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Nishida S, Takano A, Suyama Y, Kakishima S. Detection of reproductive interference between closely related Salvia species with small-scale separated distributions by multifaceted pollination and molecular analyses. JOURNAL OF PLANT RESEARCH 2024:10.1007/s10265-024-01577-6. [PMID: 39214907 DOI: 10.1007/s10265-024-01577-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Reproductive interference, an interspecific interaction in reproductive process that exerts an adverse effect, has gained attention as a contributing factor in promoting exclusive distributions between closely related species. However, detailed studies on the possibility of reproductive interference between native plants are still lacking, presumably because strong reproductive interference can rapidly realize exclusive distributions, leaving the two species apparently independent. Salvia japonica and S. lutescens are found in separate localities at a small scale, although their distributions overlap at a large scale. We investigated the possibility of reproductive interference between them through field surveys, hand-pollination experiments, evaluation of hybrid fertility, cpDNA and nrDNA genotyping, and genome-wide DNA analysis. The field survey results did not reveal apparent negative interaction in competition for pollinator services. Mixed pollination with conspecific pollen and counterpart pollen reduced seed set in S. japonica, and hybrid progeny produced by mixed pollination were less than 20% as fertile compared to the pure species. The DNA genotyping results suggested the possibility of hybridization where their distributions overlap, and the genome-wide DNA analysis results showed clear genetic differentiation between the two species as well as the existence of hybrids. These results suggest that bi-directional reproductive interference between S. japonica and S. lutescens may have led to their present separated distributions at a small scale.
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Affiliation(s)
- Sachiko Nishida
- Nagoya University Museum, Furo-Cho, Chikusa-Ku, Nagoya, 464-8601, Japan.
| | - Atsuko Takano
- University of Hyogo/ Museum of Nature and Human Activities, Yayoigaoka 6, Sanda, Hyogo, 669-1546, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Satoshi Kakishima
- Department of Botany, National Museum of Nature and Science, 4-1-1, Amakubo, Tsukuba-Shi, Ibaraki, 305-0005, Japan
- The Mt. Fuji Institute for Nature and Biology, Showa University, 4562 Kamiyoshida, Fujiyoshida, Yamanashi, 403-0005, Japan
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2
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Shinke T, Yamazaki A, Nakamura S, Kudoh H, Hosokawa M. Genetic diversification of allohexaploid Brassica hybrids (AABBCC) using a fertile octoploid with excessive C genome set (AABBCCCC). PLANTA 2024; 260:71. [PMID: 39136783 DOI: 10.1007/s00425-024-04497-w] [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: 06/13/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024]
Abstract
MAIN CONCLUSION Using octoploid somatic hybrids with excessive C genome sets, AABBCCCC, a diverse allohexaploid, AABBCC, was produced by C genome reduction through subsequent crossing with various AABB cultivars. Even when somatic hybrids are produced, the plants that are produced are rarely in themselves an innovative crop. In this study, we used somatic hybrids of Brassica juncea (AABB) and B. oleracea (CC) as model cases for the genetic diversification of the somatic hybrids. One cell of 'Akaoba Takana' (B. juncea) and two cells of 'Snow Crown' (B. oleracea) were fused to create several somatic hybrids with excessive C genomes, AABBCCCC. Using AABBCCCC somatic hybrids as mother plants and crossing with 'Akaoba Takana', the AABBCC progenies were generated. When these AABBCC plants were self-fertilized, and flow cytometric (FCM) analysis was performed on the next generations, differences in the relative amount of genome size variation were observed, depending on the different AABBCCCC parents used for AABBCC creation. Further self-progeny was obtained for AABBCC plants with a theoretical allohexaploid DNA index by FCM. However, as the DNA indices of the progeny populations varied between plants used and aneuploid individuals still occurred in the progeny populations, it was difficult to say that the allohexaploid genome was fully stabilized. Next, to obtain genetic diversification of the allohexaploid, different cultivars of B. juncea were crossed with AABBCCCC, resulting in diverse AABBCC plants. Genetic diversity can be further expanded by crossbreeding plants with different AABBCC genome sets. Although genetic stability is necessary to ensure in the later generations, the results obtained in this study show that the use of somatic hybrids with excess genomes is an effective strategy for creating innovative crops.
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Affiliation(s)
- Teppei Shinke
- Faculty of Agriculture, Kindai University, Nara, 631-8505, Japan
| | - Akira Yamazaki
- Faculty of Agriculture, Kindai University, Nara, 631-8505, Japan
| | - Soraha Nakamura
- Faculty of Agriculture, Kindai University, Nara, 631-8505, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Munetaka Hosokawa
- Faculty of Agriculture, Kindai University, Nara, 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, Nara, 631-8505, Japan.
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3
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Konaka S, Hirota SK, Sato Y, Matsumoto N, Suyama Y, Tsumura Y. Secondary contact zone and genetic introgression in closely related haplodiploid social spider mites. Heredity (Edinb) 2024:10.1038/s41437-024-00708-y. [PMID: 39090316 DOI: 10.1038/s41437-024-00708-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
How frequently hybridisation and gene flow occur in the contact zones of diverging taxa is important for understanding the speciation process. Stigmaeopsis sabelisi and Stigmaeopsis miscanthi high-aggression form (hereafter, S. miscanthi HG) are haplodiploid, social spider mites that infest the Chinese silver grass, Miscanthus sinensis. These two species are closely related and parapatrically distributed in Japan. In mountainous areas, S. sabelisi and S. miscanthi HG are often found in the highlands and lowlands, respectively, suggesting that they are in contact at intermediate altitudes. It is estimated that they diverged from their common ancestors distributed in subtropical regions (south of Japan) during the last glacial period, expanded their distribution into the Japanese Archipelago, and came to have such a parapatric distribution (secondary contact). As their reproductive isolation is strong but incomplete, hybridisation and genetic introgression are expected at their distributional boundaries. In this study, we investigated their spatial distribution patterns along the elevation on Mt. Amagi using male morphological differences, and investigated their hybridisation status using single-nucleotide polymorphisms by MIG-seq. We found their contact zone at altitudes of 150-430 m, suggesting that their contact zone is prevalent in the parapatric area, which is in line with a previous study. Interspecific mating was predicted based on the sex ratio in the contact zone. No obvious hybrids were found, but genetic introgression was detected although it was extremely low.
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Affiliation(s)
- Shota Konaka
- Master Program in Biology, Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
- Botanical Gardens, Osaka Metropolitan University 2000 Kisaichi, Katano City, Osaka, 576-0004, Japan
| | - Yukie Sato
- Faculty of Life and Environmental Sciences / Mountain Science Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Naoki Matsumoto
- Master Program in Biology, Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences / Mountain Science Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
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4
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Nakajima S, Tsuri K. Testing the applicability of environmental DNA metabarcoding to landscape genetics. Mol Ecol Resour 2024; 24:e13990. [PMID: 38923125 DOI: 10.1111/1755-0998.13990] [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: 03/07/2024] [Revised: 06/01/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
Landscape genetics is a field dealing with local genetic differences and contributes to strategic conservation planning. Recently, environmental DNA (eDNA) metabarcoding has proven useful not only for detecting species but also for assessing genetic diversity and genetic structure on a large scale such as in phylogeography. However, it remains unclear whether eDNA analysis also has sufficient power to perform the landscape genetics, which focuses on a local scale. To reveal the applicability of eDNA to landscape genetics, we conducted an eDNA metabarcoding analysis of the mitochondrial DNA D-loop region of the fluvial sculpin Cottus nozawae in the upper Sorachi River in Japan and compared the results with inferences based on traditional tissue-based approaches by the same D-loop region and genome-wide SNP data. As a result, the spatial distribution of haplotypes was generally consistent between the eDNA- and tissue-based approaches. In addition, the genetic differentiation statistics calculated using eDNA and tissue samples were highly correlated when comparing both in the D-loop region. The removal of low-frequency reads or the conversion to semi-quantitative rankings of eDNA data did not alter the correlation of genetic diversity and differentiation statistics with tissue-based approaches much. Finally, we confirmed that analyses using eDNA data can reveal patterns such as isolation-by-distance shown in previous studies on this species, indicating the applicability of eDNA to basic landscape genetics. Even though some limitations remain, eDNA may have great potential for conducting basic landscape genetics.
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Affiliation(s)
- Souta Nakajima
- Watershed Restoration Research Team, Public Works Research Institute, Tsukuba, Japan
| | - Kenji Tsuri
- Watershed Restoration Research Team, Public Works Research Institute, Tsukuba, Japan
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Mizuki M, Kaneko Y, Yukie Y, Suyama Y, Hirota SK, Sawa S, Kubo M, Yamawo A, Sasabe M, Ikeda H. Evolution of secondary metabolites, morphological structures and associated gene expression patterns in galls induced by four closely related aphid species on a host plant species. Mol Ecol 2024; 33:e17466. [PMID: 39022998 DOI: 10.1111/mec.17466] [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: 02/16/2024] [Revised: 04/12/2024] [Accepted: 04/25/2024] [Indexed: 07/20/2024]
Abstract
Gall-forming insects induce various types of galls on their host plants by altering gene expression in host plant organs, and recent studies have been conducted for gene expression in galls. However, the evolutionary trajectories of gene expression patterns and the resulting phenotypes have not yet been studied using multiple related species. We investigated the speciation and the diversification process of galls induced by four closely related aphid species (Hormaphidini) on a host plant species (Hamamelis japonica) by examining the phylogenetic congruence between the geographical divergences of aphids and the host plant, and by comparing their gene expression patterns and resulting phenotypes. Phylogenetic analysis of aphids and the host plant showed that geographical isolation among host plant populations has interrupted gene flow in aphids and accelerated the speciation process. The concentration of phenolics and the complexity of the internal structure of galls were correlated with the expression levels of genes for the biosynthesis of phenolics and morphogenesis respectively. These results suggest that the expression levels of genes for the biosynthesis of phenolics and morphogenesis have evolutionarily increased in galls accelerated by the speciation process of aphids due to the distribution change of the host plant, leading to the related phenotypic evolution. Our study showed the evolutionary process of phenotypic traits in galls in the wild from both gene expression and actual phenotype levels.
