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Yatsuyanagi T, Kanbe T, Fujii K, Inoue S, Araki H. Environmental DNA unveils deep phylogeographic structure of a freshwater fish. Mol Ecol 2024; 33:e17337. [PMID: 38558465 DOI: 10.1111/mec.17337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Phylogeography bears an important part in ecology and evolution. However, current phylogeographic studies are largely constrained by limited numbers of individual samples. Using an environmental DNA (eDNA) assay for phylogeographic analyses, this study provides detailed information regarding the history of Siberian stone loach Barbatula toni, a primary freshwater fish across the whole range of Hokkaido, Japan. Based on an eDNA metabarcoding on 293 river water samples, we detected eDNA from B. toni in 189 rivers. A total of 51 samples, representing the entire island, were then selected from the B. toni eDNA-positive sample set for the subsequent analyses. To elucidate the phylogeographic structure of B. toni, newly developed eDNA metabarcoding primers (Barba-cytb-F/R) were applied to these samples, specifically targeting their haplotypic variation in cytochrome b. After a bioinformatic processing to mitigate haplotypic false positives, a total of 50 eDNA haplotypes were identified. Two regionally restricted, genetically distinct lineages of the species were revealed as a result of phylogeographic analyses on the haplotypes and tissue-derived DNA from B. toni. According to a molecular clock analysis, they have been genetically isolated for at least 1.5 million years, suggesting their ancient origin and colonisation of Hokkaido, presumably in the glacial periods. These results demonstrate how freshwater fishes can alter their distributions over evolutionary timescales and how eDNA assay can deepen our understanding of phylogeography.
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Affiliation(s)
| | - Takashi Kanbe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kazuya Fujii
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- Fukuda Hydrologic Center, Sapporo, Japan
| | - Shouko Inoue
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hitoshi Araki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Suzuki H, Takenaka M, Tojo K. Evolutionary history of a cold-adapted limnephilid caddisfly: Effects of climate change and topography on genetic structure. Mol Phylogenet Evol 2024; 191:107967. [PMID: 38000705 DOI: 10.1016/j.ympev.2023.107967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
The distribution of organisms is influenced by complex factors such as the phylogenetic evolutionary histories of species, the physiological and ecological characteristics of organisms, climate, and geographical and geohistorical features. In this study, we focused on a caddisfly, Asynarchus sachalinensis (Trichoptera: Limnephilidae), which has adapted to cold habitats. From phylogeographic analyses based on the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) and 16S rRNA regions and the nuclear DNA (nDNA) 18S rRNA, 28S rRNA, carbamoyl-phosphate synthetase (CAD), elongation factor-1 alpha (EF1-α), and RNA polymerase II (POLII) regions, two distinct genetic clades were detected. Clade I was shown to be widely distributed from Sakhalin to Honshu, whereas Clade II was only distributed within Honshu. The distributions of these clades overlapped in Honshu. The habitats were located at relatively lower altitudes for Clade I and higher altitudes for Clade II. The divergence time of these clades was estimated to be during the Pleistocene, indicating that repeated climatic changes facilitated distributional shifts. Haplotype network and demographic analyses based on the mtDNA COI region showed contrasting genetic structures in the two clades. It was indicated that the population sizes of Clade I had expanded rapidly in a recent period, whereas Clade II had maintained stable population sizes. The habitats of Clade II were typically isolated and scattered at high altitudes, resulting in restricted migration and dispersal because of their discontinuous "Sky Island" habitats. The habitats of Clade I were located at relatively low altitudes, and it was assumed that the populations were continuous, which resulted in a higher frequency of migration and dispersal between populations. Thus, differences in the spatial scale of the adapted habitats of each clade may have resulted in different patterns of population connectivity and fragmentation associated with repeated climatic changes during the Pleistocene. Our study provided new insight into the distributional patterns of cold-adapted aquatic insects in the Japanese Archipelago. Furthermore, the distributional shifts predicted by ecological niche modeling under future climatic change conditions were different for each clade. Therefore, different principles are required in the assessment of each clade to predict temporal changes in their distributions.
