)
- Rui-Sen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu 501-3714, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yan-Qian Ding
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuji Isaji
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying-Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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48
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Han CC, Hsu KC, Fang LS, Cheng IM, Lin HD. Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan. BMC Genet 2019; 20:86. [PMID: 31752677 PMCID: PMC6868699 DOI: 10.1186/s12863-019-0788-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/31/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The freshwater species on Taiwan Island have been documented to have originated from mainland China and the Japanese islands from multiple events and by multiple colonization routes. Moreover, the sequences from the mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used for DNA barcoding to identify the species. This study used the COI sequences to identify Neocaridina species in Taiwan and to examine their geographical and temporal origins. RESULTS In total, 479 specimens were collected from 35 localities, which covered almost all rivers in Taiwan. In addition, some sequences were downloaded from GenBank. The maximum likelihood (ML) tree displayed that all sequences were sorted into 13 taxa (clades), and all sequences in Taiwan were sorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species have declined recently in Taiwan. CONCLUSIONS All results support that (1) there are four Neocaridina species in Taiwan, which are N. davidi, N. saccam, N. ketagalan and an undescribed Neocaridina species (N. sp.); (2) these four species colonized Taiwan Island in four colonization events; (3) N. sp. colonized Taiwan first; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from the Japanese islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan last; and (6) the cyclic glacial and landform changes in East Asia shaped the colonization events and population structures of the Neocaridina species.
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Affiliation(s)
- Chiao-Chuan Han
- National Museum of Marine Biology and Aquarium, Pingtung, 944 Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, 944 Taiwan
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088 China
| | - Lee-Shing Fang
- Center for Environmental Toxin and Emerging-Contaminant Research,Cheng Shiu University, Kaohsiung, 83347 Taiwan
- Department of Leisure and Sport Management, Cheng Shiu University, Kaohsiung, 83347 Taiwan
| | - I-Ming Cheng
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 80424 Taiwan
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, 701 Taiwan
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Igawa T, Sugawara H, Honda M, Tominaga A, Oumi S, Katsuren S, Ota H, Matsui M, Sumida M. Detecting inter- and intra-island genetic diversity: population structure of the endangered crocodile newt, Echinotriton andersoni, in the Ryukyus. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01219-8] [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]
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Tominaga A, Matsui M, Shimoji N, Khonsue W, Wu C, Toda M, Eto K, Nishikawa K, Ota H. Relict distribution of
Microhyla
(Amphibia: Microhylidae) in the Ryukyu Archipelago: High diversity in East Asia maintained by insularization. ZOOL SCR 2019. [DOI: 10.1111/zsc.12361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | - Naoko Shimoji
- Faculty of Education University of the Ryukyus Nishihara Japan
| | - Wichase Khonsue
- Department of Biology, Faculty of Science Chulalongkorn University Bangkok Thailand
| | - Chi‐Shiun Wu
- Department of Life Science Chinese Culture University Taipei Taiwan
| | - Mamoru Toda
- Tropical Biosphere Research Center University of the Ryukyus Nishihara Japan
| | - Koshiro Eto
- Kitakyushu Museum of Natural History & Human History Kitakyushu Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences University of Hyogo, and Museum of Nature and Human Activities Sanda Japan
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