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Affiliation(s)
- Mayu Mizuki
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
- Ina Research Inc., Ina, Nagano, Japan
| | - Yohei Kaneko
- Fukuoka Institute of Health and Environmental Sciences, Dazaifu, Fukuoka, Japan
| | | | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
- Botanical Gardens, Osaka Metropolitan University, Katano City, Osaka, Japan
| | - Shinichiro Sawa
- International Research Center for Agricultural and Environmental Biology (IRCAEB), Kumamoto Universrity | International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, Japan
| | - Minoru Kubo
- Center for Digital Green-Innovation, Nara Institute of Science and Technology, Nara, Japan
| | - Akira Yamawo
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Michiko Sasabe
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
| | - Hiroshi Ikeda
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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6
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Masuda T, Shimono Y, Kishi D, Koizumi I. Evaluation of genetic consequences of stocking on the southern-margin populations of white-spotted charr. Ecol Evol 2024; 14:e70140. [PMID: 39130102 PMCID: PMC11311121 DOI: 10.1002/ece3.70140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/03/2024] [Accepted: 07/17/2024] [Indexed: 08/13/2024] Open
Abstract
Coldwater-adapted freshwater fishes, especially their populations along warm-range margins, are most vulnerable to the climate oscillations associated with global warming. Stocking is a major strategy for avoiding the extinction of these species. However, while stocking can reverse the decline of isolated populations, it may also result in a loss of genetic diversity in the native local population due to the introgressive replacement of hatchery genes. To plan an adequate strategy for conserving locally adapted populations, the genetic impacts of stocking on native lineages should be evaluated from small river branches to wide-ranging drainage areas. We investigated the population genetic structure of white-spotted charr (Salvelinus leucomaenis) within its southern range (Lake Biwa basin, Japan). By applying genome-wide SNP analysis to the population's genetic structure, we assessed the extent of genetic introgression resulting from stocking. White-spotted charr in the Lake Biwa watershed constitutes a distinctive genetic group, within which apparent genetic differentiation was observed. The hatchery-reared fish line commonly used for supplementation stocking in the catchment was discernable from the native population, enabling us to analyze genetic introgression across the entire drainage area. Admixed individuals resulting from hatchery introgression were observed in most of the stocked sites that showed relatively high heterozygosity and nucleotide diversity. However, their genetic differentiation was much lower than that of native populations. The supplementation history as well as the road availability contributed substantially to the introgression of hatchery genes. Populations with the native genetic structure remained in the upstream regions of the tested rivers. However, their heterozygosity and nucleotide diversity were low when compared with that of the populations with hatchery supplementation. Our results shed light on the genetic impacts of stocking on isolated native populations and suggest that conventional supplementation methods cannot preserve a unique biodiversity in the distribution margin.
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Affiliation(s)
- Taro Masuda
- Laboratory of Marine Biology, Division of Applied Biological Science, Faculty of AgricultureSetsunan UniversityHirakata, OsakaJapan
| | - Yoshiko Shimono
- Laboratory of Weed Science, Graduate School of AgricultureKyoto UniversityKyotoJapan
| | - Daisuke Kishi
- Gero Branch, Gifu Prefectural Research Institute for Fisheries and Aquatic EnvironmentsGifuJapan
| | - Itsuro Koizumi
- Faculty of Environmental Earth ScienceHokkaido UniversitySapporoHokkaidoJapan
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7
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Nagata N. Phylogeography of Parnassius citrinarius Based on Mitochondrial DNA Reveals Large Differences in Genetic Structure between the Eastern and Western Japan. Zoolog Sci 2024; 41:385-391. [PMID: 39093284 DOI: 10.2108/zs230072] [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: 07/23/2023] [Accepted: 04/01/2024] [Indexed: 08/04/2024]
Abstract
The Japanese Archipelago hosts a rich butterfly fauna, and elucidating the genetic structures of multiple species is necessary to clarify their formation processes. This study aimed to reveal the genetic structure and distribution formation process of Parnassius citrinarius, which is widely distributed across the Japanese Archipelago from Hokkaido to Shikoku, through phylogeographic analysis based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence. Thirty haplotypes were revealed from 311 individuals from 47 sites, indicating significant differences in the genetic structures between the eastern and western parts of the Japanese Archipelago. In Eastern Japan, multiple genetic clusters were found, with some sites harboring two clusters. The divergence times among populations in Eastern Japan were relatively recent, and no genetic differentiation was observed between regions, including between Hokkaido and Honshu, which are separated by a narrow strait. In contrast, in Western Japan, including Shikoku, unique genetic clusters were observed in each region. The phylogenetic relationships among populations were regionally clustered, and the divergence times were relatively ancient. The distribution and genetic structure of P. citrinarius in the Japanese Archipelago have been significantly influenced by temperature fluctuations and the presence of geographical barriers during the Pleistocene glacial-interglacial cycles, including the potential formation of refugia in Western Japan.
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Affiliation(s)
- Nobuaki Nagata
- Department of Anthropology, National Museum of Nature and Science, Ibaraki 305-0005, Japan,
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8
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Sasaki T, Islam J, Hara K, Nochi T, Tanemura K. Male mice are susceptible to brain dysfunction induced by early-life acephate exposure. Front Neurosci 2024; 18:1404009. [PMID: 39050668 PMCID: PMC11266133 DOI: 10.3389/fnins.2024.1404009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
Background Acephate is a widely used organophosphate insecticide. Exposure to endocrine-disrupting chemicals, such as acephate, can interfere with neurodevelopment in childhood, increasing the risk of higher brain dysfunction later in life. Furthermore, brain dysfunction may be related to chemical exposure-related disturbances in the gut microbiota. However, the effects of early acephate exposure on the brains of adult males and females as well as on the adult gut environment remain poorly understood. Methods This study investigated the effects of perinatal acephate exposure on the central nervous system and gut microbiota of mice, including sex differences and environmentally relevant concentrations. C57BL/6 N pups were exposed to acephate (0, 0.3, 10, and 300 ppm) via the dam in their drinking water from embryonic day (E) 11.5 to postnatal day 14. We examined its effects on the central nervous system of adult males and females. Results In the male treatment group, impairments in learning and memory were detected. Immunohistochemical analysis revealed a decrease in SOX2-, NeuN-, DCX-, and GFAP-positive cells in the hippocampal dentate gyrus in males compared to the control group, whereas GFAP-positive cells were fewer in females. In addition, gut microbiota diversity was reduced in both sexes in the experimental group. Conclusion Our study demonstrates that the effects of early-life exposure to acephate are more pronounced in males than in females and can lead to a lasting impact on adult behavior, even at low doses, and that the gut microbiota may reflect the brain environment.
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Affiliation(s)
- Takahiro Sasaki
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Jahidul Islam
- Laboratory of Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Kenshiro Hara
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Tomonori Nochi
- Laboratory of Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Kentaro Tanemura
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
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Sugimoto K, Kawai R, Koizumi T, Matsuo A, Suyama Y, Mizuki I. Fine-scale clonal structure of the lingonberry Vaccinium vitis-idaea under the nurse plant Pinus pumila vegetation in an alpine region, Mt. Norikura. JOURNAL OF PLANT RESEARCH 2024; 137:619-626. [PMID: 38568301 DOI: 10.1007/s10265-024-01537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 03/06/2024] [Indexed: 07/09/2024]
Abstract
The nurse effect is a positive interaction in which a nurse plant improves the abiotic environment for another species (beneficiary plant) and facilitates its establishment. The evergreen shrub Vaccinium vitis-idaea (a beneficiary plant) grows mainly under the dwarf shrub Pinus pumila (a nurse plant) in the alpine regions of central Japan. However, whether V. vitis-idaea shrubs under various P. pumila shrubs spread through clonal growth and/or seeds remains unclear. We investigated the clonal structure of V. vitis-idaea under the nurse plant P. pumila in Japanese alpine regions. MIG-seq analysis was conducted to clarify the clonal diversity of V. vitis-idaea in isolated and patchy P. pumila plots on a ridge (PATs), and in a plot covered by dense P. pumila on a slope adjacent to the ridge (MAT) on Mt. Norikura, Japan. We detected 28 multilocus genotypes in 319 ramets of V. vitis-idaea across 11 PATs and MAT. Three genets expanded to more than 10 m in the MAT. Some genets were shared among neighboring PATs or among PATs and MAT. These findings suggest that the clonal growth of V. vitis-idaea plays an important role in the sustainability of populations. The clonal diversity of V. vitis-idaea was positively related with the spatial size of PATs and was higher in MAT than in PATs at a small scale. Therefore, the spatial spread of the nurse plant P. pumila might facilitate the nurse effect on the genetic diversity of beneficiary plants, leading to the sustainability of beneficiary populations.
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Affiliation(s)
- Kensuke Sugimoto
- Department of Biosciences, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-Ku, Tokyo, 156-8550, Japan
| | - Rio Kawai
- Department of Biosciences, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-Ku, Tokyo, 156-8550, Japan
| | - Takahiko Koizumi
- Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Ayumi Matsuo
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Inoue Mizuki
- Department of Biosciences, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-Ku, Tokyo, 156-8550, Japan.