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Affiliation(s)
- Hirohisa Suzuki
- Division of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Masaki Takenaka
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Koji Tojo
- Division of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan; Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan.
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Takenaka M, Yano K, Tojo K. Phylogeography of the true freshwater crab, Geothelphusa dehaani: Detected dual dispersal routes via land and sea. ZOOLOGY 2023; 160:126118. [PMID: 37683516 DOI: 10.1016/j.zool.2023.126118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Dispersal is an important factor that determines the potential for colonization to pioneer sites. Although most decapods employ seaward migration for reproduction with a planktonic larval phase, true freshwater crabs spend their entire life cycle in freshwater. Therefore, it is expected that genetic regionality can be easily detected. In this study, we focused on true freshwater crabs, Geothelphusa Stimpson, 1858. Herein, we reveal the evolutionary history and dispersal patterns of freshwater crustaceans. We collected and genetically analyzed 283 specimens at 138 localities across the Japanese Islands. Phylogenetic analyses were conducted on the combined dataset (mtDNA COI, 16S, and nDNA ITS1, histone H3 regions) and the data set based on the mtDNA COI region. The phylogenetic relationships detected 10 clades that were highly monophyletic. The highlights of this study were the discovery of several cryptic species or undescribed species, and the completely different heterogeneous dual dispersal pathways within a single species; i.e., both land and ocean routes. Although it was concluded that Japanese crabs are basically genetically divided by straits, strong evidence for dispersion via ocean currents was also detected (i.e., a "sweepstake"). It was also confirmed that Geothelphusa dehaani (White, 1847) could survive in seawater.
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Affiliation(s)
- Masaki Takenaka
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, Sugadairakogen 1278-294, Ueda 386-2204, Japan
| | - Koki Yano
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Nishigonaka 38, Okazaki 444-0867, Japan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan.
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Mishina T, Nomoto K, Machida Y, Hariu T, Watanabe K. Origin of scarlet gynogenetic triploid Carassius fish: Implications for conservation of the sexual-gynogenetic complex. PLoS One 2022; 17:e0276390. [PMID: 36264937 PMCID: PMC9584449 DOI: 10.1371/journal.pone.0276390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/05/2022] [Indexed: 11/22/2022] Open
Abstract
Conservation of sperm-dependent asexual (gynogenetic) species is challenging due to their complicated ecological dynamics, which requires the stable coexistence with their sperm-providing sexual relatives, who often share similar niches. A symbolic but vulnerable gynogenetic animal is the scarlet Carassius fish, or Hibuna, which is mainly found in Lake Harutori on Hokkaido, Japan. Although Hibuna in Lake Harutori has been protected as a symbol of the Natural Monument of Japan, it has recently suffered population decline. To establish an effective conservation strategy for Hibuna, we investigated its origin, reproductive mode, and genetic diversity, with reference to the surrounding wild populations, using nuclear microsatellites and mitochondrial gene sequences. Our genetic analyses revealed that the main ploidy of Hibuna was triploid or tetraploid, and it reproduces gynogenetically. However, no co-existing sexual diploid Carassius was detected among our samples, suggesting that the sexual diploids and the gynogenetic population including Hibuna would be at risk of co-extirpation. In addition, Hibuna showed high genetic/clonal diversity and most Hibuna had nonindigenous mitochondrial haplotypes that are mostly identical to those reported from goldfish. These results indicate that Hibuna most probably originated from hybridization between indigenous gynogenetic triploids and goldfish introduced about 100 years ago, involving rare sexual reproduction. This spontaneous long-term field experiment exemplifies the recently documented diversification process of gynogenetic Carassius via complex interploidy gene flow. Although the priority to be placed on the conservation of Hibuna is controversial, the maintenance of gynogenetic Carassius, including Hibuna, requires strategic conservation of sexual populations.
