101
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Magota K, Sakaguchi S, Hirota SK, Tsunamoto Y, Suyama Y, Akai K, Setoguchi H. Comparative analysis of spatial genetic structures in sympatric populations of two riparian plants, Saxifraga acerifolia and Saxifraga fortunei. AMERICAN JOURNAL OF BOTANY 2021; 108:680-693. [PMID: 33881773 DOI: 10.1002/ajb2.1644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
PREMISE The genetic structure between plant populations is facilitated by the spatial population arrangement and limited dispersal of seed and pollen. Saxifraga acerifolia, a local endemic species in Japan, is a habitat specialist that is confined to waterfalls in riparian environments. Its sister species, Saxifraga fortunei, is a generalist that is widely distributed along riverbanks. Here, we examined sympatric populations of the two Saxifraga species to test whether the differences in habitat preference and colonization process influenced regional and local genetic structures. METHODS To reveal genetic structures, we examined chloroplast microsatellite variations and genome-wide nucleotide polymorphisms obtained by genotyping by sequencing. We also estimated the gene flow among and within populations and performed landscape genetic analyses to evaluate seed and pollen movement and the extent of genetic isolation related to geographic distance and/or habitat differences. RESULTS We found strong genetic structure in the specialist S. acerifolia, even on a small spatial scale (<1 km part); each population on a different waterfall in one river system had a completely different predominant haplotype. By contrast, the generalist S. fortunei showed no clear genetic differentiation. CONCLUSIONS Our findings suggest that the level of genetic isolation was increased in S. acerifolia by the spatially fragmented habitat and limited seed and pollen dispersal over waterfalls. Habitat differentiation between the sister taxa could have contributed to the different patterns of gene flow and then shaped the contrasting genetic structures.
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Affiliation(s)
- Kana Magota
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto, 606-8501, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto, 606-8501, Japan
| | - Shun K Hirota
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihiro Tsunamoto
- Tohoku Research Center, Forestry and Forest Products Research Institute, 92-25 Nabeyashiki, Shimo-kuriyagawa, Morioka, Iwate, 020-0123, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Kensei Akai
- International Center for Island Studies Amami Station, Kagoshima University, Naze-Minatomachi 15-1, Amami, Kagoshima, 894-0026, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto, 606-8501, Japan
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102
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Hirata M, Mitsuyuki C, Moritsuka E, Chhang P, Tagane S, Toyama H, Sokh H, Rueangruea S, Suddee S, Suyama Y, Yahara T, Teshima KM, Tachida H, Kusumi J. Evaluating the genetic diversity in two tropical leguminous trees, Dalbergia cochinchinensis and D. nigrescens, in lowland forests in Cambodia and Thailand using MIG-seq. Genes Genet Syst 2021; 96:41-53. [PMID: 33731512 DOI: 10.1266/ggs.20-00026] [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] [Indexed: 11/23/2022] Open
Abstract
It is vital to measure the levels of genetic diversity and differentiation between populations in a species to understand the current genetic structure and evolution of the species. Here, MIG-seq (multiplexed inter-simple sequence repeat genotyping by sequencing) was employed to assess the genetic variation in two tropical leguminous tree species, Dalbergia cochinchinensis and D. nigrescens, in Cambodia and Thailand. Sequence data for 255-618 loci, each with an approximate length of 100 bp, were obtained, and the nucleotide diversity, Tajima's D and FST were computed. The estimates calculated from the data obtained by MIG-seq were compared to those obtained by Sanger sequencing of nine nuclear coding genes in D. cochinchinensis in our previous study. The nucleotide diversity at the MIG-seq loci was slightly higher than that at silent sites in the coding loci, whereas the FST values at the MIG-seq loci were generally lower than those at the coding loci, although the differences were not significant. Moreover, nucleotide diversities within populations of the two species were similar to each other, at approximately 0.005. Three and four population clusters were genetically recognized in D. cochinchinensis and D. nigrescens, respectively. Although the populations were differentiated from each other, the levels of differentiation among them, as measured by FST, were higher in D. cochinchinensis than in D. nigrescens. This indicates higher levels of gene flow between the populations in the latter species. We recommend using MIG-seq for quick surveys of genetic variation because it is cost-effective and results in smaller variance in the estimates of population genetic parameters.
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Affiliation(s)
- Moeko Hirata
- Graduate School of Systems Life Sciences, Kyushu University
| | | | - Etsuko Moritsuka
- Department of Biology, Faculty of Science, Kyushu University.,Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University
| | - Phourin Chhang
- Institute of Forest and Wildlife Research Development, Forestry Administration
| | - Shuichiro Tagane
- Department of Biology, Faculty of Science, Kyushu University.,The Kagoshima University Museum, Kagoshima University
| | - Hironori Toyama
- Department of Biology, Faculty of Science, Kyushu University.,Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies
| | - Heng Sokh
- Institute of Forest and Wildlife Research Development, Forestry Administration
| | - Sukid Rueangruea
- The Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation
| | - Somran Suddee
- The Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation
| | | | | | | | | | - Junko Kusumi
- Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University
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103
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Kobayashi H, Shirasawa K, Fukino N, Hirakawa H, Akanuma T, Kitashiba H. Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions. DNA Res 2021; 27:5739440. [PMID: 32065621 PMCID: PMC7315352 DOI: 10.1093/dnares/dsaa001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/11/2020] [Indexed: 11/24/2022] Open
Abstract
Radish (Raphanus sativus L.) is cultivated around the world as a vegetable crop and exhibits diverse morphological and physiological features. DNA polymorphisms are responsible for differences in traits among cultivars. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse radish accessions using the double-digest restriction site-associated DNA sequencing (ddRAD-Seq) method. A total of 52,559 SNPs was identified in a collection of over 500 radish accessions (cultivated and wild) from East Asia, South and Southeast Asia, and the Occident and Near East. In addition, 2,624 SNP sites without missing data (referred to as common SNP sites) were identified among 510 accessions. Genetic diversity analyses, based on the common SNP sites, divided the cultivated radish accessions into four main groups, each derived from four geographical areas (Japan, East Asia, South and Southeast Asia, and the Occident and Near East). Furthermore, we discuss the origin of cultivated radish and its migration from the West to East Asia. SNP data generated in this work will facilitate further genetic studies on the radish breeding and production of DNA markers.
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Affiliation(s)
- Hiroto Kobayashi
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Nobuko Fukino
- Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu 514-2392, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takashi Akanuma
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
| | - Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
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104
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Wachi N, Gau JJ, Fujie S, Fukano K, Maeto K. Genomic population structure of sympatric sexual and asexual populations in a parasitic wasp, Meteorus pulchricornis (Hymenoptera: Braconidae), inferred from six hundred single-nucleotide polymorphism loci. Mol Ecol 2021; 30:1612-1623. [PMID: 33634920 DOI: 10.1111/mec.15834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 01/22/2021] [Accepted: 02/04/2021] [Indexed: 11/28/2022]
Abstract
In spite of the two-fold reproductive advantage, asexual reproduction is not common in nature, probably due to the associated genetic deterioration or reduced genetic variation. To understand how genetic diversity is maintained in existing asexual populations, we investigated the genetic diversity and population structure of sympatric sexual and asexual populations of a parasitic wasp, Meteorus pulchricornis, using 614 genome-wide single nucleotide polymorphisms. The genetic structures of the apomictic asexual populations were distinct, showing considerable genetic differentiation among them. Most of the asexual populations were highly differentiated from the sympatric sexual population; some asexual individuals could not be distinguished from members of the sexual population. Furthermore, significantly fewer multilocus genotypes were identified in the asexual populations (1-7) compared to the sexual population (42), which is consistent with their apomictic nature. The observed patterns of fixed heterozygous sites suggest that most asexual populations had the same evolutionary origin and have long since evolved individually; the detected gene flow between the sexual population and a few asexual population may indicate independent origins of asexuality. The potential role of occasional males in apomictic wasps is also discussed.
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Affiliation(s)
- Nakatada Wachi
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Jin-Je Gau
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Shunpei Fujie
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan.,Osaka Museum of Natural History, Higashisumiyoshi, Osaka, Japan
| | - Kenya Fukano
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Kaoru Maeto
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
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105
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Kurata S, Sakaguchi S, Hirota SK, Kurashima O, Suyama Y, Nishida S, Ito M. Refugia within refugium of Geranium yesoense (Geraniaceae) in Japan were driven by recolonization into the southern interglacial refugium. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Recent studies have found that geographical fragmentation and recurrent colonization result in complex genetic structures in refugial areas. This phenomenon, known as ‘refugia within refugium’, has been identified from many geographical locations. In Japan, the high-elevation mountains of central Honshu provided an interglacial refugium for alpine plants. Here we focused on the Geranium yesoense complex, which exhibits increased morphological variation in the refugial area, to determine whether this variation was shaped by recurrent colonization, range fragmentation or phenotypic changes independent of population history. We analysed single nucleotide polymorphism data and chloroplast genome sequences. Diversification in the G. yesoense species complex occurred in the mid-Pleistocene. The varieties are distinct entities and suggest the presence of a genetic cluster with highly disjunct distributions, occurring both in northern Japan and in southern refugial areas in central Honshu. Demographic analysis suggests that a single ancestral variety (var. nipponicum) evolved in the alpine region of central Honshu, and that subsequent migration from one of the two diverged northern varieties (var. pseudopratense) led to secondary contact with var. nipponicum during the last glacial period. Recolonization into refugial populations in central Honshu and hybridization between diverged populations have resulted in complex genetic structures among refugial populations.