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10
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Schnittler M, Inoue M, Shchepin ON, Fuchs J, Chang H, Lamkowski P, Knapp R, Horn K, Bennert HW, Bog M. Hybridization and reticulate evolution in Diphasiastrum (flat-branched clubmosses, Lycopodiaceae) - New data from the island of Taiwan and Vietnam. Mol Phylogenet Evol 2024; 196:108067. [PMID: 38561082 DOI: 10.1016/j.ympev.2024.108067] [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: 12/01/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
In the species groups related to Diphasiastrum multispicatum and D. veitchii, hybridization was investigated in samples from northern and southern Vietnam and the island of Taiwan, including available herbarium specimens from southeast Asia. The accessions were analyzed using flow cytometry (living material only), Sanger sequencing and multiplexed inter-simple sequence repeat genotyping by sequencing. We detected two cases of ancient hybridization involving different combinations of parental species; both led via subsequent duplication to tetraploid taxa. A cross D. multispicatum × D. veitchii from Malaysia represents D. wightianum, a tetraploid taxon according to reported DNA content measurements of dried material (genome formulas MM, VV and MMVV, respectively). The second case involves D. veitchii and an unknown diploid parent (genome formula XX). Three hybridogenous taxa (genome formulas VVX, VVXX, VVVX) were discernable by a combination of flow cytometry and molecular data. Taxon I (VVX, three clones found on Taiwan island) is apparently triploid. Taxon II represents another genetically diverse and sexual tetraploid species (VVXX) and can be assigned to D. yueshanense, described from Taiwan island but occurring as well in mainland China and Vietnam. Taxon III is as well most likely tetraploid (VVVX) and represented by at least one, more likely two, clones from Taiwan island. Taxa I and III are presumably asexual and new to science. Two independently inherited nuclear markers recombine only within, not between these hybrids, pointing towards reproductive isolation. We present an evolutionary scheme which explains the origin of the hybrids and the evolution of new and fully sexual species by hybridization and subsequent allopolyploidization in flat-branched clubmosses.
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Affiliation(s)
- M Schnittler
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Soldmannstraße 15, D-17487 Greifswald, Germany
| | - M Inoue
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Soldmannstraße 15, D-17487 Greifswald, Germany
| | - O N Shchepin
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Soldmannstraße 15, D-17487 Greifswald, Germany
| | - J Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Stadt Seeland, D-06466 OT Gatersleben, Germany
| | - H Chang
- Division of Botany, Endemic Species Research Institute, 1, Ming Seng E. Road, Jiji, Nantou 552, Taiwan, ROC
| | - P Lamkowski
- Nature Conservation and Land Use Planning, University of Applied Sciences Neubrandenburg, Brodaer Straße 2, D-17033 Neubrandenburg, Germany
| | - R Knapp
- Steigestraße 78, D-69412 Eberbach, Germany
| | - K Horn
- Büro für angewandte Geobotanik und Landschaftsökologie (BaGL), Frankenstraße 2, D-91077 Dormitz, Germany
| | - H W Bennert
- Evolution and Biodiversity of Plants, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - M Bog
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Soldmannstraße 15, D-17487 Greifswald, Germany.
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Simonov E, Lopatina NV, Titov SV, Ivanova AD, Brandler OV, Surin VL, Matrosova VA, Dvilis AE, Oreshkova NV, Kapustina SY, Golenishchev FN, Ermakov OA. Traditional multilocus phylogeny fails to fully resolve Palearctic ground squirrels (Spermophilus) relationships but reveals a new species endemic to West Siberia. Mol Phylogenet Evol 2024; 195:108057. [PMID: 38471598 DOI: 10.1016/j.ympev.2024.108057] [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: 10/05/2023] [Revised: 02/29/2024] [Accepted: 03/09/2024] [Indexed: 03/14/2024]
Abstract
Previous efforts to reconstruct evolutionary history of Palearctic ground squirrels within the genus Spermophilus have primarily relied on a single mitochondrial marker for phylogenetic data. In this study, we present the first phylogeny with comprehensive taxon sampling of Spermophilus via a conventional multilocus approach utilizing five mitochondrial and five nuclear markers. Through application of the multispecies coalescent model, we constructed a species tree revealing four distinct clades that diverged during the Late Miocene. These clades are 1) S. alaschanicus and S. dauricus from East Asia; 2) S. musicus and S. pygmaeus from East Europe and northwestern Central Asia; 3) the subgenus Colobotis found across Central Asia and its adjacent regions and encompassing S. brevicauda, S. erythrogenys, S. fulvus, S. major, S. pallidicauda, S. ralli, S. relictus, S. selevini, and S. vorontsovi sp. nov.; and 4) a Central/Eastern Europe and Asia Minor clade comprising S. citellus, S. taurensis, S. xanthoprymnus, S. suslicus, and S. odessanus. The latter clade lacked strong support owing to uncertainty of taxonomic placement of S. odessanus and S. suslicus. Resolving relationships within the subgenus Colobotis, which radiated rapidly, remains challenging likely because of incomplete lineage sorting and introgressive hybridization. Most of modern Spermophilus species diversified during the Early-Middle Pleistocene (2.2-1.0 million years ago). We propose a revised taxonomic classification for the genus Spermophilus by recognizing 18 species including a newly identified one (S. vorontsovi sp. nov.), which is found only in a limited area in the southeast of West Siberia. Employing genome-wide single-nucleotide polymorphism genotyping, we substantiated the role of the Ob River as a major barrier ensuring robust isolation of this taxon from S. erythrogenys. Despite its inherent limitations, the traditional multilocus approach remains a valuable tool for resolving relationships and can provide important insights into otherwise poorly understood groups. It is imperative to recognize that additional efforts are needed to definitively determine phylogenetic relationships between certain species of Palearctic ground squirrels.
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Affiliation(s)
- Evgeniy Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Frunze Str. 11, Novosibirsk 630091, Russia.
| | - Natalia V Lopatina
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Frunze Str. 11, Novosibirsk 630091, Russia
| | - Sergey V Titov
- Department of Zoology and Ecology, Penza State University, Krasnaya Str. 40, Penza 440026, Russia
| | - Anastasiya D Ivanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow 119991, Russia
| | - Oleg V Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Vadim L Surin
- National Medical Research Center for Hematology, Novyy Zykovskiy Pr. 4, Moscow 125167, Russia
| | - Vera A Matrosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow 119991, Russia
| | - Alisa E Dvilis
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Frunze Str. 11, Novosibirsk 630091, Russia
| | - Nataliya V Oreshkova
- Federal Research Center Krasnoyarsk Science Center, Siberian Branch of Russian Academy of Sciences, Akademgorodok Str. 50, Krasnoyarsk 660036, Russia; Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodnyy Ave. 79, Krasnoyarsk 660041, Russia; V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Akademgorodok Str. 50/28, Krasnoyarsk 660036, Russia; Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodnyy Ave. 79, Krasnoyarsk 660041, Russia
| | - Svetlana Yu Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Fedor N Golenishchev
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Emb. 1, Saint Petersburg 199034, Russia
| | - Oleg A Ermakov
- Department of Zoology and Ecology, Penza State University, Krasnaya Str. 40, Penza 440026, Russia.
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Nishimura K, Kokaji H, Motoki K, Yamazaki A, Nagasaka K, Mori T, Takisawa R, Yasui Y, Kawai T, Ushijima K, Yamasaki M, Saito H, Nakano R, Nakazaki T. Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2296-2317. [PMID: 38459738 DOI: 10.1111/tpj.16708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/14/2024] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
Next-generation sequencing (NGS) library construction often involves using restriction enzymes to decrease genome complexity, enabling versatile polymorphism detection in plants. However, plant leaves frequently contain impurities, such as polyphenols, necessitating DNA purification before enzymatic reactions. To overcome this problem, we developed a PCR-based method for expeditious NGS library preparation, offering flexibility in number of detected polymorphisms. By substituting a segment of the simple sequence repeat sequence in the MIG-seq primer set (MIG-seq being a PCR method enabling library construction with low-quality DNA) with degenerate oligonucleotides, we introduced variability in detectable polymorphisms across various crops. This innovation, named degenerate oligonucleotide primer MIG-seq (dpMIG-seq), enabled a streamlined protocol for constructing dpMIG-seq libraries from unpurified DNA, which was implemented stably in several crop species, including fruit trees. Furthermore, dpMIG-seq facilitated efficient lineage selection in wheat and enabled linkage map construction and quantitative trait loci analysis in tomato, rice, and soybean without necessitating DNA concentration adjustments. These findings underscore the potential of the dpMIG-seq protocol for advancing genetic analyses across diverse plant species.