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Affiliation(s)
- Tappei Mishina
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
- Laboratory for Chromosome Segregation, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Japan
- * E-mail:
| | | | | | - Tsutomu Hariu
- Kushiro Public University of Economics, Kushiro, Hokkaido, Japan
| | - Katsutoshi Watanabe
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
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Suzuki T, Kuhara N, Tojo K. Phylogeography of Kisaura Ross (Trichoptera: Philopotamidae) of the Japanese Archipelago and the character displacement evolution observed in a secondary contact area between genetically differentiated intra-specific lineages. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
In this study we present evidence of an ongoing speciation event in the Japanese Archipelago. The Kisaura nozakii species complex (Philopotamidae) is a group of a small trichopteran insects, and it has been reported that this species has large differences between populations in the copulatory organs (genitalia) of males. Therefore, we conducted molecular phylogenetic analyses based on the mtDNA COI region (658 bp) and genome-wide nDNA single nucleotide polymorphisms (SNPs) (16 254 loci) using the K. nozakii species complex and a sister-species, K. borealis. We also conducted principal component analyses (PCA) based on the forewing length and seven morphological characteristics of the male genitalia. It was revealed that the K. nozakii species complex is composed of multiple allopatrically differentiated genetic lineages. However, two genetic lineages were distributed sympatrically/parapatrically in the western area of the Japanese Archipelago, and the occurrence of ‘character displacement’ in the male genitalia was detected in this area. We consider that the evolutionary event in this species complex has high potential to become a model case for elucidating the processes of speciation and species diversification.
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Affiliation(s)
- Tomoya Suzuki
- Faculty of Science, Shinshu University , Asahi, Matsumoto, Nagano , Japan
| | | | - Koji Tojo
- Faculty of Science, Shinshu University , Asahi, Matsumoto, Nagano , Japan
- Institute of Mountain Science, Shinshu University , Asahi, Matsumoto, Nagano , Japan
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Pliocene origins, Pleistocene refugia, and postglacial range expansions in southern devil scorpions (Vaejovidae: Vaejovis carolinianus). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00505-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Harigai W, Saito A, Suzuki H, Yamamoto M. Genetic Diversity of Ligidium Isopods in Hokkaido and Niigata, Northern Japan, Based on Mitochondrial DNA Analysis. Zoolog Sci 2021; 37:417-428. [PMID: 32972082 DOI: 10.2108/zs200017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/24/2020] [Indexed: 11/17/2022]
Abstract
The genetic diversity of the genus Ligidium in Hokkaido and Niigata, northern Japan, was investigated by analyzing the cytochrome c oxidase subunit 1 (CO1) region in the mitochondrial DNA (mtDNA). The genetic diversity in Hokkaido was much lower than that in Niigata. Nine different operational taxonomic units (OTUs) were identified. Only a single OTU, most likely Ligidium japonicum, was found in Hokkaido, whereas all nine OTUs were found in Niigata. Using the mtDNA evolutionary rate determined for the marine invertebrate Haptosquilla pulchella (Miers, 1880), population expansion for OTU1 in Hokkaido was estimated to have occurred at 12,600 years BP, suggesting that Ligidium underwent a bottleneck due to glacial cooling, and the population then expanded after postglacial warming. Assuming that the expansion of the OTU1 population occurred at 9600 years BP, when the sea surface temperature rose offshore of Tokachi in the Northwestern Pacific, the evolutionary rate (µ) of the mtDNA CO1 region in Ligidium is calculated as: 0.087 (95% confidence intervals: min: 0.042-max: 0.12) (substitutions/site/million years). The presence of a haplotype common to Hokkaido and Niigata implies that the haplotype migrated across the Tsugaru Strait. Considering that geological evidence indicates that the Tsugaru Strait was continuously present even during the last glacial maximum when the sea level was at its lowest, accidental transport by human beings or animals might have been critical to the migration of Ligidium.