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Affiliation(s)
- Seikan Kurata
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Aza-yomogida, Naruko Onsen, Osaki City, Miyagi, Japan
| | - Osamu Kurashima
- National Museum of Nature and Science, Ueno-koen, Taito-ku, Tokyo, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Aza-yomogida, Naruko Onsen, Osaki City, Miyagi, Japan
| | - Sachiko Nishida
- Nagoya University Museum, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Motomi Ito
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
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106
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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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107
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High-Throughput Genotyping Technologies in Plant Taxonomy. Methods Mol Biol 2021; 2222:149-166. [PMID: 33301093 DOI: 10.1007/978-1-0716-0997-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Molecular markers provide researchers with a powerful tool for variation analysis between plant genomes. They are heritable and widely distributed across the genome and for this reason have many applications in plant taxonomy and genotyping. Over the last decade, molecular marker technology has developed rapidly and is now a crucial component for genetic linkage analysis, trait mapping, diversity analysis, and association studies. This chapter focuses on molecular marker discovery, its application, and future perspectives for plant genotyping through pangenome assemblies. Included are descriptions of automated methods for genome and sequence distance estimation, genome contaminant analysis in sequence reads, genome structural variation, and SNP discovery methods.
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108
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Park JS, Jin DP, Choi BH. Insights into genomic structure and evolutionary processes of coastal Suaeda species in East Asia using cpDNA, nDNA, and genome-wide SNPs. Sci Rep 2020; 10:20950. [PMID: 33262390 PMCID: PMC7708624 DOI: 10.1038/s41598-020-78041-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/27/2020] [Indexed: 11/30/2022] Open
Abstract
Species in the genus Suaeda have few diagnostic characters and substantial morphological plasticity. Hence, regional floras do not provide clear taxonomic information for Suaeda spp. in East Asia. In order to assess the taxonomy of four species in the genus Suaeda (S. australis, S. maritima, S. japonica, and S. heteroptera), cpDNA (rpl32-trnL and trnH-psbA), nDNA (ITS), and MIG-seq analyses were carried out. Genome-wide SNP results indicated three lineages: (1) S. australis in Korea and S. maritima in Japan, (2) S. maritima in Korea and S. heteroptera in China, and (3) S. japionica. In phylogenetic trees and genotype analyses, cpDNA and nDNA results showed discrepancies, while S. japonica and S. maritima in Korea, and S. heteroptera in China shared the same haplotype and ribotype. We suggest that the shared haplotype may be due to chloroplast capture. Based on our results, we assume that S. japonica was formed by homoploid hybrid speciation between the two lineages.
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Affiliation(s)
- Jong-Soo Park
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Dong-Pil Jin
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Byoung-Hee Choi
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
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109
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Zhang W, Liu K, Zhang P, Cheng W, Zhang Y, Li L, Yu Z, Chen M, Chen L, Li L, Zhang X. All-in-one approaches for rapid and highly specific quantifcation of single nucleotide polymorphisms based on ligase detection reaction using molecular beacons as turn-on probes. Talanta 2020; 224:121717. [PMID: 33378999 DOI: 10.1016/j.talanta.2020.121717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/17/2020] [Accepted: 09/28/2020] [Indexed: 11/27/2022]
Abstract
Rapid, simple, specific and sensitive approaches for single nucleotide polymorphisms (SNPs) detection are essential for clinical diagnosis. In this study, all-in-one approaches, consisting of the whole detection process including ligase detection reaction (LDR) and real time quantitative polymerase chain reaction performed in one PCR tube by a one-step operation on a real-time PCR system using molecular beacon (MB) as turn-on probe, were developed for rapid, simple, specific and sensitive quantifcation of SNPs. High specificity of the all-in-one approach was achieved by using the LDR, which employs a thermostable and single-base discerning Hifi Taq DNA ligase to ligate adjacently hybridized LDR-specific probes. In addition, a highly specific probe, MB, was used to detect the products of all-in-one approach, which doubly enhances the specificity of the all-in-one approach. The linear dynamic range and high sensitivity of mutant DNA (MutDNA) and wild-type DNA (WtDNA) all-in-one approaches for the detection of MutDNA and WtDNA were studied in vitro, with a broad linear dynamic range of 0.1 fM to 1 pM and detection limits of 65.3 aM and 31.2 aM, respectively. In addition, the MutDNA and WtDNA all-in-one approaches were able to accurately detect allele frequency changes as low as 0.1%. In particular, the epidermal growth factor receptor T790M MutDNA frequency in the tissue of five patients with non-small cell lung cancer detected by all-in-one approaches were in agreement with clinical detection results, indicating the excellent practicability of the developed approaches for the quantification of SNPs in real samples. In summary, the developed all-in-one approaches exhibited promising potential for further applications in clinical diagnosis.
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Affiliation(s)
- Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; Department of Pediatric Oncology Surgery, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Kangbo Liu
- Biological Testing Room, Henan Medical Equipment Inspection Institute, Henan Medical Equipment Inspection and Testing Engineering Technology Research Center, Henan Medical Equipment Biotechnology and Application Engineering Research Center, Zhengzhou, 450000, China
| | - Pin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Linfei Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Mengmeng Chen
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China.
| | - Lin Chen
- Henan Joint International Research Laboratory of Drug Discovery of Small Molecules, Zhengzhou Key Laboratory of Synthetic Biology of Natural Products, Huanghe Science and Technology College, 450063, Zhengzhou, China.
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; Departments of Neonatology, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Xianwei Zhang
- Department of Pediatric Oncology Surgery, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China.
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110
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Affiliation(s)
- Naoyuki Nakahama
- Institute of Natural and Environmental Sciences, University of Hyogo Sanda City Japan
- The Museum of Nature and Human Activities, Hyogo Sanda City Japan
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111
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Yorisue T, Iguchi A, Yasuda N, Mizuyama M, Yoshioka Y, Miyagi A, Fujita Y. Extensive gene flow among populations of the cavernicolous shrimp at the northernmost distribution margin in the Ryukyu Islands, Japan. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191731. [PMID: 33204436 PMCID: PMC7657918 DOI: 10.1098/rsos.191731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Marine cave habitats in the Ryukyu Islands, Indo-West Pacific, are located at the northern edge of the distribution of many cave-dwelling species. At distribution margins, gene flow is often more restricted than that among core populations due to the smaller effective population size. Here, we used high-throughput sequencing technology to investigate the gene flow pattern among three sampling sites of a marine cave-dwelling species at the margin of its distribution range. We collected individuals of the barbouriid shrimp Parhippolyte misticia from three marine caves in the Ryukyu Islands and performed population genetic analyses by means of multiplexed inter-simple sequence repeat genotyping by sequencing. Based on 62 single-nucleotide polymorphism markers, no clear population structure or directional gene flow pattern was found among the three sites. These results were unexpected because previous studies of other stygobitic shrimps in this region did find significant population genetic structures and northward directional gene flow patterns. Together, these inconsistent findings imply that marine cave-dwelling species in the region have different mechanisms of larval dispersal. Future studies on larval ecology and the biotic and abiotic factors influencing gene flow patterns are needed to clarify the mechanisms underlying the population dynamics of marine cave-dwelling species.
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Affiliation(s)
- Takefumi Yorisue
- Integrative Aquatic Biology, Onagawa Field Center, Graduate School of Agricultural Science, Tohoku University, 3-1 Mukai, Konori-hama, Onagawa, Oshika, Miyagi 986-2242, Japan
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
- Institute of Natural and Environmental Sciences, University of Hyogo, 6 Yayoigaoka, Sanda, Hyogo 669-1546, Japan
- Division of Nature and Environmental Management, Museum of Nature and Human Activities, Hyogo, 6 Yayoigaoka, Sanda, Hyogo 669-1546, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Nina Yasuda
- Department of Marine Biology and Environmental Science, Faculty of Agriculture, University of Miyazaki, Gakuenkibana-dai Nishi 1-1, Miyazaki 889-2192, Japan
| | - Masaru Mizuyama
- Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905, Henoko, Nago, Okinawa 905-2192, Japan
| | - Aika Miyagi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905, Henoko, Nago, Okinawa 905-2192, Japan
| | - Yoshihisa Fujita
- General Educational Center, Okinawa Prefectural University of Arts, 1-4, Shuri Tounokura-cho, Naha-shi, Okinawa 903-8602, Japan
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112
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A Narrow Endemic or a Species Showing Disjunct Distribution? Studies on Meehania montis-koyae Ohwi (Lamiaceae). PLANTS 2020; 9:plants9091159. [PMID: 32911695 PMCID: PMC7570357 DOI: 10.3390/plants9091159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 11/26/2022]
Abstract
Meehania montis-koyae Ohwi (Lamiaceae), which has been considered a narrow endemic and endangered species in Japan, was found in eastern China in 2011. China and Japan belong to the same floristic region and share many plant species, but it is very rare that Japanese narrow endemic species are newly found outside of the country. We examined herbarium specimens of both countries, and conducted analyses of molecular phylogenetics, population genetics, and divergence time estimation using two nuclear (ITS and ETS) gene regions and MIG-seq data. Chinese plants tend to become larger than Japanese, and they are different in leaf shape and floral features. Molecular phylogenetic analysis shows Chinese and Japanese M. montis-koyae are the closest relatives to each other. Population genetic analysis indicates no current gene flow between the Chinese and Japanese populations, and divergence time analysis shows they were separated during the late Miocene. We reach the conclusion that Chinese and Japanese M. montis-koyae have already become distinct biological entities, and a new taxon name Meehania zheminensis A. Takano, Pan Li, G.-H.Xia is proposed for the Chinese plants. A key to Asian Meehania species is provided.