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Affiliation(s)
- Kazusa Nishimura
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Hiroyuki Kokaji
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Ko Motoki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Akira Yamazaki
- Faculty of Agriculture, Kindai University, 3327-204, Nakamachi, Nara City, Nara, 631-8505, Japan
| | - Kyoka Nagasaka
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Mori
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Rihito Takisawa
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu City, Shiga, 520-2194, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Kawai
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Masanori Yamasaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2 no-cho, Nishi-ku, Niigata City, Niigata, 950-2181, Japan
| | - Hiroki Saito
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, 1091-1 Maezato-Kawarabaru, Ishigaki, Okinawa, 907-0002, Japan
| | - Ryohei Nakano
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
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Yuhara T, Ohtsuki H, Hirota SK, Suyama Y, Urabe J. Contrasting population genetic structure of three semi-terrestrial brachyuran crabs on the coast of the Japanese archipelago. Ecol Evol 2024; 14:e11484. [PMID: 38846710 PMCID: PMC11154805 DOI: 10.1002/ece3.11484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 04/16/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024] Open
Abstract
Anthropogenic activities have reduced ecotones between the ocean and land, which is likely to threaten the population of brackish-water brachyuran crabs. To assess the current status of these crabs, we examine the population genetic structures of three semi-terrestrial brachyuran crabs widely distributed along the coast of the Japan and to clarify factors determining their genetic structures. We collected 184 Orisarma dehaani, 252 Chiromantes haematocheir, and 151 Helice tridens crabs from 36 localities of the Japanese archipelago. Genome-wide SNP data from these crabs were analyzed using MIG-seq. Bayesian clustering of STRUCTURE and DAPC analysis were used to identify genetically disturbed populations and to visualize genetic differentiation between local populations. Genetic population structure showed clear differentiation between populations on the Pacific coast of the Tohoku region and on other Japanese coasts in O. dehaani, but not in C. haematocheir or H. tridens. The inbreeding coefficient of O. dehaani was significantly higher on the Pacific coast of the Tohoku region compared to other Japanese coasts. C. haematocheir and H. tridens had homogeneous genetic structures along the Japanese coast, but showed genetic differentiation of a local population at their range limits. Thus, O. dehaani showed little gene flow and clear genetic differentiation between populations in the Tohoku Pacific region and those on other Japanese coasts due to ocean currents. Although such a regional differentiation was not found in C. haematocheir and H. tridens, one population of C. haematocheir was genetically isolated at the edge of its distribution range and likely vulnerable to environmental changes.
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Affiliation(s)
- Takeshi Yuhara
- Graduate School of Life SciencesTohoku UniversitySendaiMiyagiJapan
- Present address:
National Institute for Environmental StudiesTsukubaIbarakiJapan
| | - Hajime Ohtsuki
- Graduate School of Life SciencesTohoku UniversitySendaiMiyagiJapan
| | - Shun K. Hirota
- Graduate School of Agricultural SciencesTohoku UniversityOsakiMiyagiJapan
- Botanical GardensOsaka Metropolitan UniversityKatanoOsakaJapan
| | - Yoshihisa Suyama
- Graduate School of Agricultural SciencesTohoku UniversityOsakiMiyagiJapan
| | - Jotaro Urabe
- Graduate School of Life SciencesTohoku UniversitySendaiMiyagiJapan
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Iwata H, Ito T, Park JS, Kokubugata G, Kakezawa A, Kurosawa T, Nishimura A, Noda H, Takayama K. Intraspecific divergence in a coastal plant, Euphorbia jolkinii, at a major biogeographic boundary in East Asia. AMERICAN JOURNAL OF BOTANY 2024; 111:e16327. [PMID: 38725176 DOI: 10.1002/ajb2.16327] [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: 08/24/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 05/29/2024]
Abstract
PREMISE Quaternary climatic fluctuations and long-distance seed dispersal across the sea are critical factors affecting the distribution of coastal plants, but the spatiotemporal nature of population expansion and distribution change of East Asian coastal plants during this period are rarely examined. To explore this process, we investigated the genome-wide phylogenetic patterns of Euphorbia jolkinii Boiss. (Euphorbiaceae), which grows widely on littoral areas of Japan, Korea, and Taiwan. METHODS We used plastome sequences and genome-wide single nucleotide polymorphisms in samples across the species range to reveal phylogeographic patterns and spatiotemporal distributional changes. We conducted ecological niche modeling for the present and the last glacial maximum (LGM). RESULTS Genetic differentiation was observed between the northern and southern populations of E. jolkinii, separated by the major biogeographic boundary, the Tokara Gap. These two groups of populations differentiated during the glacial period and subsequently intermingled in the intermorainic areas of the central Ryukyu Islands after the LGM. Ecological niche models suggested that the potential range of E. jolkinii was restricted to southern Kyushu; however, it was widespread in the southern Ryukyu Islands and Taiwan during the LGM. CONCLUSIONS This study provides evidence of genetic differentiation among coastal plant populations separated by the prominent biogeographical boundary. Although coastal plants are typically expected to maintain population connectivity through sea-drifted seed dispersal, our findings suggest that genetic differences may arise because of a combination of limited gene flow and changes in climate during the glacial period.
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Affiliation(s)
- Hiroyuki Iwata
- Department of Botany, Faculty of Science, Kyoto University, Kyoto, Japan
| | - Takuro Ito
- Botanical Gardens, Tohoku University, Sendai, Japan
| | - Jong-Soo Park
- Honam National Institute of Biological Resources, Mokpo-si, Jeollanam-do, South Korea
| | - Goro Kokubugata
- Department of Botany, National Museum of Nature and Science, Amakubo, Tsukuba, Japan
| | | | - Takahide Kurosawa
- Faculty of Symbiotic System Science, Fukushima University, Fukushima, Japan
| | - Akihiro Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroshi Noda
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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15
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Yang J, Park CG, Cho MS, Kim SC. Wasabi Gone Wild? Origin and Characterization of the Complete Plastomes of Ulleung Island Wasabi ( Eutrema japonicum; Brassicaceae) and Other Cultivars in Korea. Genes (Basel) 2024; 15:457. [PMID: 38674391 PMCID: PMC11049635 DOI: 10.3390/genes15040457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Korean wasabi occurs naturally on the young oceanic, volcanic Ulleung Island off the east coast of the Korean Peninsula. Although the Ulleung Island wasabi is reported as Eutrema japonicum and has been suggested to be morphologically identical to cultivars in Korea, very little is known about its taxonomic identity and relationship with other cultivars. In this study, we sequenced the complete chloroplast DNA sequences of three naturally occurring Ulleung Island wasabi plants and six cultivars ('Daewang', 'Daruma', 'Micado', 'Orochi', 'Green Thumb', and 'Shogun') from continental Korea and determined the taxonomic identity of Korean wasabi on Ulleung Island. The size and organization of the complete chloroplast genomes of the nine accessions were nearly identical to those of previously reported wasabi cultivars. In addition, phylogenetic analysis based on the complete plastomes suggested that Ulleung Island wasabi most likely comprises various wasabi cultivars with three chlorotypes ('Shogun', 'Green Thumb', and a unique Chusan type). Based on the complete plastomes, we identified eight chlorotypes for the major wasabi cultivars and the Ulleung Island wasabi. Two major groups (1-'Mazuma' and 'Daruma', and 2-'Fujidaruma'/'Shimane No. 3'/Ulleung Island wasabi/five cultivars in Korea) were also identified based on mother line genealogical history. Furthermore, different types of variations (mutations, insertions/deletions (indels), mononucleotide repeats, and inversions) in plastomes were identified to distinguish different cultivar lines and five highly divergent hotspots. The nine newly obtained complete plastomes are valuable organelle genomic resources for species identification and infraspecific phylogeographic studies on wild and cultivated wasabi.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea;
| | - Cheon Gyoo Park
- Gangwondo Agricultural Research and Extension Services, Wild Vegetable Reseaerch Institute, Alpine Agricultural Experiment Station, Taebaek-si 26046, Republic of Korea;
| | - Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Republic of Korea;
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Republic of Korea;
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Saito R, Nemoto Y, Kondo NI, Kanda K, Takeda T, Beasley JC, Tamaoki M. Study on the relationship between the dispersal of wild boar (Sus scrofa) and the associated variability of Cesium-137 concentrations in its muscle Post-Fukushima Daiichi Nuclear Power Plant accident. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170328. [PMID: 38301788 DOI: 10.1016/j.scitotenv.2024.170328] [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: 11/19/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024]
Abstract
After the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident in 2011, the wild boar (Sus scrofa) population within the Fukushima Evacuation Zone (FEZ) increased substantially in size and distribution. This growing population and their potential dispersal from the FEZ, where they are exposed to high levels of radionuclides, into the surrounding landscape underscores the need to better understand boar movement patterns in order to establish policies for managing shipping restrictions for boar meat and develop management strategies. In this study, we quantified the genetic population structure of boar in and around Fukushima prefecture using sequence data of the mitochondrial DNA control region and MIG-seq analysis using 348 boar samples to clarify boar dispersal patterns. Among boar samples, seven Asian haplotypes and one European haplotype were detected. The European haplotype originated from hybridization between domestic pigs and native boar in the evacuation zone after the accident and was detected in 15 samples across a broad geographic area. Our MIG-seq analysis revealed genetic structure of boar was significantly different between boar inhabiting the eastern (including FEZ. i.e., East clade) and western (i.e., West clade) regions in Fukushima prefecture. In addition, we investigated the relationships between boar dispersal and Cesium (Cs)-137 activity concentrations in boar muscle using MIG-seq genetic data in Nihonmatsu city, located in the central-northern region of Fukushima. High Cs-137 activity concentrations, exceeding 1000 Bq/kg, in boar muscle had a significantly high probability of belonging to the East clade within localized regions. Thus, our results provide evidence of the spatial scale of dispersal of individuals or offspring of boar from the FEZ. Results of this research also indicate that dispersal of individuals between areas with different Cs-137 contamination levels is one of the biggest factors contributing to variation in Cs-137 activity concentration in boar muscle within localized regions.