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Affiliation(s)
- Wakana Harigai
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan,
| | - Aya Saito
- Department of Earth and Planetary Sciences, School of Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Masanobu Yamamoto
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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Zhang Z, Kass JM, Mammola S, Koizumi I, Li X, Tanaka K, Ikeda K, Suzuki T, Yokota M, Usio N. Lineage‐level distribution models lead to more realistic climate change predictions for a threatened crayfish. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13225] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Zhixin Zhang
- Graduate School of Marine Science and Technology Tokyo University of Marine Science and Technology Tokyo Japan
| | - Jamie M. Kass
- Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University Tancha, Onna‐son, Kunigami‐gun Okinawa Japan
| | - Stefano Mammola
- Molecular Ecology Group (MEG) Water Research Institute National Research Council of Italy (CNR‐IRSA) Verbania Pallanza Italy
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (LUOMUS) University of Helsinki Helsinki Finland
| | - Itsuro Koizumi
- Faculty of Environmental Earth Science Hokkaido University Sapporo Japan
| | - Xuecao Li
- College of Land Science and Technology China Agricultural University Beijing China
| | - Kazunori Tanaka
- Faculty of Humanities and Human Sciences Hokkaido University Sapporo Japan
| | | | - Toru Suzuki
- Department of Environmental and Symbiotic Sciences College of Agriculture, Food and Environmental Sciences Rakuno Gakuen University Ebetsu Japan
| | - Masashi Yokota
- Graduate School of Marine Science and Technology Tokyo University of Marine Science and Technology Tokyo Japan
| | - Nisikawa Usio
- Institute of Nature and Environmental Technology Kanazawa University Kanazawa Japan
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Pârvulescu L, Iorgu EI, Zaharia C, Ion MC, Satmari A, Krapal AM, Popa OP, Miok K, Petrescu I, Popa LO. The future of endangered crayfish in light of protected areas and habitat fragmentation. Sci Rep 2020; 10:14870. [PMID: 32913322 PMCID: PMC7483723 DOI: 10.1038/s41598-020-71915-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 07/28/2020] [Indexed: 11/09/2022] Open
Abstract
The long-term survival of a species requires, among other things, gene flow between populations. Approaches for the evaluation of fragmentation in the frame of freshwater habitats consider only a small amount of the information that combined demography and geography are currently able to provide. This study addresses two species of Austropotamobius crayfish in the light of population genetics, spatial ecology and protected areas of the Carpathians. Advancing the classical approaches, we defined ecological distances upon the rasterised river network as a surrogate of habitat resistance to migration, quantifying the deviations from the species´ suitability range for a set of relevant geospatial variables in each cell of the network. Molecular analyses revealed the populations of the two Austropotamobius crayfish species are clearly distinct, lacking hybridisation. Comparing pairs of populations, we found, in some cases, a strong disagreement regarding genetic and ecological distances, potentially due to human-mediated translocations or the geophysical phenomena of regressive erosion, which may have led to unexpected colonisation routes. Protected areas were found to offer appropriate local habitat conditions but failed to ensure connectivity. The methodology applied in this study allowed us to quantify the contribution of each geospatial (environmental) variable to the overall effect of fragmentation, and we found that water quality was the most important variable. A multilevel approach proved to reveal a better understanding of drivers behind the distribution patterns, which can lead to more adequate conservation measures.