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113
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Genetic Structure and Population Demography of White-Spotted Charr in the Upstream Watershed of a Large Dam. WATER 2020. [DOI: 10.3390/w12092406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
White-spotted charr (Salvelinus leucomaenis leucomaenis) is an anadromous fish that has been severely harmed by human land-use development, particularly through habitat fragmentation. However, the anthropogenic impacts on populations of this species have not been evaluated, except those on small dammed-off populations. Using multiplexed ISSR genotyping by sequencing, we investigated the genetic structure of white-spotted charr in four tributaries in the upper section of the Kanayama Dam in the Sorachi River, Hokkaido Island, Japan. There were no distinct genetic structures (FST = 0.014), probably because some active individuals migrate frequently among tributaries. By model-flexible demographic simulation, historical changes in the effective population size were inferred. The result indicates that the population size has decreased since the end of the last glacial period, with three major population decline events, including recent declines that were probably associated with recent human activities. Nevertheless, populations in the watershed upstream of the Kanayama Dam are still expected to be at low risk of immediate extinction, owing to the large watershed size and the limited number of small check dams. An effective conservation measure for sustaining the white-spotted charr population is to maintain high connectivity between tributaries, such as by providing fishways in check dams during construction.
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SNP Genotyping with Target Amplicon Sequencing Using a Multiplexed Primer Panel and Its Application to Genomic Prediction in Japanese Cedar, Cryptomeria japonica (L.f.) D.Don. FORESTS 2020. [DOI: 10.3390/f11090898] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Along with progress in sequencing technology and accumulating knowledge of genome and gene sequences, molecular breeding techniques have been developed for predicting the genetic potential of individual genotypes and for selecting superior individuals. For Japanese cedar (Cryptomeria japonica (L.f.) D.Don), which is the most common coniferous species in Japanese forestry, we constructed a custom primer panel for target amplicon sequencing in order to simultaneously determine 3034 informative single nucleotide polymorphisms (SNPs). We performed primary evaluation of the custom primer panel with actual sequencing and in silico PCR. Genotyped SNPs had a distribution over almost the entire region of the C. japonica linkage map and verified the high reproducibility of genotype calls compared to SNPs obtained by genotyping arrays. Genotyping was performed for 576 individuals of the F1 population, and genomic prediction models were constructed for growth and wood property-related traits using the genotypes. Amplicon sequencing with the custom primer panel enables efficient obtaining genotype data in order to perform genomic prediction, manage clones, and advance forest tree breeding.
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115
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Ito H, Nakajima N, Onuma M, Murayama M. Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis. Animals (Basel) 2020; 10:ani10081375. [PMID: 32784782 PMCID: PMC7459485 DOI: 10.3390/ani10081375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The Tsushima leopard cat, Prionailurus bengalensis euptilurus, is a small regional population of the Amur leopard cat and is only found on Tsushima Island in Japan. A breeding program will require adequate information on parentage, kinship, and inbreeding for this population. Hence, there is an urgent need to develop this information in order to conserve the population and its genetic diversity. We performed GRAS-Di analysis to investigate the genetic diversity and genetic structure of the Tsushima leopard cat. We identified between 133 and 158 single-nucleotide polymorphism (SNP) markers in three different genotyping methods. These SNP markers can be used in identification of individuals and parentage. In addition, structure analysis using these markers demonstrated the similar genetic composition of the samples from 48 Tsushima leopard cats, and indicated Tsushima leopard cats have no subpopulations. We have provided genetic markers that are useful for conservation of the Tsushima leopard cat, such as individual identification and parentage. Moreover, we have also clarified units for conservation of the Tsushima leopard cat population from structure analysis. Abstract The Tsushima leopard cat (Prionailurus bengalensis euptilurus) lives on Tsushima Island in Japan and is a regional population of the Amur leopard cat; it is threatened with extinction. Its genetic management is important because of the small population. We used genotyping by random amplicon sequencing-direct (GRAS-Di) to develop a draft genome and explore single-nucleotide polymorphism (SNP) markers. The SNPs were analyzed using three genotyping methods (mapping de novo, to the Tsushima leopard cat draft genome, and to the domestic cat genome). We examined the genetic diversity and genetic structure of the Tsushima leopard cat. The genome size was approximately 2.435 Gb. The number of SNPs identified was 133–158. The power of these markers was sufficient for individual and parentage identifications. These SNPs can provide useful information about the life of the Tsushima leopard cat and the pairings and for the introduction of founders to conserve genetic diversity with ex situ conservation. We identified that there are no subpopulations of the Tsushima leopard cat. The identifying units will allow for a concentration of efforts for conservation. SNPs can be applied to the analysis of the leopard cat in other regions, making them useful for comparisons among populations and conservation in other small populations.
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Affiliation(s)
- Hideyuki Ito
- Kyoto City Zoo, Kyoto 606-8333, Japan
- Wildlife Research Center, Kyoto University, Kyoto 606-8203, Japan;
- Correspondence: ; Tel.: +81-75-771-0211; Fax: +81-75-752-1974
| | - Nobuyoshi Nakajima
- Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba 305-8506, Japan; (N.N.); (M.O.)
| | - Manabu Onuma
- Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba 305-8506, Japan; (N.N.); (M.O.)
| | - Miho Murayama
- Wildlife Research Center, Kyoto University, Kyoto 606-8203, Japan;
- Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba 305-8506, Japan; (N.N.); (M.O.)
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Sato H, Ohta R, Murakami N. Molecular prospecting for cryptic species of the Hypholoma fasciculare complex: toward the effective and practical delimitation of cryptic macrofungal species. Sci Rep 2020; 10:13224. [PMID: 32764692 PMCID: PMC7413530 DOI: 10.1038/s41598-020-70166-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/24/2020] [Indexed: 11/11/2022] Open
Abstract
Many macrofungal cryptic species remain unidentified. A possible solution is to increase the number of loci analyzed and use rigorous statistics for macrofungal species delimitation. To validate this assumption, cryptic species of the Hypholoma fasciculare complex, a group of common wood-decomposing fungi, were attempted to be delineated. Massively parallel sequencing of mitochondrial ribosomal RNA (mt_rRNA), nuclear ribosomal internal transcribed spacer (ITS) region, and 24 single-copy genes were performed for 96 specimens collected in Japan. Then, the species boundaries were inferred using comparative gene genealogies (mt_rRNA vs. ITS), Bayesian Poisson tree process (bPTP) model for the phylogeny of concatenated nuclear sequences, and analysis of molecular variance (AMOVA) for single nucleotide polymorphisms. In both the mt_rRNA and ITS phylogenies, the H. fasciculare complex was not divided into well-supported clades. Nevertheless, based on the bPTP, two mitochondrial haplotypes were inferred to represent distinct species (H. fasciculare and H. subviride). The results of AMOVA also indicated that the differentiation of nuclear loci can be explained mostly by differences between haplotype. These results suggest that it is necessary to increase the number of target loci to 20 or more and use both phylogeny-based and population genetics-based statistics for the accurate delimitation of macrofungal species.
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Affiliation(s)
- Hirotoshi Sato
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
| | - Ryoma Ohta
- Makino Herbarium, Tokyo Metropolitan University, Hachioji, Tokyo, 192-0397, Japan
| | - Noriaki Murakami
- Makino Herbarium, Tokyo Metropolitan University, Hachioji, Tokyo, 192-0397, Japan
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117
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Cronin AL, Azuma N, Miyazaki S, Oguri E, Schwarz MP, Ito F. Geographic patterns in colonial reproductive strategy in Myrmecina nipponica: Links between biogeography and a key polymorphism in ants. J Evol Biol 2020; 33:1192-1202. [PMID: 33448532 DOI: 10.1111/jeb.13659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/15/2020] [Accepted: 05/25/2020] [Indexed: 11/26/2022]
Abstract
The ability to express different phenotypes can help define species distributions by allowing access to, and exploitation of, new environments. Social insects employ two markedly different reproductive strategies with contrasting cost/benefit characteristics: independent colony foundation (ICF), which is associated with high dispersal range and high risk, and dependent colony foundation (DCF), characterized by low risk but low dispersal. The ant Myrmecina nipponica employs both of these strategies, with the frequency of each apparently varying between populations. We combine molecular data with data on reproductive strategy from different populations of this species throughout Japan to explore how this polymorphism is linked to environmental factors and whether this relationship can help explain the current and historical biogeography of this species. Reproductive strategy exhibited a strong geographic pattern, with ICF predominant in southern populations and DCF more common in northern and southern highland populations. Molecular analyses clearly divided populations into broad geographic regions, with the southern lowland populations basal to (southern highland (+ northern)) populations. Intra-population polymorphism in colony-founding strategy was widespread, and polymorphism was reconstructed as the likely ancestral state. The frequency of different strategies was linked with climate, with DCF more common in colder areas. A recent inferred origin to the northern lineage suggests that colonization of northern Japan was a rapid event coincident with warming at the end of the Last Glacial Maxima, likely facilitated by the cold-adaptive advantages of DCF. We discuss how such polymorphisms could help explain the biogeography of this and other social insects.