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Affiliation(s)
- Rie Saito
- Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken, SC 29802, USA; Fukushima Prefectural Centre for Environmental Creation, 10-2 Fukasaku, Miharu, Fukushima 963-7700, Japan; Fukushima Regional Collaborative Research Center, National Institute for Environmental Studies, 10-2 Fukasaku, Miharu, Fukushima 963-7700, Japan.
| | - Yui Nemoto
- Okutama Practice Forest, Tokyo University of Agriculture, 2137 Hikawa, Okutama, Tokyo 198-0212, Japan
| | - Natsuko Ito Kondo
- Biodiversity Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Kosuke Kanda
- Fukushima Prefectural Centre for Environmental Creation, 10-2 Fukasaku, Miharu, Fukushima 963-7700, Japan
| | - Toshimasa Takeda
- Fukushima Regional Collaborative Research Center, National Institute for Environmental Studies, 10-2 Fukasaku, Miharu, Fukushima 963-7700, Japan
| | - James C Beasley
- Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken, SC 29802, USA; Warnell School of Forestry and Natural Resources, University of Georgia, Drawer E, Aiken, SC 29802, USA
| | - Masanori Tamaoki
- Fukushima Regional Collaborative Research Center, National Institute for Environmental Studies, 10-2 Fukasaku, Miharu, Fukushima 963-7700, Japan; Biodiversity Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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17
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Pejhanmehr M, Kantar MB, Yorkston M, Morden CW. Population genetics of Sida fallax Walp. (Malvaceae) in the Hawaiian Islands. FRONTIERS IN PLANT SCIENCE 2024; 15:1304078. [PMID: 38495376 PMCID: PMC10941843 DOI: 10.3389/fpls.2024.1304078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
Introduction Sida fallax (Malvaceae) is the most widespread and variable taxon of Malvaceae in the Hawaiian Islands, growing with a diversity of morphological forms in different habitats including Midway Atoll, Nihoa, and all the main islands. Morphological variation exists within and among populations. The study aimed to investigate the genetic variation within and among populations from various habitats and geographic locations throughout the Hawaiian range of S. fallax. Methods A total of 124 samples, with up to five samples per population where possible, were collected from 26 populations across six of the main Hawaiian Islands (Kaua'i, O'ahu, Maui, Moloka'i, Lāna'i, and Hawai'i) and Nihoa in the Northwestern Hawaiian Islands. The sampling strategy encompassed collecting populations from different habitats and geographic locations, including coastal and mountain ecotypes, with many intermediate morphological forms. Multiplexed ISSR genotyping by sequencing (MIG-seq) was used to detect single nucleotide polymorphisms (SNP) and genetic differences among individuals and populations were evaluated using PCO analyses. Results The relationship of FST with the geographical distance between the populations was assessed using the Mantel test. The results showed that populations on a single island were more closely related to each other and to populations on islands within their respective groups than they were to populations on other islands. Discussion The overall genetic relationships among islands were, to a large extent, predictive based on island position within the chain and, to a lesser extent, within island topography.
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Affiliation(s)
| | - Michael Benjamin Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawaiʻi, Honolulu, HI, United States
| | - Mitsuko Yorkston
- School of Life Sciences, University of Hawaiʻi, Honolulu, HI, United States
| | - Clifford W. Morden
- School of Life Sciences, University of Hawaiʻi, Honolulu, HI, United States
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Novaes DR, Sujii PS, Rodrigues CA, Silva KMNB, Machado AFP, Inoue-Nagata AK, Nakasu EYT, Togni PHB. Natural habitat connectivity and organic management modulate pest dispersal, gene flow, and natural enemy communities. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2938. [PMID: 38071736 DOI: 10.1002/eap.2938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 12/24/2023]
Abstract
The simplification and fragmentation of agricultural landscapes generate effects on insects at multiple spatial scales. As each functional group perceives and uses the habitat differently, the response of pest insects and their associated natural enemies to environmental changes varies. Therefore, landscape structure may have consequences on gene flow among pest populations in space. This study aimed to evaluate the effects of local and landscape factors, at multiple scales, on the local infestation, gene flow and broad dispersion dynamics of the pest insect Bemisia tabaci (Genn.) Middle East-Asia Minor 1 (MEAM-1, former biotype B) (Hemiptera: Aleyrodidae) and its associated natural enemies in a tropical agroecosystem. We evaluated the abundance of B. tabaci populations and their natural enemy community in 20 tomato farms in Brazil and the gene flow between farms from 2019 to 2021. Landscapes dominated by agriculture resulted in larger B. tabaci populations and higher gene flow, especially in conventional farms. A higher density of native vegetation patches disfavored pest populations, regardless of the management system. The results revealed that whitefly responds to intermediate spatial scales and that landscape factors interact with management systems to modulate whitefly populations on focal farms. Conversely, whitefly natural enemies benefited from higher amounts of natural vegetation at small spatial scales, while the connectivity between natural habitat patches was beneficial for natural enemies regardless of the distance from the focal farm. The resulting dispersion model predicts that the movement of whiteflies between farms increases as the amount of natural vegetation decreases. Our findings demonstrate that landscape features, notably landscape configuration, can mediate infestation episodes, as they affect pest insects and natural enemies in opposite ways. We also showed that landscape features interact with farm traits, which highlights the need for management strategies at multiple spatial scales. In conclusion, we demonstrated the importance of the conservation of natural areas as a key strategy for area-wide ecological pest management and the relevance of organic farming to benefit natural enemy communities in tropical agroecosystems.
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Affiliation(s)
- Danyelle R Novaes
- Programa de Pós-Graduação em Ecologia, Universidade de Brasília (UnB), Brasília, Brazil
| | - Patricia S Sujii
- Programa de Pós-Graduação em Ecologia, Universidade de Brasília (UnB), Brasília, Brazil
- Centro de Ensino Unificado do Distrito Federal, Brasília, Brazil
| | - Camila A Rodrigues
- Instituto Federal Goiano, Goiânia, Brazil
- Programa de Pós-Graduação em Zoologia, Universidade de Brasília (UnB), Brasília, Brazil
| | - Karen M N B Silva
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília (UnB), Brasília, Brazil
| | - Amanda F P Machado
- Programa de Pós-Graduação em Ecologia, Universidade de Brasília (UnB), Brasília, Brazil
| | - Alice K Inoue-Nagata
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Hortaliças, Brasília, Brazil
| | - Erich Y T Nakasu
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Hortaliças, Brasília, Brazil
| | - Pedro H B Togni
- Departamento de Ecologia, Universidade de Brasília (UnB), Brasília, Brazil
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Furuta T, Yamamoto T. MCPtaggR: R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison. DNA Res 2024; 31:dsad027. [PMID: 38134958 PMCID: PMC10799318 DOI: 10.1093/dnares/dsad027] [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: 10/18/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023] Open
Abstract
Reduced representation sequencing (RRS) offers cost-effective, high-throughput genotyping platforms such as genotyping-by-sequencing (GBS). RRS reads are typically mapped onto a reference genome. However, mapping reads harbouring mismatches against the reference can potentially result in mismapping and biased mapping, leading to the detection of error-prone markers that provide incorrect genotype information. We established a genotype-calling pipeline named mappable collinear polymorphic tag genotyping (MCPtagg) to achieve accurate genotyping by eliminating error-prone markers. MCPtagg was designed for the RRS-based genotyping of a population derived from a biparental cross. The MCPtagg pipeline filters out error-prone markers prior to genotype calling based on marker collinearity information obtained by comparing the genome sequences of the parents of a population to be genotyped. A performance evaluation on real GBS data from a rice F2 population confirmed its effectiveness. Furthermore, our performance test using a genome assembly that was obtained by genome sequence polishing on an available genome assembly suggests that our pipeline performs well with converted genomes, rather than necessitating de novo assembly. This demonstrates its flexibility and scalability. The R package, MCPtaggR, was developed to provide functions for the pipeline and is available at https://github.com/tomoyukif/MCPtaggR.
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Affiliation(s)
- Tomoyuki Furuta
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Toshio Yamamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
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20
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Taichi N, Nakahama N, Ohmido N, Ushimaru A. Habitat diversification associated with urban development has a little effect on genetic structure in the annual native plant Commelina communis in an East Asian megacity. Ecol Evol 2024; 14:e10975. [PMID: 38384819 PMCID: PMC10880129 DOI: 10.1002/ece3.10975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024] Open
Abstract
Urban development greatly alters the natural and semi-natural habitats of native plants. Urbanisation results in a range of diverse habitats including remnant agricultural lands, urban parks, and roadside habitats. This habitat diversity often promotes trait divergence within urban areas. However, the mechanisms by which diverse urban habitats influence the population genetic structure of individual plant species remain poorly understood. We investigated the effects of urbanisation on genetic diversity and structure within 24 Commelina communis populations across diverse habitat types (rural agricultural land, urban agricultural land, urban park land, and urban roadsides) within the Kyoto-Osaka-Kobe megacity in Japan. We conducted multiplexed inter-simple sequence repeat genotyping to compare genetic diversity among populations in different habitats. We also examined the correlation between Nei's genetic distance and geographic and environmental distances and performed principal coordinate analysis (PCoA) to evaluate genetic differentiation among urban habitats. There were no significant differences in genetic diversity indices between urban and rural populations and among urban habitat types. Although we detected no isolation-by-distance structure in population pairs of the same habitat type and in those of different habitats, the difference in surrounding landscape facilitated genetic differentiation not only between urban and rural habitats but also between different urban habitats. PCoA revealed no clear genetic differentiation among rural and urban habitat populations. Our findings indicate that the establishment of diverse habitat types through urbanisation has no and little impact on genetic diversity and structure, respectively, in C. communis, likely due to its high selfing rate and ability to adapt to urban conditions.