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Affiliation(s)
- Lucian Pârvulescu
- Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, 300115, Timisoara, Romania.
| | - Elena-Iulia Iorgu
- "Grigore Antipa" National Museum of Natural History, 011341, Bucharest, Romania.
| | - Claudia Zaharia
- Department of Mathematics, Faculty of Mathematics and Computer Science, West University of Timisoara, 300223, Timisoara, Romania
| | - Mihaela C Ion
- Institute of Biology Bucharest, Romanian Academy, 060031, Bucharest, Romania
- Faculty of Biology, University of Bucharest, 050095, Bucharest, Romania
| | - Alina Satmari
- Department of Geography, Faculty of Chemistry, Biology, Geography, West University of Timisoara, 300223, Timisoara, Romania
| | - Ana-Maria Krapal
- "Grigore Antipa" National Museum of Natural History, 011341, Bucharest, Romania
| | - Oana-Paula Popa
- "Grigore Antipa" National Museum of Natural History, 011341, Bucharest, Romania
| | - Kristian Miok
- Department of Informatics, Faculty of Mathematics and Computer Science, West University of Timisoara, 300223, Timisoara, Romania
| | - Iorgu Petrescu
- "Grigore Antipa" National Museum of Natural History, 011341, Bucharest, Romania
| | - Luis-Ovidiu Popa
- "Grigore Antipa" National Museum of Natural History, 011341, Bucharest, Romania
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Graham MR, Santibáñez‐López CE, Derkarabetian S, Hendrixson BE. Pleistocene persistence and expansion in tarantulas on the Colorado Plateau and the effects of missing data on phylogeographical inferences from RADseq. Mol Ecol 2020; 29:3684-3701. [DOI: 10.1111/mec.15588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Matthew R. Graham
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | | | - Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology Museum of Comparative Zoology Harvard University Cambridge MA USA
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Next generation sequencing-aided comprehensive geographic coverage sheds light on the status of rare and extinct populations of Aporia butterflies (Lepidoptera: Pieridae). Sci Rep 2020; 10:13970. [PMID: 32811885 PMCID: PMC7434888 DOI: 10.1038/s41598-020-70957-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/07/2020] [Indexed: 11/08/2022] Open
Abstract
The Black-veined White Aporia crataegi (Linnaeus, 1758), a common and widespread butterfly ranging from northwestern Africa to Europe and Asia, has been extinct in Britain since the 1920s and is on a steady decline in several other parts of its range. In order to investigate genetic diversity within A. crataegi and its correspondence with current subspecies-level taxonomy, we barcoded 173 specimens from across its range including, for the first time, extinct populations from Britain and Korea. Using next generation sequencing we also obtained a sequence for Aporia joubini, a peculiar taxon from China known only by its type specimen collected in the early twentieth century. Our phylogenetic analysis placed A. joubini sister to A. oberthuri, although further taxon sampling may reveal a different scheme. Within A. crataegi, we observed a shallow and weak mitogenomic structure with only a few distinct lineages in North Africa, Sicily, Iran, and Japan. Eurasian populations, including those extinct in Britain and Korea, clustered into a large set of closely allied lineages, consistent with a recent expansion during the Late Pleistocene glacial period. This study highlights the importance of museum collections and the unique opportunities they provide in documenting species diversity and helping conservation efforts.
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Yano K, Takenaka M, Tojo K. Genealogical Position of Japanese Populations of the Globally Distributed Mayfly Cloeon dipterum and Related Species (Ephemeroptera, Baetidae): A Molecular Phylogeographic Analysis. Zoolog Sci 2020; 36:479-489. [PMID: 31833319 DOI: 10.2108/zs190049] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/11/2019] [Indexed: 11/17/2022]
Abstract
In the present study, we add genetic data of the mayfly Cloeon dipterum collected from the Japanese Islands to the established molecular phylogenetic knowledge in the mitochondrial COI gene of Cloeon mayflies. Cloeon dipterum is a typical cosmopolitan species that includes six intraspecific haplotype groups. The present phylogenetic analysis revealed that haplotypes of the Japanese C. dipterum constitute a seventh group together with a haplotype from Korea. This East Asian group forms a sister group with previously known European and North American haplotype groups (i.e., the clade CT1 to CT3). The present phylogenetic analysis further revealed the occurrence of two described species (C. dipterum and Cloeon ryogokuensis) and possibly three species (Cloeon sp. 1 to 3) in Japan. Consideration is given to the degree of genetic differentiation, divergence time, and differentiation process among these seven genetic groups.