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Affiliation(s)
- Adam L Cronin
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Noriko Azuma
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Japan
| | - Satoshi Miyazaki
- Department of Agri-production Sciences, College of Agriculture, Tamagawa University, Machida, Tokyo, Japan
| | - Emiko Oguri
- Systematic Botany Laboratory, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Michael P Schwarz
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Fuminori Ito
- Faculty of Agriculture, Kagawa University, Miki, Japan
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118
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Assessments of fine-scale spatial patterns of SNPs in an old-growth beech forest. Heredity (Edinb) 2020; 125:240-252. [PMID: 32606418 DOI: 10.1038/s41437-020-0334-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 11/09/2022] Open
Abstract
The spatial patterns of non-neutral genetic variations at fine spatial scales and their possible associations with microenvironments have not been well-documented for tree populations. Based on 25-32 SNP markers, we examine whether non-neutral SNPs and their associations with microenvironments can be detected in FcMYB1603, a gene homologous to that encoding a protein induced by drought stress in Arabidopsis thaliana for the 166 adult trees in a 1-ha plot in a mature population of Fagus crenata. In the 83 individuals of a younger cohort of below canopy trees, the nonsynonymous SNP at locus FcMYB1603_684 exhibited a spatial signature representing a departure from the expected spatial patterns of neutral genetic variation. Evaluations of non-neutrality for this locus were robust against the potential risks of false positives due to the low number of SNP loci, a low criterion set for minor allele frequency, and any edge effect on the trees' spatial structure. An older cohort exhibited no signal of the existence of non-neutral genetic variation, suggesting that temporal fluctuation in the microenvironmental conditions on the forest floor may have exposed different cohorts to different magnitudes of selection pressure. Although genotypes of the locus showed a spatial association with a microenvironmental variable potentially related to soil moisture, the present study was subject to a limitation due to the generally low polymorphism of nonsynonymous loci within the single plot, which suggests that it will be important to replicate the study design in order to carry out research on fine-scale non-neutral genetic variations.
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Yorisue T, Iguchi A, Yasuda N, Yoshioka Y, Sato T, Fujita Y. Evaluating the effect of overharvesting on genetic diversity and genetic population structure of the coconut crab. Sci Rep 2020; 10:10026. [PMID: 32572270 PMCID: PMC7308380 DOI: 10.1038/s41598-020-66712-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 02/20/2020] [Indexed: 11/19/2022] Open
Abstract
Birgus latro (coconut crab) is an edible crustacean that has experienced serious overharvesting throughout its whole habitat range; however, the negative effects of overharvesting on the genetic diversity within B. latro populations have not been elucidated. Here, we report sex ratio, body size, and genetic diversity in populations of B. latro in the Ryukyu Islands where large-male-biased overharvesting of B. latro has continued. In 2 of the study populations, the sex ratio was significantly skewed toward females, and in all of the study populations large males were rare, which we attributed to sex- and size-biased overharvesting. We found no differences in genetic diversity between small and large individuals, suggesting that genetic diversity, even among the large (i.e., old) individuals, may have had already been negatively affected by overharvesting. Continued monitoring of sex ratio, body size and genetic diversity are needed for effective management of the study populations.
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Affiliation(s)
- Takefumi Yorisue
- Integrative Aquatic Biology, Onagawa Field Center, Graduate School of Agricultural Science, Tohoku University, 3-1 Mukai, Konori-hama, Onagawa, Oshika, Miyagi, 986-2242, Japan.
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan, AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan, AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
| | - Nina Yasuda
- Department of Marine Biology and Environmental Science, Faculty of Agriculture, University of Miyazaki, Gakuenkibana-dai Nishi 1-1, Miyazaki, 889-2192, Japan
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905, Henoko, Nago, Okinawa, 905-2192, Japan
| | - Taku Sato
- Research Center for Marine Invertebrates, National Research Institute of Fisheries and Environment of Inland Sea, Japan Fisheries Research and Education Agency, Momoshima, Onomichi, Hiroshima, 722-0061, Japan
| | - Yoshihisa Fujita
- Okinawa Prefectural University of Arts, 1-4, Shuri Tonokura-cho, Naha-shi, Okinawa, 903-8602, Japan
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120
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Strijk JS, Binh HT, Ngoc NV, Pereira JT, Slik JWF, Sukri RS, Suyama Y, Tagane S, Wieringa JJ, Yahara T, Hinsinger DD. Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea. PLoS One 2020; 15:e0232936. [PMID: 32442164 PMCID: PMC7244142 DOI: 10.1371/journal.pone.0232936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 04/24/2020] [Indexed: 11/21/2022] Open
Abstract
Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.
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Affiliation(s)
- Joeri S. Strijk
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
| | | | | | - Joan T. Pereira
- Sabah Forestry Department, Forest Research Centre, Sandakan, Sabah, Malaysia
| | - J. W. Ferry Slik
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Rahayu S. Sukri
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Yoshihisa Suyama
- Kawatabi Field Science Centre, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, Kagoshima, Japan
| | | | - Tetsukazu Yahara
- Center for Asian Conservation Ecology, Kyushu University, Fukuoka, Japan
| | - Damien D. Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l′Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
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121
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Zhang M, Yahara T, Tagane S, Rueangruea S, Suddee S, Moritsuka E, Suyama Y. Cryptocarya kaengkrachanensis, a new species of Lauraceae from Kaeng Krachan National Park, southwest Thailand. PHYTOKEYS 2020; 140:139-157. [PMID: 32194319 PMCID: PMC7066263 DOI: 10.3897/phytokeys.140.34574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
A new species of Lauraceae, Cryptocarya kaengkrachanensis M.Z.Zhang, Yahara & Tagane, from Kaeng Krachan National Park, Phetchaburi Province, southwestern Thailand, is described and illustrated. This species is morphologically most similar to C. amygdalina in that its leaves are pinnately veined, leathery, and apparently glabrous (but microscopically hairy) abaxially, twigs are yellowish brown hairy, and fruits are 1.36 to 1.85 times longer than width. However, C. kaengkrachanensis is distinguished from C. amygdalina in having the leaves of ovate and elliptic (vs. oblong-lanceolate) with leaf aspect ratio (length:width) from 1.38 to 2.28 (vs. 2.46-3.43), and ovoid fruits (vs. ellipsoid) with stalk distinctly swollen (vs. not or only slightly swollen). In addition, phylogenetic trees constructed based on internal transcribed spacer sequences (ITS) and genome-wide SNPs using MIG-seq showed that C. kaengkrachanensis is not sister to C. amygdalina and is distinct from all the other Cryptocarya species hitherto recognized in Thailand. Analysis including other species demonstrates that C. floribunda should be a synonym of C. amygdalina, but we recognize C. scortechinii as a distinct species.
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Affiliation(s)
- Meng Zhang
- Department of Biology, Kyushu University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu UniversityFukuokaJapan
| | - Tetsukazu Yahara
- Department of Biology, Kyushu University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu UniversityFukuokaJapan
| | - Shuichiro Tagane
- Department of Biology, Kyushu University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu UniversityFukuokaJapan
- The Kagoshima University Museum, Kagoshima University, 1-21-30 Korimoto, Kagoshima, 890-0065, JapanKagoshima UniversityKagoshimaJapan
| | - Sukid Rueangruea
- Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, 10900, ThailandDepartment of National ParksBangkokThailand
| | - Somran Suddee
- Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, 10900, ThailandDepartment of National ParksBangkokThailand
| | - Etsuko Moritsuka
- Department of Biology, Kyushu University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu UniversityFukuokaJapan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversitySendaiJapan
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122
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Tsujimoto M, Araki KS, Honjo MN, Yasugi M, Nagano AJ, Akama S, Hatakeyama M, Shimizu-Inatsugi R, Sese J, Shimizu KK, Kudoh H. Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq. AOB PLANTS 2020; 12:plz080. [PMID: 32002176 PMCID: PMC6983914 DOI: 10.1093/aobpla/plz080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66 617 scaffolds with N50 = 6086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets.
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Affiliation(s)
| | - Kiwako S Araki
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
- Faculty of Life Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
| | - Masaki Yasugi
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
- Faculty of Engineering, Utsunomiya University, Yoto, Utsunomiya, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
- Faculty of Agriculture, Ryukoku University, Yokatani, Seta Ohe-cho, Otsu, Japan
| | - Satoru Akama
- National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
- Functional Genomics Center Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Jun Sese
- National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo, Japan
- Humanome Lab., Inc. 2-4-10-2F, Tsukiji, Chuo-ku, Tokyo, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka-ku, Yokohama, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
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Nagasawa K, Setoguchi H, Maki M, Goto H, Fukushima K, Isagi Y, Suyama Y, Matsuo A, Tsunamoto Y, Sawa K, Sakaguchi S. Genetic consequences of plant edaphic specialization to solfatara fields: Phylogenetic and population genetic analysis of Carex angustisquama (Cyperaceae). Mol Ecol 2019; 29:3234-3247. [PMID: 31800130 DOI: 10.1111/mec.15324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 11/29/2022]
Abstract
Edaphic specialization is one of the main drivers of plant diversification and has multifaceted effects on population dynamics. Carex angustisquama is a sedge plant growing only on heavily acidified soil in solfatara fields, where only extremophytes can survive. Because of the lack of closely related species in similar habitats and its disjunct distribution, the species offers ideal settings to investigate the effects of adaptation to solfatara fields and of historical biogeography on the genetic consequences of plant edaphic specialization to solfatara fields. Here, genome-wide single nucleotide polymorphisms were used to reveal the phylogenetic origin of C. angustisquama, and 16 expressed sequence tag-simple sequence repeat markers were employed to infer population demography of C angustisquama. Molecular phylogenetic analysis strongly indicated that C. angustisquama formed a monophyletic clade with Carex doenitzii, a species growing on nonacidified soil in the sympatric subalpine zone. The result of population genetic analysis showed that C. angustisquama has much lower genetic diversity than the sister species, and notably, all 16 loci were completely homozygous in most individuals of C. angustisquama. Approximate Bayesian computation analysis supported the model that assumed hierarchical declines of population size through its evolutionary sequence. We propose that the edaphic specialist in solfatara fields has newly attained the adaptation to solfatara fields in the process of speciation. Furthermore, we found evidence of a drastic reduction in genetic diversity in C. angustisquama, suggesting that the repeated founder effects associated with edaphic specialization and subsequent population demography lead to the loss of genetic diversity of this extremophyte in solfatara fields.