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Affiliation(s)
- Nakata Taichi
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
| | - Naoyuki Nakahama
- Institute of Natural and Environmental SciencesUniversity of HyogoSandaJapan
- Museum of Nature and Human ActivitiesHyogoJapan
| | - Nobuko Ohmido
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
| | - Atushi Ushimaru
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
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21
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Tsunenari K, Ito T, Yokota M, Shibabayashi M, Endo C, Chung KF, Suyama Y, Matsuo A, Abe A, Naiki A, Setoguchi H, Makino T, Isagi Y. Double migration of the endangered Tricyrtis formosana (Liliaceae) in Japan. Sci Rep 2024; 14:957. [PMID: 38200076 PMCID: PMC10781951 DOI: 10.1038/s41598-024-51431-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
The Ryukyu Islands of Japan are a biodiversity hotspot due to geographical and historical factors. Tricyrtis formosana is a perennial herbaceous plant that commonly found in Taiwan. But only a few populations have been identified in a limited habitat on Iriomote Island, while populations of unknown origin occur near human settlements in an area on the main island of Okinawa. To better understand these populations of the phylogenetic uniqueness and intrinsic vulnerability, we conducted comparative analyses including (1) phylogeny and population structure with MIG-seq data, (2) photosynthesis-related traits of plants grown under common conditions and (3) transcriptome analysis to detect deleterious variations. Results revealed that T. formosana was split into two clades by the congeners and that Iriomote and Okinawa populations independently derived from ancestral Taiwanese populations in each clade. Photosynthetic efficiency was lowest in the Iriomote population, followed by Okinawa and Taiwan. Transcriptome analysis showed that the Iriomote population accumulated more deleterious variations, suggesting intrinsic vulnerability. These results indicate that each T. formosana population in Japan is phylogenetically unique and has been independently dispersed from Taiwan, and that the Iriomote population presents a high conservation difficulty with a unique photosynthesis-related characteristic and a larger amount of deleterious variations.
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Affiliation(s)
- Kaori Tsunenari
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
- Japan Broadcasting Cooporation, Tokyo, Japan.
| | - Takuro Ito
- The Center for Academic Resources and Archives, Tohoku University, Sendai, Japan
| | | | | | - Chiharu Endo
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kuo-Fang Chung
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Ayumi Matsuo
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Atsushi Abe
- Okinawa Churashima Foundation Research Institute, Botanical Laboratory, Okinawa, Japan
| | - Akiyo Naiki
- Tropical Biosphere Research Center, University of the Ryukyus, Taketomi, Okinawa, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Takashi Makino
- Graduate School of Life Science, Tohoku University, Sendai, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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22
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Gutiérrez-Ortega JS, Pérez-Farrera MA, Matsuo A, Sato MP, Suyama Y, Calonje M, Vovides AP, Kajita T, Watano Y. The phylogenetic reconstruction of the Neotropical cycad genus Ceratozamia (Zamiaceae) reveals disparate patterns of niche evolution. Mol Phylogenet Evol 2024; 190:107960. [PMID: 37918683 DOI: 10.1016/j.ympev.2023.107960] [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: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
The cycad genus Ceratozamia comprises 40 species from Mexico, Guatemala, Belize, and Honduras, where cycads occur throughout climatically varied montane habitats. Ceratozamia has the potential to reveal the history and processes of species diversification across diverse Neotropical habitats in this region. However, the species relationships within Ceratozamia and the ecological trends during its evolution remain unclear. Here, we aimed to clarify the phylogenetic relationships, the timing of clade and species divergences, and the niche evolution throughout the phylogenetic history of Ceratozamia. Genome-wide DNA sequences were obtained with MIG-seq, and multiple data-filtering steps were used to optimize the dataset used to construct an ultrametric species tree. Divergence times among branches and ancestral niches were estimated. The niche variation among species was evaluated, summarized into two principal components, and their ancestral states were reconstructed to test whether niche shifts among branches can be explained by random processes, under a Brownian Motion model. Ceratozamia comprises three main clades, and most species relationships within the clades were resolved. Ceratozamia has diversified since the Oligocene, with major branching events occurring during the Miocene. This timing is consistent with fossil evidence, the timing estimated for other Neotropical plant groups, and the major geological events that shaped the topographic and climatic variation in Mexico. Patterns of niche evolution in the genus do not accord with the Brownian Motion model. Rather, non-random evolution with shifts towards more seasonal environments at high latitudes, or shifts towards humid or dry environments at low latitudes explain the diversification of Ceratozamia. We present a comprehensive phylogenetic reconstruction for Ceratozamia and identify for the first time the environmental factors involved in clade and species diversification within the genus. This study alleviates the controversies regarding the species relationships in the genus and provides the first evidence that latitude-associated environmental factors may influence processes of niche evolution in cycads.
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Affiliation(s)
| | - Miguel Angel Pérez-Farrera
- Herbario Eizi Matuda, Laboratorio de Ecología Evolutiva, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez 29039, Mexico.
| | - Ayumi Matsuo
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Mitsuhiko P Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | | | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., 91070 Xalapa, Mexico
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa 907-1541, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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23
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Tamaki I, Mizuno M, Ohtsuki T, Shutoh K, Tabata R, Tsunamoto Y, Suyama Y, Nakajima Y, Kubo N, Ito T, Noma N, Harada E. Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced. Sci Rep 2023; 13:20746. [PMID: 38007576 PMCID: PMC10676423 DOI: 10.1038/s41598-023-48079-4] [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: 07/07/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023] Open
Abstract
Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300-400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese V. sepium is not introduced but is native.
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Affiliation(s)
- Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan
- Gifu Prefectural Research Institute for Forests, 1128-1 Sodai, Mino, Gifu, 501-3714, Japan
| | - Mizuo Mizuno
- Gifu Pharmaceutical University, 5-6-1 Mitahora-Higashi, Gifu, 502-8585, Japan
| | - Tatsuo Ohtsuki
- Lake Biwa Museum, 1091 Oroshimo, Kusatsu, Shiga, 525-0001, Japan
| | - Kohtaroh Shutoh
- The Hokkaido University Museum, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Ryoichi Tabata
- Lake Biwa Museum, 1091 Oroshimo, Kusatsu, Shiga, 525-0001, Japan
| | - Yoshihiro Tsunamoto
- Research Institute of Energy, Environment and Geology, Hokkaido Research Organization, Kita 19 Nishi 12, Kita-ku, Sapporo, Hokkaido, 060-0819, Japan
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yusuke Nakajima
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan
| | - Naoki Kubo
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan
| | - Takeru Ito
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan
| | - Naohiko Noma
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan
| | - Emiko Harada
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka, Hikone, Shiga, 522-8533, Japan.
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Yahara T, Hirota SK, Fujii S, Kokami Y, Fuse K, Sato H, Tagane S, Suyama Y. Molecular phylogeny and taxonomy of Hosta (Asparagaceae) on Shikoku Island, Japan, including five new species, one new subspecies, and two new status assignments. PHYTOKEYS 2023; 235:137-187. [PMID: 38020470 PMCID: PMC10680290 DOI: 10.3897/phytokeys.235.99140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 10/04/2023] [Indexed: 12/01/2023]
Abstract
Japan has 16 native species of the genus Hosta Tratt. (Asparagaceae). A recent study on Hosta based on field surveys and molecular phylogenetic analyses resulted in the discovery of six unknown taxa in Kochi Prefecture, Shikoku Island, southwestern Japan. We aimed to identify these unknown taxa. Therefore, we constructed a finely resolved phylogeny for 320 Hosta samples collected from the Honshu, Shikoku, and Kyushu Islands using multiplex inter-simple sequence repeat genotyping by sequencing (MIG-seq). Based on this phylogenetic analysis and related morphological observations, we describe five new species, H.longipedicellatasp. nov., H.minazukiflorasp. nov., H.polyneuronoidessp. nov., H.samukazemontanasp. nov., and H.takiminazukiflorasp. nov. and one new subspecies, H.takiminazukiflorasubsp.grandissubsp. nov. In addition, we propose two new status assignments, H.tardivasubsp.densinerviacomb. and stat. nov. and H.scabrinerviastat. nov. We also propose classifying H.kikutiivar.tosana as a species, H.tosana. Further studies that combine MIG-seq with careful morphological observations are needed for Hosta plants on all Japanese islands, which may result in the discovery of even more undescribed species.
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Affiliation(s)
- Tetsukazu Yahara
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shun K. Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
- Botanical Gardens, Osaka Metropolitan University, 2000 Kisaichi, Katano, Osaki 576-0004, JapanOsaka Metropolitan UniversityOsakiJapan
| | - Seiko Fujii
- The Kochi Prefectural Makino Botanical Garden, Godai-san 4200-6, Kochi 781-8125, JapanThe Kochi Prefectural Makino Botanical GardenKochiJapan
| | - Yasushi Kokami
- The Kochi Prefectural Makino Botanical Garden, Godai-san 4200-6, Kochi 781-8125, JapanThe Kochi Prefectural Makino Botanical GardenKochiJapan
| | - Kengo Fuse
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Hiroyuki Sato
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, 1-21-30 Korimoto, Kagoshima, 890-0065, JapanKagoshima UniversityKagoshimaJapan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
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25
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Wang WY, Yamada A. Scrutinising an inscrutable bark-nesting ant: Exploring cryptic diversity in the Rhopalomastix javana (Hymenoptera: Formicidae) complex using DNA barcodes, genome-wide MIG-seq and geometric morphometrics. PeerJ 2023; 11:e16416. [PMID: 38025712 PMCID: PMC10657568 DOI: 10.7717/peerj.16416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Overlooking cryptic species diversity has grave implications on assessments of climate change impacts on biodiversity, ecosystems and organismal populations. Discriminating between cryptic species has long been challenging even for seasoned taxonomists, as interspecies morphological differences are often indiscernible by visual observation. Multi-disciplinary methods involving genetic analyses in conjunction with quantitative morphological data, should therefore be used to investigate boundaries between cryptic species. We adopted an integrated approach combining analyses of mitochondrial COI barcodes, a genome-wide dataset obtained via multiplexed inter-simple sequence repeats (ISSRs) genotyping by sequencing (MIG-seq), and geometric morphometrics to investigate species divergences in the inscrutable Rhopalomastix javana species complex. Objective clustering of COI suggested five putative molecular species units divergent from each other by thresholds within 4.2-10.6% uncorrected pairwise distance. Phylogenetic analyses based on concatenated MIG-seq data also recovered and strongly supported the monophyly of five major lineages in agreement with COI clusters. Co-ancestry analyses based on MIG-seq data using fineRADstructure resolved variable patterns of admixture linked to geography, and potential genetic drift within some putative species. Geometric morphometric analyses of specimen images further detected statistically significant differences in at least one of three anatomical aspects (Head, Meso, Profile) between all pairs of putative species. Head shape (full-face view) was determined to be the most informative character for species diagnosis, with relatively high classification accuracy. Thin-plate spline deformation grids highlighted areas of high variation between species in each shape for deeper taxonomic scrutiny. The presence of species from multiple distinct lineages existing in near-sympatry firmly demonstrates that R. javana comprises more than one closely-related species, but exact species boundaries are difficult to ascertain. Differences in elevation and its associated abiotic effects on ant adaptations and reproductive phenology may contribute to restricting gene flow and maintaining species boundaries between sympatric populations of the R. javana complex. We further assess the advantages and limitations of geometric morphometrics as a taxonomic tool. Despite its drawbacks, our combined approach has helped draw important insights on cryptic diversity in R. javana, and also identified gaps of knowledge that await address. Results from this study will inform and prime future in-depth taxonomic investigation on the R. javana complex, including formal descriptions and establishment of the five putative species.