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Affiliation(s)
- Koki Yano
- Department of Biology, Graduate School of Science and Technology, Shinshu University, Matsumoto, Nagano 390-8621, Japan.,Department of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Masaki Takenaka
- Department of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, Nagano 390-8621, Japan, .,Institute of Mountain Science, Interdisciplinary Cluster for Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan,
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Sherpa S, Blum MGB, Després L. Cold adaptation in the Asian tiger mosquito's native range precedes its invasion success in temperate regions. Evolution 2019; 73:1793-1808. [DOI: 10.1111/evo.13801] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/06/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Stéphanie Sherpa
- Université Grenoble Alpes CNRS, UMR 5553 LECA F‐38000 Grenoble France
| | - Michael G. B. Blum
- Université Grenoble Alpes CNRS, UMR 5525 TIMC‐IMAG F‐38000 Grenoble France
| | - Laurence Després
- Université Grenoble Alpes CNRS, UMR 5553 LECA F‐38000 Grenoble France
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Phylogeography of freshwater planorbid snails reveals diversification patterns in Eurasian continental islands. BMC Evol Biol 2018; 18:164. [PMID: 30400816 PMCID: PMC6219199 DOI: 10.1186/s12862-018-1273-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/08/2018] [Indexed: 01/19/2023] Open
Abstract
Background Islands have traditionally been the centre of evolutionary biological research, but the dynamics of immigration and differentiation at continental islands have not been well studied. Therefore, we focused on the Japanese archipelago, the continental islands located at the eastern end of the Eurasian continent. While the Japanese archipelago is characterised by high biodiversity and rich freshwater habitats, the origin and formation mechanisms of its freshwater organisms are not clear. In order to clarify the history of the planorbid gastropod fauna, we conducted phylogenetic analysis, divergence time estimation, ancestral state reconstruction, and lineage diversity estimations. Results Our analyses revealed the formation process of the planorbid fauna in the Japanese archipelago. Most lineages in the Japanese archipelago have closely related lineages on the continent, and the divergence within the Japanese lineages presumably occurred after the late Pliocene. In addition, each lineage is characterised by different phylogeographical patterns, suggesting that immigration routes from the continent to the Japanese archipelago differ among lineages. Furthermore, a regional lineage diversity plot showed that the present diversity in the Japanese archipelago potentially reflects the differentiation of lineages within the islands after the development of the Japanese archipelago. Conclusions Although additional taxon sampling and genetic analysis focused on each lineage are needed, our results suggest that immigration from multiple routes just prior to the development of the Japanese archipelago and subsequent diversification within the islands are major causes of the present-day diversity of the Japanese planorbid fauna. Electronic supplementary material The online version of this article (10.1186/s12862-018-1273-3) contains supplementary material, which is available to authorized users.
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Kobayashi H, Haino Y, Iwasaki T, Tezuka A, Nagano AJ, Shimada S. ddRAD-seq based phylogeographic study of Sargassum thunbergii (Phaeophyceae, Heterokonta) around Japanese coast. MARINE ENVIRONMENTAL RESEARCH 2018; 140:104-113. [PMID: 29895505 DOI: 10.1016/j.marenvres.2018.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Using genome-wide SNP data obtained from high-throughput techniques based on double digest restriction site-associated DNA sequencing (ddRAD-seq), we elucidated the migration history and genetic diversity of the Japanese population of the ecologically important brown seaweed Sargassum thunbergii (Mertens ex Roth) Kuntze. STRUCTURE and NeighborNet analyses showed a clear genetic differentiation among populations of four geographic regions: Kyushu (POP1); Sea of Japan (POP2); Hokkaido and Tohoku (POP3); and Pacific coast from Kyushu to Kanto (POP4). Approximate Bayesian Computation (ABC) analysis indicated that POP4 diverged first, followed by the separation between POP2 (the largest effective population size) and POP3; POP1 was the last to form, shaped by the mixture of POP2 (73%) and POP4 (27%). High genetic diversity was detected in POP1 and POP2, whereas low genetic diversity was detected in POP3 and POP4. These results indicated that S. thunbergii populations of Kyushu and the Sea of Japan might have been maintained as large and stable populations gathered different lineages from China, Korea and/or Japan.