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Affiliation(s)
- Koki Nagasawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | | | - Hayato Goto
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Ayumi Matsuo
- Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Yoshihiro Tsunamoto
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Japan
| | | | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
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124
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Honjo MN, Kudoh H. Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation. AOB PLANTS 2019; 11:plz076. [PMID: 31832127 PMCID: PMC6899346 DOI: 10.1093/aobpla/plz076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/26/2019] [Indexed: 05/21/2023]
Abstract
Local adaptation is assumed to occur when populations differ in a phenotypic trait or a set of traits, and such variation has a genetic basis. Here, we introduce Arabidopsis halleri and its life history as a perennial model system to study population differentiation and local adaptation. Studies on altitudinal adaptation have been conducted in two regions: Mt. Ibuki in Japan and the European Alps. Several studies have demonstrated altitudinal adaptation in ultraviolet-B (UV-B) tolerance, leaf water repellency against spring frost and anti-herbivore defences. Studies on population differentiation in A. halleri have also focused on metal hyperaccumulation and tolerance to heavy metal contamination. In these study systems, genome scans to identify candidate genes under selection have been applied. Lastly, we briefly discuss how RNA-Seq can broaden phenotypic space and serve as a link to underlying mechanisms. In conclusion, A. halleri provides us with opportunities to study population differentiation and local adaptation, and relate these to the genetic systems underlying target functional traits.
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Affiliation(s)
- Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
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125
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Hirano T, Saito T, Tsunamoto Y, Koseki J, Prozorova L, Do VT, Matsuoka K, Nakai K, Suyama Y, Chiba S. Role of ancient lakes in genetic and phenotypic diversification of freshwater snails. Mol Ecol 2019; 28:5032-5051. [DOI: 10.1111/mec.15272] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Takahiro Hirano
- Department of Biological Sciences University of Idaho Moscow ID USA
| | - Takumi Saito
- Department of Biology Faculty of Science Toho University Funabashi Japan
| | - Yoshihiro Tsunamoto
- Tohoku Research Center Forestry and Forest Products Research Institute Morioka Japan
| | - Joichiro Koseki
- Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Larisa Prozorova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
| | - Van Tu Do
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | | | | | - Yoshihisa Suyama
- Kawatabi Field Science Center Graduate School of Agricultural Science Tohoku University Osaki Japan
| | - Satoshi Chiba
- Graduate School of Life Sciences Tohoku University Sendai Japan
- Center for Northeast Asian Studies Tohoku University Sendai Japan
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126
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Takata K, Taninaka H, Nonaka M, Iwase F, Kikuchi T, Suyama Y, Nagai S, Yasuda N. Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype. PeerJ 2019; 7:e7769. [PMID: 31598424 PMCID: PMC6779117 DOI: 10.7717/peerj.7769] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/27/2019] [Indexed: 11/20/2022] Open
Abstract
Background Precious corals known as coralliid corals (Anthozoa: Octocorallia) play an important role in increasing the biodiversity of the deep sea. Currently, these corals are highly threatened because of overfishing that has been brought on by an increased demand and elevated prices for them.The deep sea precious corals Pleurocorallium elatius and P. konojoi are distributed in Japanese waters and have distinct morphological features: (1) the terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) the autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status to allow for their conservation. Methodology We collected a total of 87 samples (60 of Corallium japonicum and 27 of P. konojoi) from around the Ryukyu Islands and Shikoku Island, which are geographically separated by approximately 1,300 km. We used a multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs with which to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared. Results P. elatius and P. konojoi share a same mtDNA haplotype, which has been previously reported. However, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs. Conclusion This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of the conservation of these two species, especially P. elatius, whose population has been dramatically depleted over the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for defining closely related octocoral species that were otherwise indistinguishable using traditional genetic markers (mtDNA and EF).
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Affiliation(s)
- Kenji Takata
- Graduate School of Agriculture, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.,Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Hiroki Taninaka
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Masanori Nonaka
- Okinawa Churashima Foundation Reseach Center, Motobu, Okinawa, Japan
| | | | - Taisei Kikuchi
- Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Nina Yasuda
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan
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Yoshihara Y, Sasaki T, Nyambayar D, Matsuki Y, Baba Y, Suyama Y. Testing the effects of plant species loss on multiple ecosystem functions based on extinction scenarios. Basic Appl Ecol 2019. [DOI: 10.1016/j.baae.2019.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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128
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Ito H, Inoue-Murayama M. The Tsushima leopard cat exhibits extremely low genetic diversity compared with the Korean Amur leopard cat: Implications for conservation. PeerJ 2019; 7:e7297. [PMID: 31341743 PMCID: PMC6637929 DOI: 10.7717/peerj.7297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 06/14/2019] [Indexed: 11/20/2022] Open
Abstract
We examined genetic diversity of the wild Tsushima leopard cat-a regional population of the Amur leopard cat-using microsatellite markers. In addition, we compared genetic diversity of the Tsushima leopard cat with that of the Korean population of Amur leopard cat. Although bias should be considered when applying cross-species amplification, the Tsushima leopard cat showed a lower index of molecular genetic diversity than did the Korean population. These results were consistent with those obtained using other genetic markers, such as mitochondrial DNA and Y chromosome sequences. This low genetic diversity of the wild Tsushima leopard cat may be derived from the founding population. Furthermore, our results suggest that the captive populations held in Japanese zoos may show extremely low genetic diversity, leading to difficulties in genetic management of the Tsushima leopard cat. Moreover, the two regional populations were clearly separated using these marker sets. In the present study, we demonstrated that the genetic diversity of the Tsushima leopard cat is extremely low compared with that of the continental regional population. Importantly, the Japanese captive population for ex situ conservation was derived from a founding population with extremely low genetic diversity; hence, we assume that both the captive and wild populations showed extremely low genetic diversities. Our findings emphasize the need to develop carefully considered management strategies for genetic conservation.
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Affiliation(s)
- Hideyuki Ito
- Kyoto City Zoo, Kyoto, Kyoto, Japan.,Wildlife Research Center, Kyoto University, Kyoto, Kyoto, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Kyoto, Japan.,Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba, Japan
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129
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Hosoya S, Hirase S, Kikuchi K, Nanjo K, Nakamura Y, Kohno H, Sano M. Random PCR-based genotyping by sequencing technology GRAS-Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes. Mol Ecol Resour 2019; 19:1153-1163. [PMID: 31009151 DOI: 10.1111/1755-0998.13025] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/06/2019] [Accepted: 04/15/2019] [Indexed: 01/15/2023]
Abstract
While various technologies for high-throughput genotyping have been developed for ecological studies, simple methods tolerant to low-quality DNA samples are still limited. In this study, we tested the availability of a random PCR-based genotyping-by-sequencing technology, genotyping by random amplicon sequencing, direct (GRAS-Di). We focused on population genetic analysis of estuarine mangrove fishes, including two resident species, the Amboina cardinalfish (Fibramia amboinensis, Bleeker, 1853) and the Duncker's river garfish (Zenarchopterus dunckeri, Mohr, 1926), and a marine migrant, the blacktail snapper (Lutjanus fulvus, Forster, 1801). Collections were from the Ryukyu Islands, southern Japan. PCR amplicons derived from ~130 individuals were pooled and sequenced in a single lane on a HiSeq2500 platform, and an average of three million reads was obtained per individual. Consensus contigs were assembled for each species and used for genotyping of single nucleotide polymorphisms by mapping trimmed reads onto the contigs. After quality filtering steps, 4,000-9,000 putative single nucleotide polymorphisms were detected for each species. Although DNA fragmentation can diminish genotyping performance when analysed on next-generation sequencing technology, the effect was small. Genetic differentiation and a clear pattern of isolation-by-distance was observed in F. amboinensis and Z. dunckeri by means of principal component analysis, FST and the admixture analysis. By contrast, L. fulvus comprised a genetically homogeneous population with directional recent gene flow. These genetic differentiation patterns reflect patterns of estuary use through life history. These results showed the power of GRAS-Di for fine-grained genetic analysis using field samples, including mangrove fishes.