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Affiliation(s)
- Wendy Y. Wang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Aiki Yamada
- Systematic Zoology Laboratory, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
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26
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Yamato M, Yagita M, Kusakabe R, Shimabukuro K, Yamana K, Suetsugu K. Impact of mycoheterotrophy on the growth of Gentiana zollingeri (Gentianaceae), as suggested by size variation, morphology, and 13C abundance of flowering shoots. JOURNAL OF PLANT RESEARCH 2023; 136:853-863. [PMID: 37713005 DOI: 10.1007/s10265-023-01496-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/03/2023] [Indexed: 09/16/2023]
Abstract
Gentiana zollingeri is an annual photosynthetic plant that employs a mycoheterotrophic growth strategy during its underground seedling stage (initial mycoheterotrophy). Notably, the morphological characteristics of its flowering shoots, such as shoot size, leaf size, and leaf color, are highly variable, and it was hypothesized that these variations may be linked to nutritional mode. The morphological characteristics of G. zollingeri individuals were thus investigated alongside environmental factors, 13C abundance, and diversity of colonizing arbuscular mycorrhizal (AM) fungi. The majority of G. zollingeri flowering individuals were found to exhibit a high affinity for the specific AM fungi that exclusively colonize roots of the mycoheterotrophic seedlings, while other phylogenetically diverse AM fungi could also be detected. The leaves to shoot dry weight ratio (leaf ratio) was negatively correlated with the canopy openness in the habitat, suggesting that leaf development is impeded in sunny conditions. Furthermore, the shoot weight of G. zollingeri was positively correlated with leaf 13C abundance. Given that 13C enrichment can provide indirect evidence of mycoheterotrophy in AM plants, the results suggest that the utilization of carbon obtained through mycoheterotrophy, at least during the underground seedling stage, is crucial for G. zollingeri.
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Affiliation(s)
- Masahide Yamato
- Faculty of Education, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
| | - Mai Yagita
- Faculty of Education, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Ryota Kusakabe
- Graduate School of Horticulture, Chiba University, 648, Matsudo, Chiba, 271-8510, Japan
| | - Keito Shimabukuro
- Faculty of Education, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Kohei Yamana
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
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27
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Kagawa O, Hirota SK, Saito T, Uchida S, Watanabe H, Miyazoe R, Yamaguchi T, Matsuno T, Araki K, Wakasugi H, Suzuki S, Kobayashi G, Miyazaki H, Suyama Y, Hanyuda T, Chiba S. Host-Shift Speciation Proceeded with Gene Flow in Algae Covering Shells. Am Nat 2023; 202:721-732. [PMID: 37963116 DOI: 10.1086/726221] [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] [Indexed: 11/16/2023]
Abstract
AbstractHost shifts represent the advancement of a novel niche and often lead to speciation in symbionts. However, its mechanisms are not well understood. Here, we focused on the alga Pseudocladophora conchopheria growing on the shells of intertidal snails. Previous surveys have shown that the alga has host specificity-only attaching to the shell of Lunella correensis-but we discovered that the alga attaches to the shells of multiple sympatric snails. A genome-wide single-nucleotide polymorphism analysis (MIG-seq) was performed to determine whether host-associated speciation occurred in the algae. As a result, there was no gene flow or limited gene flow among the algae from different hosts, and some algae were genetically differentiated among hosts. In addition, the demographic estimate revealed that speciation with gene flow occurred between the algae from different hosts. Therefore, these results support the idea that host-shift speciation gradually proceeded with gene flow in the algae, providing insight into the early evolution of host shifts.
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28
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Fukutani K, Matsui M, Nishikawa K. Population genetic structure and hybrid zone analyses for species delimitation in the Japanese toad ( Bufo japonicus). PeerJ 2023; 11:e16302. [PMID: 37901459 PMCID: PMC10607272 DOI: 10.7717/peerj.16302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated during isolation. The Japanese toad, Bufo japonicus, is distributed on the main islands of Japan. In the present study, we applied multiplexed inter-simple sequence repeat genotyping by sequencing to achieve the fine-scale resolution of the genetic cluster in B. j. japonicus and B. j. formosus. We also elucidated hybridization patterns and gene flow degrees across contact zones between the clusters identified. Using SNP data, we found four genetic clusters in B. j. japonicus and B. j. formosus and three contact zones of the cluster pairs among these four clusters. The two oldest diverged lineages, B. j. japonicus and B. j. formosus, formed a narrow contact zone consistent with species distinctiveness. Therefore, we recommend that these two subspecies be elevated to the species level. In contrast, the less diverged pairs of two clusters in B. j. japonicus and B. j. formosus, respectively, admixed over a hundred kilometers, suggesting that they have not yet developed strong reproductive isolation and need to be treated as conspecifics. These results will contribute to resolving taxonomic confusion in Japanese toads.
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Affiliation(s)
- Kazumi Fukutani
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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29
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Kikkawa HS, Sato MP, Matsuo A, Sasaki T, Suyama Y, Tsuge K. Discrimination of Camellia cultivars using iD-NA analysis. Sci Rep 2023; 13:17674. [PMID: 37848466 PMCID: PMC10582245 DOI: 10.1038/s41598-023-44404-z] [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: 05/02/2023] [Accepted: 10/07/2023] [Indexed: 10/19/2023] Open
Abstract
Recently, many new cultivars have been taken abroad illegally, which is now considered an international issue. Botanical evidence found at a crime scene provides valuable information about the origin of the sample. However, botanical resources for forensic evidence remain underutilized because molecular markers, such as microsatellites, are not available without a limited set of species. Multiplexed intersimple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and its analysis method, identification of not applicable (iD-NA), have been used to determine several genome-wide genetic markers, making them applicable to all plant species, including those with limited available genetic information. Camellia cultivars are popular worldwide and are often planted in many gardens and bred to make new cultivars. In this study, we aimed to analyze Camellia cultivars/species through MIG-seq. MIG-seq could discriminate similar samples, such as bud mutants and closely related samples that could not be distinguished based on morphological features. This discrimination was consistent with that of a previous study that classified cultivars based on short tandem repeat (STR) markers, indicating that MIG-seq has the same or higher discrimination ability as STR markers. Furthermore, we observed unknown phylogenetic relationships. Because MIG-seq can be applied to unlimited species and low-quality DNA, it may be useful in various scientific fields.
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Affiliation(s)
- Hitomi S Kikkawa
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.
| | - Mitsuhiko P Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Ayumi Matsuo
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Takanori Sasaki
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Kouichiro Tsuge
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
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30
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Suetsugu K, Nozaki T, Hirota SK, Funaki S, Ito K, Isagi Y, Suyama Y, Kaneko S. Phylogeographical evidence for historical long-distance dispersal in the flightless stick insect Ramulus mikado. Proc Biol Sci 2023; 290:20231708. [PMID: 37817589 PMCID: PMC10565398 DOI: 10.1098/rspb.2023.1708] [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: 07/30/2023] [Accepted: 09/13/2023] [Indexed: 10/12/2023] Open
Abstract
Exploring how organisms overcome geographical barriers to dispersal is a fundamental question in biology. Passive long-distance dispersal events, although infrequent and unpredictable, have a considerable impact on species range expansions. Despite limited active dispersal capabilities, many stick insect species have vast geographical ranges, indicating that passive long-distance dispersal is vital for their distribution. A potential mode of passive dispersal in stick insects is via the egg stage within avian digestive tracts, as suggested by experimental evidence. However, detecting such events under natural conditions is challenging due to their rarity. Therefore, to indirectly assess the potential of historical avian-mediated dispersal, we examined the population genetic structure of the flightless stick insect Ramulus mikado across Japan, based on a multifaceted molecular approach [cytochrome oxidase subunit I (COI) haplotypes, nuclear simple sequence repeat markers and genome-wide single nucleotide polymorphisms]. Subsequently, we identified unique phylogeographic patterns, including the discovery of identical COI genotypes spanning considerable distances, which substantiates the notion of passive long-distance genotypic dispersal. Overall, all the molecular data revealed the low and mostly non-significant genetic differentiation among populations, with identical or very similar genotypes across distant populations. We propose that long-distance dispersal facilitated by birds is the plausible explanation for the unique phylogeographic pattern observed in this flightless stick insect.