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Affiliation(s)
- Honoka Kobayashi
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Yuka Haino
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Takaya Iwasaki
- Faculty of Science, Kanagawa University, Tsuchiya 2946, Hiratsuka, Kanagawa, 259-1293, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
| | - Satoshi Shimada
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan.
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Miyamoto Y, Narimatsu M, Nara K. Effects of climate, distance, and a geographic barrier on ectomycorrhizal fungal communities in Japan: A comparison across Blakiston's Line. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Miranda I, Gomes KM, Ribeiro FB, Araujo PB, Souty-Grosset C, Schubart CD. Molecular systematics reveals multiple lineages and cryptic speciation in the freshwater crayfish Parastacus brasiliensis (von Martens, 1869) (Crustacea : Decapoda : Parastacidae). INVERTEBR SYST 2018. [DOI: 10.1071/is18012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The characterisation of intraspecific genetic diversity in representatives of the South American crayfish genus Parastacus Huxley, 1879 is here carried out for the first time by comparing populations of Parastacus brasiliensis (von Martens, 1869) as currently defined. Phylogenetic reconstructions based on mitochondrial and nuclear markers indicate the existence of multiple lineages, of which only one can be considered as P. brasiliensis sensu stricto. In addition, there are seven other lineages, one of which is the subspecies Parastacus brasiliensis promatensis Fontoura & Conter, 2008, which is here elevated to species level. We thereby increase to 14 the number of recognised species within Parastacus in South America. Genetic distances among P. brasiliensis sensu stricto and the lineages ‘A’, ‘B’ and ‘C’ increase with geographical distances, suggesting isolation by distance as an important driver of diversification, and eventually speciation, in these burrowing crayfishes. Parastacus brasiliensis occurs mainly in the Guaíba Lake basin and studied populations show limited connectivity and gene flow, probably due to habitat fragmentation. On the basis of genetic and distribution data, the conservation status of P. brasiliensis sensu stricto is confirmed as Near Threatened (NT). These findings lead us to encourage the establishment of preservation areas for isolated populations. The importance of preserving the newly recognised distinct gene pools in order to maintain overall genetic diversity is emphasised.
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Bláha M, Patoka J, Kozák P, Kouba A. Unrecognized diversity in New Guinean crayfish species (Decapoda, Parastacidae): The evidence from molecular data. Integr Zool 2017; 11:457-468. [PMID: 27264730 DOI: 10.1111/1749-4877.12211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The phylogenetic relationships among imported ornamental crayfish belonging to the genus Cherax were inferred from a combined dataset of 3 mitochondrial genes (COI, 16S and 12S) and by comparison with available GenBank sequences of 14 Cherax species. Furthermore, the concordance of previously described species obtained from a wholesaler (Cherax boesemani, C. holthuisi and C. peknyi) with available GenBank sequences was verified based on COI with special respect to comparison with sequences assigned as Cherax species. Recently described species C. gherardiae, C. pulcher and C. subterigneus belong to the northern group of Cherax species. Comparison and analysis with other GenBank COI sequences show previously unreported diversity of New Guinean species, suggesting 5 putative new species. Surprisingly, species assigned to the subgenus Astaconephrops do not form a monophyletic clade; this subgenus should be reappraised relative to the purported typical morphological characteristic of the uncalcified patch on male chelae. Increasing importation of crayfish underscores the importance of accurate species identification. Use of basic molecular methods is a necessary requisite for documenting occurrence, abundance and population trends of target species. Consequently, it helps to support eventual conservation decision-making by stakeholders.