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Affiliation(s)
- Sho Hosoya
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Japan
| | - Kusuto Nanjo
- Department of Applied Aquabiology, National Fisheries University, Shimonoseki, Japan
| | - Yohei Nakamura
- Department of Agriculture, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Hiroyoshi Kohno
- Okinawa Regional Research Center, Tokai University, Taketomi, Japan
| | - Mitsuhiko Sano
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
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130
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Tsurui‐Sato K, Sato Y, Kato E, Katoh M, Kimura R, Tatsuta H, Tsuji K. Evidence for frequency-dependent selection maintaining polymorphism in the Batesian mimic Papilio polytes in multiple islands in the Ryukyus, Japan. Ecol Evol 2019; 9:5991-6002. [PMID: 31161014 PMCID: PMC6540699 DOI: 10.1002/ece3.5182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/22/2019] [Accepted: 03/29/2019] [Indexed: 11/23/2022] Open
Abstract
Batesian mimicry is a well-studied adaptation for predation avoidance, in which a mimetic species resembles an unpalatable model species. Batesian mimicry can be under positive selection because of the protection gained against predators, due to resemblance to unpalatable model species. However, in some mimetic species, nonmimetic individuals are present in populations, despite the benefits of mimicry. The mechanism for evolution of such mimetic polymorphism remains an open question. Here, we address the hypothesis that the abundance of mimics is limited by that of the models, leading to mimetic polymorphism. In addition, other forces such as the effects of common ancestry and/or isolation by distance may explain this phenomenon. To investigate this question, we focused on the butterfly, Papilio polytes, that exhibits mimetic polymorphism on multiple islands of the Ryukyus, Japan, and performed field surveys and genetic analysis. We found that the mimic ratio of P. polytes was strongly correlated with the model abundance observed on each of the five islands, suggesting negative frequency-dependent selection is driving the evolution of polymorphism in P. polytes populations. Molecular phylogenetic analysis indicated that the southern island populations are the major source of genetic diversity, and the middle and northern island populations arose by relatively recent migration. This view was also supported by mismatch distribution and Tajima's D analyses, suggesting a recent population expansion on the middle and northern islands, and stable population persistence on the southern islands. The frequency of the mimetic forms within P. polytes populations is thus explained by variations in the model abundance rather than by population structure. Thus, we propose that predation pressure, rather than neutral forces, have shaped the Batesian mimicry polymorphism in P. polytes observed in the Ryukyus.
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Affiliation(s)
- Kaori Tsurui‐Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Yukuto Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Emi Kato
- Department of Agro‐Environmental Sciences, Faculty of AgricultureUniversity of the RyukyusOkinawaJapan
| | - Mitsuho Katoh
- Department of Agro‐Environmental Sciences, Faculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of MedicineUniversity of the RyukyusOkinawaJapan
| | - Haruki Tatsuta
- Department of Agro‐Environmental Sciences, Faculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Kazuki Tsuji
- Department of Agro‐Environmental Sciences, Faculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
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131
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Matos-Maraví P, Duarte Ritter C, Barnes CJ, Nielsen M, Olsson U, Wahlberg N, Marquina D, Sääksjärvi I, Antonelli A. Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies. PeerJ 2019; 7:e6727. [PMID: 31106048 PMCID: PMC6499058 DOI: 10.7717/peerj.6727] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.
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Affiliation(s)
- Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Camila Duarte Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | | | - Martin Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Urban Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanical Garden, Kew, Richmond, Surrey, UK
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132
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Hirano T, Saito T, Tsunamoto Y, Koseki J, Ye B, Do VT, Miura O, Suyama Y, Chiba S. Enigmatic incongruence between mtDNA and nDNA revealed by multi-locus phylogenomic analyses in freshwater snails. Sci Rep 2019; 9:6223. [PMID: 30996240 PMCID: PMC6470147 DOI: 10.1038/s41598-019-42682-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/05/2019] [Indexed: 02/08/2023] Open
Abstract
Phylogenetic incongruence has frequently been encountered among different molecular markers. Recent progress in molecular phylogenomics has provided detailed and important information for evolutionary biology and taxonomy. Here we focused on the freshwater viviparid snails (Cipangopaludina chinensis chinensis and C. c. laeta) of East Asia. We conducted phylogenetic analyses and divergence time estimation using two mitochondrial markers. We also performed population genetic analyses using genome-wide SNPs. We investigated how and which phylogenetic patterns reflect shell morphology. The results showed these two species could be separated into four major mitochondrial clades, whereas the nuclear clusters supported two groups. The phylogenetic patterns of both mtDNA and nDNA largely reflected the geographical distribution. Shell morphology reflected the phylogenetic clusters based on nDNA. The findings also showed these two species diversified in the Pliocene to early Pleistocene era, and occurred introgressive hybridisation. The results also raise the taxonomic issue of the two species.
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Affiliation(s)
- Takahiro Hirano
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.
| | - Takumi Saito
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
| | - Yoshihiro Tsunamoto
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Joichiro Koseki
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
| | - Bin Ye
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Satoshi Chiba
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
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133
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Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing. Heredity (Edinb) 2019; 123:371-383. [PMID: 30809077 DOI: 10.1038/s41437-019-0198-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 01/28/2019] [Accepted: 02/01/2019] [Indexed: 12/17/2022] Open
Abstract
The evolution of a species depends on multiple forces, such as demography and natural selection. To understand the trajectory and driving forces of evolution of a target species, it is first necessary to uncover that species' population history, such as past and present population sizes, subdivision and gene flow, by using appropriate genetic markers. Cryptomeria japonica is a long-lived monoecious conifer species that is distributed in Japan. There are two main lines (omote-sugi and ura-sugi), which are distinguished by apparent differences in morphological traits that may have contributed to their local adaptation. The evolution of these morphological traits seems to be related to past climatic changes in East Asia, but no precise estimate is available for the divergence time of these two lines and the subsequent population dynamics in this species. Here, we analyzed the nucleotide variations at 120 nuclear genes in 94 individuals by using amplicon sequencing in combination with high-throughput sequencing technologies. Our analysis indicated that the population on Yakushima Island, the southern distribution limit of C. japonica in Japan, diverged from the other populations 0.85 million years ago (MYA). The divergence time of the other populations on mainland Japan was estimated to be 0.32 MYA suggesting that the divergence of omote-sugi and ura-sugi might have occurred before the last glacial maximum. Although we found modest levels of gene flow between the present populations, the long-term isolation and environmental heterogeneity caused by climatic changes might have contributed to the differentiation of the lines and their local adaptation.
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Matsui M, Okawa H, Nishikawa K, Aoki G, Eto K, Yoshikawa N, Tanabe S, Misawa Y, Tominaga A. Systematics of the Widely Distributed Japanese Clouded Salamander, Hynobius nebulosus (Amphibia: Caudata: Hynobiidae), and Its Closest Relatives. CURRENT HERPETOLOGY 2019. [DOI: 10.5358/hsj.38.32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Masafumi Matsui
- 1Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto 606–8501, JAPAN
| | | | - Kanto Nishikawa
- 1Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto 606–8501, JAPAN
| | - Gen Aoki
- 3Doshisha International Junior/Senior High School, 60–1 Tatara-Miyakodani, Kyotanabe, Kyoto 610–0321
| | - Koshiro Eto
- 4Kitakyushu Museum of Natural History & Human History, Higashida 2–4–1, Yahatahigashi-ku, Kitakyushu
| | - Natsuhiko Yoshikawa
- 5Center for Molecular Biodiversity Research, National Museum of Nature and Science, 4–1–1 Amakubo, T
| | - Shingo Tanabe
- 6Kamikatsura-Higashi-no-Kuchi-Cho, Nishikyo-ku, Kyoto 615–8221, JAPAN
| | - Yasuchika Misawa
- 7Civil Engineering and Eco-Technology Consultants, Minamisenba 1–15–14, Chuo-ku, Osaka 542–0081, JAP
| | - Atsushi Tominaga
- 8Faculty of Education, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903–0213, JAPAN
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135
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Ando H. Genetic and ecological conservation issues for oceanic island birds, revealed by a combination of the latest molecular techniques and conventional field work. Ecol Res 2019. [DOI: 10.1111/1440-1703.1062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haruko Ando
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies Ibaraki Japan
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136
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Richards ZT, Yasuda N, Kikuchi T, Foster T, Mitsuyuki C, Stat M, Suyama Y, Wilson NG. Integrated evidence reveals a new species in the ancient blue coral genus Heliopora (Octocorallia). Sci Rep 2018; 8:15875. [PMID: 30367122 PMCID: PMC6203795 DOI: 10.1038/s41598-018-32969-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/17/2018] [Indexed: 12/11/2022] Open
Abstract
Maintaining the accretion potential and three dimensional structure of coral reefs is a priority but reef-building scleractinian corals are highly threatened and retreating. Hence future reefs are predicted to be dominated by non-constructional taxa. Since the Late Triassic however, other non-scleractinian anthozoans such as Heliopora have contributed to tropical and subtropical reef-building. Heliopora is an ancient and highly conserved reef building octocoral genus within the monospecific Family Helioporidae, represented by a single extant species - H. coerulea, Pallas, 1766. Here we show integrated morphological, genomic and reproductive evidence to substantiate the existence of a second species within the genus Heliopora. Importantly, some individuals of the new species herein described as Heliopora hiberniana sp. nov. feature a white skeleton indicating that the most diagnostic and conserved Heliopora character (the blue skeleton) can be displaced. The new species is currently known only from offshore areas in north Western Australia, which is a part of the world where coral bleaching events have severely impacted the scleractinian community over the last two decades. Field observations indicate individuals of both H. coerulea and H. hiberniana sp. nov. were intact after the 2016 Scott Reef thermal stress event, and we discuss the possibility that bleaching resistant non-scleractinian reef builders such as Heliopora could provide new ecological opportunities for the reconfiguration of future reefs by filling empty niches and functional roles left open by the regression of scleractinian corals.
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Affiliation(s)
- Zoe T Richards
- Western Australian Museum, Welshpool, WA, 6106, Australia.
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6845, Australia.
| | - Nina Yasuda
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Taisei Kikuchi
- Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Taryn Foster
- Australian Institute of Marine Science, Crawley, Perth, WA, 6009, Australia
| | - Chika Mitsuyuki
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Michael Stat
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6845, Australia
- Department of Biological Sciences, Macquarie University, Sydney, 2109, Australia
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Nerida G Wilson
- Western Australian Museum, Welshpool, WA, 6106, Australia
- University of Western Australia, Crawley, Perth, Western Australia, 6009, Australia
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137
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Nagata N, Kitamura JI, Inaba O, Kumagai M, Fujimoto Y, Sota T. Phylogeography of Endangered Bitterling Acheilognathus melanogaster Endemic to Eastern Japan. Zoolog Sci 2018; 35:396-401. [PMID: 30298778 DOI: 10.2108/zs180033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The bitterling Acheilognathus melanogaster is a critically endangered primary freshwater fish endemic to the Pacific side of eastern Japan. To elucidate A. melanogaster genetic structure, we investigated phylogeography in nine populations, using gene sequences of mitochondrial Cytochrome b (Cytb), as well as nuclear Rhodopsin (Rho) and glycosyltransferase (Glyt). We found four Cytb-based geographical clusters unevenly divided between the northern and southern regions, with smaller groups in the south. Of the nuclear genes, Glyt did not show geographical differentiation, whereas Rho formed two clusters: one widely occurring and another restricted to central regions. Genetic diversity was generally higher in southern than in northern populations. Our results suggest that conservation of southern local populations is particularly important in maintaining the genetic diversity of this endangered fish.
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Affiliation(s)
- Nobuaki Nagata
- 1 Division of Collections Conservation, National Museum of Nature and Science, Ibaraki 305-0005, Japan.,2 Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Miyagi 980-8578, Japan
| | | | - Osamu Inaba
- 4 Minamisoma City Museum, Fukushima 975-0051, Japan
| | - Masahiro Kumagai
- 5 Tsuchiura Nature Conservation Association, Ibaraki 300-0043, Japan
| | - Yasufumi Fujimoto
- 6 Miyagi Prefectural Izunuma-Uchinuma Environmental Foundation, Miyagi 989-5504, Japan
| | - Teiji Sota
- 7 Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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138
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Campbell EO, Brunet BMT, Dupuis JR, Sperling FAH. Would an
RRS
by any other name sound as
RAD
? Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13038] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Erin O. Campbell
- Department of Biological SciencesCW405 Biosciences CentreUniversity of Alberta Edmonton Alberta Canada
| | - Bryan M. T. Brunet
- Department of Biological SciencesCW405 Biosciences CentreUniversity of Alberta Edmonton Alberta Canada
| | - Julian R. Dupuis
- Department of Plant and Environmental Protection SciencesUniversity of Hawai'i at Mãnoa Honolulu Hawai'i
| | - Felix A. H. Sperling
- Department of Biological SciencesCW405 Biosciences CentreUniversity of Alberta Edmonton Alberta Canada
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139
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Considering evolutionary processes in cycad conservation: identification of evolutionarily significant units within Dioon sonorense (Zamiaceae) in northwestern Mexico. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1079-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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140
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Matsuo K, Fujii T, Tokuda M, Ganaha-Kikumura T, Yukawa J, Yamagishi K. Descriptions of two new species of Platygaster Latreille that attack gall midges (Diptera, Cecidomyiidae) with notes on their biology (Hymenoptera, Platygastridae). Zookeys 2018:113-125. [PMID: 29755259 PMCID: PMC5945789 DOI: 10.3897/zookeys.754.23296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/03/2018] [Indexed: 11/18/2022] Open
Abstract
Platygasteringeniosus Matsuo & Yamagishi, sp. n. and P.urniphila Matsuo & Yamagishi, sp. n. (Hymenoptera: Platygastridae) are described from Japan. The former species is an egg-larval solitary parasitoid of Masakimyiapustulae Yukawa and Sunose (Diptera: Cecidomyiidae). The latter species is an egg-larval gregarious parasitoid of Rhopalomyialongitubifex (Shinji) (Diptera: Cecidomyiidae).
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Affiliation(s)
- Kazunori Matsuo
- Biosystematics Laboratory, Faculty of Social and Cultural Studies, Kyushu University, Fukuoka812-0395, Japan
| | - Tomohisa Fujii
- NARO Kyushu Okinawa Agricultural Research Center, Kumamoto 861-1192, Japan
| | - Makoto Tokuda
- Laboratory of Systems Ecology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | | | - Junichi Yukawa
- Entomological Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Kenzou Yamagishi
- Entomological Laboratory, Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan
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141
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Niimi K, Usami K, Fujita Y, Abe M, Furukawa M, Suyama Y, Sakai Y, Kamioka M, Shibata N, Park EJ, Sato S, Kiyono H, Yoneyama H, Kitazawa H, Watanabe K, Nochi T, Aso H. Development of immune and microbial environments is independently regulated in the mammary gland. Mucosal Immunol 2018; 11:643-653. [PMID: 29346344 DOI: 10.1038/mi.2017.90] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 09/21/2017] [Indexed: 02/04/2023]
Abstract
Breastfeeding is important for mammals, providing immunological and microbiological advantages to neonates, together with the nutritional supply from the mother. However, the mechanisms of this functional diversity in the mammary gland remain poorly characterized. Here, we show that, similar to the gastrointestinal tract, the mammary gland develops immune and microbial environments consisting of immunoglobulin A (IgA) and the microflora, respectively, both of which are important for protecting neonates and the mother from infectious diseases. The IgA production and microflora development are coordinated in the gastrointestinal tract but seem to be independently regulated in the mammary gland. In particular, the chemokine (C-C motif) ligand 28 and poly-Ig receptor, crucial molecules for the IgA production in milk, were expressed normally in germ-free lactating mice but were almost undetectable in postweaning mothers, regardless of the microflora presence. Our findings offer insights into potentially improving the quality of breastfeeding, using both immunological and microbiological approaches.
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Affiliation(s)
- K Niimi
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - K Usami
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Y Fujita
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - M Abe
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - M Furukawa
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Y Suyama
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Y Sakai
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - M Kamioka
- International Research and Development Center for Mucosal Vaccine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - N Shibata
- International Research and Development Center for Mucosal Vaccine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - E J Park
- International Research and Development Center for Mucosal Vaccine, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Molecular Pathobiology and Cell Adhesion Biology, Graduate School of Medicine, Mie University, Mie, Japan
| | - S Sato
- International Research and Development Center for Mucosal Vaccine, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Mucosal Vaccine and Adjuvant Project, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - H Kiyono
- International Research and Development Center for Mucosal Vaccine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - H Yoneyama
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - H Kitazawa
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - K Watanabe
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - T Nochi
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan.,International Research and Development Center for Mucosal Vaccine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - H Aso
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
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142
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Gutiérrez-Ortega JS, Salinas-Rodríguez MM, Martínez JF, Molina-Freaner F, Pérez-Farrera MA, Vovides AP, Matsuki Y, Suyama Y, Ohsawa TA, Watano Y, Kajita T. The phylogeography of the cycad genus Dioon (Zamiaceae) clarifies its Cenozoic expansion and diversification in the Mexican transition zone. ANNALS OF BOTANY 2018; 121:535-548. [PMID: 29293877 PMCID: PMC5838841 DOI: 10.1093/aob/mcx165] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Background and Aims Biogeographic transition zones are promising areas to study processes of biogeographic evolution and its influence on biological groups. The Mexican transition zone originated due to the overlap of Nearctic and Neotropical biota, which promoted great biological diversification. However, since most previous studies in this area were focused on revealing the phylogeography of Nearctic plants, how historical biogeographic configuration influenced the expansion and diversification of the Neotropical flora remains almost unknown. Using the cycad genus Dioon (Zamiaceae), this study aimed to test whether the biogeographic provinciality of the Mexican transition zone reflects the history of diversification of Neotropical plants. Methods Two chloroplast DNA (cpDNA) regions were analysed from 101 specimens of 15 Dioon species to reveal the distribution of haplogroups. In addition, genome-wide single nucleotide polymorphisms (SNPs) from 84 specimens were used to test the concordance between phylogenetic clusters and the biogeographic provinces. An ultrametric tree was constructed from the sequences containing SNPs to reconstruct the biogeographic events of vicariance and dispersal of Dioon across the Neotropical biogeographic provinces. Key Results Four Dioon lineages with strong phylogeographic structures were recognized using both cpDNA and SNP data. The lineages correspond to two clades that originated from a common ancestor in Eastern Mexico. One clade expanded and diversified in South-east Mexico and Central America. Another clade diversified into three lineages that dispersed to North-east, South and North-west Mexico. Each lineage was biogeographically delimitated. Biogeographic provinces might have provided disparate ecological conditions that facilitated speciation in Dioon since the Miocene. Conclusions The current genetic structure and species diversity of Dioon depict the history of expansion and diversification of the northernmost Neotropical provinces. Past biogeographic connectivities were favoured by elevated topographies, since mountain systems served as corridors for the migration of Dioon and as refugia of tropical communities that diversified during the formation of modern Neotropical forests.