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Affiliation(s)
- Martin Bláha
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Jiří Patoka
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Praha, Czech Republic
| | - Pavel Kozák
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Antonín Kouba
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
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Clavero M, Nores C, Kubersky-Piredda S, Centeno-Cuadros A. Interdisciplinarity to reconstruct historical introductions: solving the status of cryptogenic crayfish. Biol Rev Camb Philos Soc 2015; 91:1036-1049. [DOI: 10.1111/brv.12205] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 05/28/2015] [Accepted: 06/05/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Miguel Clavero
- Estación Biológica de Doñana-CSIC; Américo Vespucio s.n. 41092 Sevilla Spain
| | - Carlos Nores
- Indurot, Universidad de Oviedo; Campus de Mieres 3006 Mieres Asturias, Spain
| | - Susanne Kubersky-Piredda
- Minerva Research Group; Bibliotheca Hertziana, Max Planck Institute for Art History; Via Gregoriana 28 I-00187 Rome Italy
| | - Alejandro Centeno-Cuadros
- Department of Molecular Biology & Biochemical Engineering; University Pablo de Olavide; Carretera de Utrera km 1 41013 Seville Spain
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Morii Y, Yokoyama J, Kawata M, Davison A, Chiba S. Evidence of introgressive hybridization between the morphologically divergent land snailsAinohelixandEzohelix. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12466] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yuta Morii
- Graduate School of Life Sciences; Tohoku University; Sendai Miyagi 980-8576 Japan
| | - Jun Yokoyama
- Department of Biology; Faculty of Science; Yamagata University; Kojirakawa Yamagata 990-8560 Japan
| | - Masakado Kawata
- Graduate School of Life Sciences; Tohoku University; Sendai Miyagi 980-8576 Japan
| | - Angus Davison
- Centre for Genetics and Genomics; School of Life Sciences; University of Nottingham; Nottingham NG7 2RD UK
| | - Satoshi Chiba
- Graduate School of Life Sciences; Tohoku University; Sendai Miyagi 980-8576 Japan
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Jean CT, Wu CY, Tsai KC, Wang WK, Hsu YY, Chang YM, Lin HD. Population genetic structure in the endemic cyprinid fish Microphysogobio alticorpus in Taiwan: Evidence for a new phylogeographical area. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Osborne MJ, Perkin JS, Gido KB, Turner TF. Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes. Mol Ecol 2014; 23:5663-79. [PMID: 25327780 DOI: 10.1111/mec.12970] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/06/2014] [Accepted: 10/15/2014] [Indexed: 11/28/2022]
Abstract
We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic-spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic-spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most tributary basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross-basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and in response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA
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Yamada M, Ishibashi R, Toyoda K, Kawamura K, Komaru A. Phylogeography of the Brackish Water ClamCorbicula japonicaAround the Japanese Archipelago Inferred from Mitochondrial COII Gene Sequences. Zoolog Sci 2014; 31:168-79. [DOI: 10.2108/zsj.31.168] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Clavero M, Villero D. Historical Ecology and Invasion Biology: Long-Term Distribution Changes of Introduced Freshwater Species. Bioscience 2013. [DOI: 10.1093/biosci/bit014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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25
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Graham MR, Jaeger JR, Prendini L, Riddle BR. Phylogeography of Beck’s Desert Scorpion, Paruroctonus becki, reveals Pliocene diversification in the Eastern California Shear Zone and postglacial expansion in the Great Basin Desert. Mol Phylogenet Evol 2013; 69:502-13. [DOI: 10.1016/j.ympev.2013.07.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 07/10/2013] [Accepted: 07/29/2013] [Indexed: 11/28/2022]
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