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Affiliation(s)
| | - María Magdalena Salinas-Rodríguez
- Herbario Isidro Palacios, Instituto de Investigaciones de Zonas Desérticas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - José F Martínez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Mexico
| | - Francisco Molina-Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Mexico
- Instituto de Geología, Estación Regional del Noroeste, Universidad Nacional Autónoma de México, Hermosillo, Mexico
| | - Miguel Angel Pérez-Farrera
- Laboratorio de Ecología Evolutiva, Herbario Eizi Matuda, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico
| | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Mexico
| | - Yu Matsuki
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Yomogida, Naruko-onsen, Osaki, Miyagi, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Yomogida, Naruko-onsen, Osaki, Miyagi, Japan
| | - Takeshi A Ohsawa
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa , Japan
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143
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Yoichi W, Kawamata I, Matsuki Y, Suyama Y, Uehara K, Ito M. Phylogeographic analysis suggests two origins for the riparian azalea Rhododendron indicum (L.) Sweet. Heredity (Edinb) 2018; 121:594-604. [PMID: 29479059 DOI: 10.1038/s41437-018-0064-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 11/09/2022] Open
Abstract
Ecological speciation is an important factor in the diversification of plants. The distribution of the woody species Rhododendron indicum, which grows along rivers and is able to withstand water flow when rivers flood (i.e. it is a rheophyte), is disjunct, in contrast to the widespread distribution of its relative, Rhododendron kaempferi. This study aimed to elucidate the phylogenetic relationships between R. indicum and R. kaempferi and the evolutionary processes that gave rise to them. The sequences of three non-coding chloroplast DNA regions (total length 1977 bp) were obtained from 21 populations covering the ranges of the two species. In addition, genome-wide SNPs were genotyped from 20 populations using a genotyping by sequencing method. Leaf morphologies were measured for eight representative populations. Two chloroplast DNA haplotypes, which were detected in R. indicum, were shared between the two species. Genome-wide SNPs identified two lineages in R. indicum and these lineages did not constitute a monophyletic group. Each of these two lineages was related to geographically close populations of R. kaempferi. Leaf morphology, which is a characteristic feature in rheophytes, was not differentiated between the two lineages in R. indicum. The morphological similarity between the two heterogeneous lineages may be a result of parallel evolution from R. kaempferi or of introgressive hybridization between the species due to strong selective pressure imposed by flooding.
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Affiliation(s)
- Watanabe Yoichi
- Graduate School of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba, 271-8510, Japan.
| | - Izumi Kawamata
- Faculty of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba, 271-8510, Japan
| | - Yu Matsuki
- Graduate School of Agricultural Science, Tohoku University, Naruko-onsen Yomogida 232-3, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Naruko-onsen Yomogida 232-3, Osaki, Miyagi, 989-6711, Japan
| | - Koichi Uehara
- College of Liberal Arts and Sciences, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba, 263-8522, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153-8902, Japan
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144
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Binh HT, Ngoc NV, Tagane S, Toyama H, Mase K, Mitsuyuki C, Strijk JS, Suyama Y, Yahara T. A taxonomic study of Quercus langbianensis complex based on morphology and DNA barcodes of classic and next generation sequences. PHYTOKEYS 2018; 95:37-70. [PMID: 29674926 PMCID: PMC5904329 DOI: 10.3897/phytokeys.95.21126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/28/2018] [Indexed: 06/01/2023]
Abstract
The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised based on evidence obtained from field observations, morphological comparison of herbarium specimens and molecular analyses using both classic and next generation DNA markers. Based on Bayesian inference using rbcL, matK and ITS regions and Neighbour-joining tree using genome-wide sequences amplified with multiplexed inter-simple sequence repeat (ISSR) primers (MIG-seq), the authors recognised ten species in the complex in Vietnam and Cambodia, three of which are newly described in this paper: Q. baolamensissp. nov., Q. bidoupensissp. nov. and Q. honbaensissp. nov. These new species are all phenotypically similar to Q. langbianensiss. str. in having lanceolate to oblanceolate leaf shape, upper 4-5/6-serrated leaf margin, acute or acuminate leaf apex and bracts of cupule arranged in 5-9 rings but distinguished both morphologically and phylogenetically. In molecular phylogenetic reconstructions, Q. bidoupensis is not close to any other species. In the Bayesian tree, Q. honbaensis is sister to both Q. blaoensis and Q. camusiae that are found in the same locality but morphologically distinct and those three species are sister to Q. langbianensiss. str., while Quercus baolamensis is not sister to Q. langbianensiss. str. in both the Bayesian tree and MIG-seq tree. In addition, Q. cambodiensis and Q. baniensis previously reduced to Q. langbianensiss. lat. have been recognised as distinct species. Six species were in need of lectotypification and that is undertaken herein.
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Affiliation(s)
- Hoang Thi Binh
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Nguyen Van Ngoc
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Shuichiro Tagane
- Centre for Asian Conservation Ecology, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Hironori Toyama
- Centre for Asian Conservation Ecology, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Keiko Mase
- Centre for Asian Conservation Ecology, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Chika Mitsuyuki
- Kawatabi Field Science Centre, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Joeri Sergej Strijk
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation (under state evaluation status), College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, PR China
- State Key Laboratory for Conservation and Utilisation of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi 530005, PR China
| | - Yoshihisa Suyama
- Kawatabi Field Science Centre, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Tetsukazu Yahara
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
- Centre for Asian Conservation Ecology, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
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145
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Binh HT, Ngoc NV, Bon TN, Tagane S, Suyama Y, Yahara T. A new species and two new records of Quercus (Fagaceae) from northern Vietnam. PHYTOKEYS 2018; 92:1-15. [PMID: 29362550 PMCID: PMC5770563 DOI: 10.3897/phytokeys.92.21831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/20/2017] [Indexed: 06/01/2023]
Abstract
A new species, Quercus xuanlienensis Binh, Ngoc & Bon, is described from Xuan Lien Nature Reserve, Vietnam. The new species is morphologically similar to Q. edithiae Skan, in having 8-11 pairs of secondary veins, bowl-shaped cupules and ellipsoid to cylindrical-ellipsoid and basally convex nuts. It differs in having serrulate leaf margins only at apical 1/5-1/7, almost entire margins of bracts on cupule and much longer nuts. The species is also similar to Q. fleuryi Hickel & A. Camus in having leaves glabrous on both surfaces with only an apically serrulate margin but differs in having shorter petioles, cupules enclosing 1/5 of the nut and much longer nuts. In addition, Q. disciformis Chun & Tsiang. and Q. bella Chun & Tsiang., previously known from China, are newly recorded from Ba Vi National Park, Vietnam.
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Affiliation(s)
- Hoang Thi Binh
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Nguyen Van Ngoc
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Trinh Ngoc Bon
- Department of Forest Phytodiversity, Silviculture Research Institute, Vietnamese Academy of Forest Sciences, Hanoi, Vietnam
| | | | | | - Tetsukazu Yahara
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
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146
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Bao B, Pan Y, Gu B, Chen J, Xu Y, Su P, Liu Y, Tong L, Wang L. Highly sensitive detection of nucleic acids using a cascade amplification strategy based on exonuclease III-assisted target recycling and conjugated polyelectrolytes. Analyst 2018; 143:4267-4272. [DOI: 10.1039/c8an01024b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A ratiometric and cascade amplification strategy that combines the signal amplification and effecitive FRET property of CPEs with the Exo III-assisted target recycling method has been developed for DNA detection.
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Affiliation(s)
- Biqing Bao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Yanrui Pan
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Bingbing Gu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Jia Chen
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Yu Xu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Peng Su
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Yunfei Liu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Li Tong
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
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147
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Takahashi Y. Genome-wide population genetic analysis identifies evolutionary forces establishing continuous population divergence. Ecol Res 2017. [DOI: 10.1007/s11284-017-1459-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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148
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Kang J, Ma X, He S. Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq. Sci Rep 2017; 7:2813. [PMID: 28588195 PMCID: PMC5460224 DOI: 10.1038/s41598-017-02853-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.
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Affiliation(s)
- Jingliang Kang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuhui Ma
- College of Animal Science, Guizhou University, Guizhou, 550025, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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149
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Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. THE NEW PHYTOLOGIST 2017; 214:924-942. [PMID: 28370025 DOI: 10.1111/nph.14470] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/07/2016] [Indexed: 05/14/2023]
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Keith D Bennett
- Department of Geography & Sustainable Development, School of Geography & Geosciences, University of St Andrews, St Andrews, Fife, KY16 9AL, UK
- Marine Laboratory, Queen's University Belfast, Portaferry, BT22 1LS, UK
| | - Gentile Francesco Ficetola
- CNRS, Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), Grenoble, F-38000, France
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Inger Greve Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Jamie R Wood
- Long-term Ecology Lab, Landcare Research, PO Box 69040, Lincoln Canterbury, 7640, New Zealand
| | - Mikkel Winther Pedersen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
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150
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Affiliation(s)
- Josephine R. Paris
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Jamie R. Stevens
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois at Urbana–Champaign Urbana IL 61801 USA
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