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Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
- Institute for Advanced Research, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Tomonari Nozaki
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shun K. Hirota
- Botanical Gardens, Osaka Metropolitan University, 2000 Kisaichi, Katano City, Osaka 576-0004, Japan
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Shoichi Funaki
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobeotsu, Nankoku, Kochi 783-8502, Japan
| | - Katsura Ito
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobeotsu, Nankoku, Kochi 783-8502, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Shingo Kaneko
- Graduate School of Symbiotic Systems Science and Technology, Fukushima University, Fukushima, Fukushima 960-1296, Japan
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Minami M, Tanaka R, Mori T, Fujii T, Tsuchida T, Shibata T. Population genetic structure of wild Angelica acutiloba, A. acutiloba var. iwatensis, and their hybrids by atpF-atpA intergenic spacer in chloroplast DNA and genome-wide SNP analysis using MIG-seq. J Nat Med 2023; 77:1009-1021. [PMID: 37581741 DOI: 10.1007/s11418-023-01742-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/03/2023] [Indexed: 08/16/2023]
Abstract
Sampling surveys of Angelica acutiloba and A. acutiloba var. iwatensis, which are medicinal plants endemic to Japan, were conducted in the Chubu region in the central area of the main island of Japan. A. acutiloba grows in riverbeds in mountainous areas, while A. acutiloba. var. iwatensis grows on slopes near mountain ridges at 1000 m above sea level or on constantly collapsing rocky slopes and bare fields on developed land along asphalt roads in valleys of mountainous areas. Specimens of two wild Angelica species collected in this region were examined for maternal lineage by DNA polymorphism analysis of the atpF-atpA region for chloroplast DNA using direct sequencing and genomic component analysis by genome-wide SNP using MIG-seq. In this study area, while all A. acutiloba populations were monophyletic in both maternal and ancestral lineages, A. acutiloba var. iwatensis were genetically heterogeneous due to being composed of three maternal and three ancestral lineages to various degrees. In addition, a natural hybrid population with maternal lineage presumed to be A. acutiloba and paternal lineage A. acutiloba var. iwatensis was also found. In the present study, we report that the combined method of atpF-atpA and MIG-seq analyses is a useful tool for determining the population genetic structure of two wild Angelica species and for identifying hybrids.
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Affiliation(s)
- Motoyasu Minami
- College of Bioscience & Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan.
| | - Ryusaku Tanaka
- College of Bioscience & Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Takako Mori
- College of Bioscience & Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Taichi Fujii
- College of Bioscience & Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Takashi Tsuchida
- Central R&D Laboratory, Kobayashi Pharmaceutical Co., Ltd., 1-30-3 Toyokawa, Ibaraki, Osaka, 567-0057, Japan
| | - Toshiro Shibata
- Green Innovation Co., Ltd., 2-302, 4-21-2 Matsushiro, Tsukuba, Ibaraki, 305-0035, Japan
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Niwa K, Nishikawa K, Matsui M, Kanamori S, Kuro-O M. Taxonomic reassessment of salamanders (genus Hynobius) from Tsushima Islands, Japan, with a resurrection of Hynobius tagoi Dunn, 1923 (Amphibia: Caudata). Zootaxa 2023; 5339:201-236. [PMID: 38221056 DOI: 10.11646/zootaxa.5339.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Indexed: 01/16/2024]
Abstract
To clarify the taxonomic status of salamanders from Tsushima Islands, Japan, we examined two species of salamanders, Hynobius tsuensis and Hynobius sp. from Tsushima Islands, and compared them with H. nebulosus from Kyushu. We found that the three taxa differ from each other in nuclear DNA, adult morphology, and egg-sac shape, and consider them to be independent species. Based on the investigation of type specimens of the synonyms, we identified Hynobius sp. as H. tagoi Dunn, 1923 and redescribe it herein. Also, we designate a neotype for H. tsuensis and redescribe H. tsuensis. The distribution areas of the two species partly overlap but they were distinguishable by their body colorations: H. tsuensis has uniformly blackish tail sides and a distinct yellow stripe on the upper tail edge; whereas H. tagoi has brown tail sides with numerous dark stippling and without a distinct yellow stripe on the upper tail edge.
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Affiliation(s)
- Keita Niwa
- 1Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu; Sakyo-ku; Kyoto 606-8501; JAPAN. Present affiliation: Akita Prefectural Office; Sanno 4-1-1; Akita 010-8570; JAPAN..
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu; Sakyo-ku; Kyoto 606-8501; JAPAN. Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN..
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu; Sakyo-ku; Kyoto 606-8501; JAPAN..
| | - Sally Kanamori
- Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN..
| | - Masaki Kuro-O
- Faculty of Agriculture and Life Science; Hirosaki University; Bunkyo-cho 3; Hirosaki; Aomori 036-8561; JAPAN..
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Choi I, Han E, Wojciechowski MF, Heo T, Park J, Yang J, Gantsetseg A, Cheon K, Tamaki I, Lee J. The genetic structure and demographic history of Zabelia tyaihyonii, endemic to Korean limestone karst forests, based on genome-wide SNP markers. Ecol Evol 2023; 13:e10252. [PMID: 37404698 PMCID: PMC10316687 DOI: 10.1002/ece3.10252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Similar to the global phenomenon, many plant species endemic to Korean limestone karst forests are at risk of extinction due to human intervention. Zabelia tyaihyonii is a familiar shrub, called "Hardy abelia" and "Fragrant abelia" growing in the karst forests of Korea, where it is one of the most threatened species. We investigated the genetic structure and demographic history of Z. tyaihyonii, which allow us to develop appropriate conservation and management strategies. The genetic structure was evaluated using a total of 187 samples from 14 populations, covering the entire distribution of Z. tyaihyonii in South Korea. We utilized 254 and 1753 SNP loci obtained via MIG-seq (Multiplexed ISSR Genotyping by sequencing) for structure and demographic analyses, respectively. The population demographic modeling was performed with site frequency spectrum. To gain further historical insights, we also employed ENM (Ecological Niche Modeling). We found two distinct clusters (CLI and CLII) of ancient origin (ca. 490 ka). Despite CLII experiencing a more severe bottleneck, both clusters showed similar levels of genetic diversity, indicating mutual historical gene flow. Their historical distribution range seems to have changed very little. We proposed a historical distribution scenario for Z. tyaihyonii, taking into account its intrinsic factors, and emphasized a more complex response to Quaternary climate change beyond simple allopatric speciation models. These findings provide valuable insights for conservation and management strategies for Z. tyaihyonii.
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Affiliation(s)
- In‐Su Choi
- Department of Biological Sciences and BiotechnologyHannam UniversityDaejeonKorea
| | - Eun‐Kyeong Han
- Department of Biology EducationChonnam National UniversityGwangjuKorea
| | | | - Tae‐Im Heo
- Division of Baekdudaegan Biodiversity ConservationBaekdudaegan National ArboretumBonghwaKorea
| | - Jong‐Soo Park
- Division of BotanyHonam National Institute of Biological ResourcesMokpoKorea
| | - Jong‐Cheol Yang
- Division of Baekdudaegan Biodiversity ConservationBaekdudaegan National ArboretumBonghwaKorea
| | | | | | | | - Jung‐Hyun Lee
- Department of Biology EducationChonnam National UniversityGwangjuKorea
- School of Life SciencesArizona State UniversityTempeArizonaUSA
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Nishio S, Moriya S, Kunihisa M, Takeuchi Y, Imai A, Takada N. Rapid and easy construction of a simplified amplicon sequencing (simplified AmpSeq) library for marker-assisted selection. Sci Rep 2023; 13:10575. [PMID: 37386134 PMCID: PMC10310812 DOI: 10.1038/s41598-023-37522-1] [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: 05/10/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023] Open
Abstract
Marker-assisted selection (MAS) is fundamental for plant breeding programs, as it can identify desirable seedlings at a young stage and reduce the cost, time and space needed for plant maintenance, especially for perennial crops. To facilitate the process of genotyping, which is time consuming and laborious, we developed a simplified amplicon sequencing (simplified AmpSeq) library construction method for next-generation sequencing that can be applied to MAS in breeding programs. The method is based on one-step PCR with a mixture of two primer sets: the first consisting of tailed target primers, the second of primers that contain flow-cell binding sites, indexes and tail sequences complementary to those in the first set. To demonstrate the process of MAS using s implified AmpSeq, we created databases of genotypes for important traits by using cultivar collections including triploid cultivars and segregating seedlings of Japanese pear (Pyrus pyrifolia Nakai), Japanese chestnut (Castanea crenata Sieb. et Zucc.) and apple (Malus domestica Borkh.). Simplified AmpSeq has the advantages of high repeatability, ability to estimate allele number in polyploid species and semi-automatic evaluation using target allele frequencies. Because this method provides high flexibility for designing primer sets and targeting any variant, it will be useful for plant breeding programs.
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Affiliation(s)
- Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan.
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, Morioka, Iwate, 020-0123, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Yukie Takeuchi
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Atsushi Imai
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Norio Takada
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
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Tomimori Y, Matsui M, Okawa H, Nishikawa K, Tanabe S, Kamasaka R. Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae). Zootaxa 2023; 5293:145-160. [PMID: 37518493 DOI: 10.11646/zootaxa.5293.1.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Indexed: 08/01/2023]
Abstract
Hynobius akiensis sensu lato has recently been split into three species based on short sequence analyses of cyt-b gene of mtDNA and without data of nuclear DNA, and strange sympatric distribution in some areas has been indicated in two species. We analyzed nuclear DNA marker (SNPs) and complete sequence of cyt-b in H. akiensis sensu lato to reassess species delimitation and genetic introgression among species. As a result, we found two lineages with discordant mitochondrial and nuclear DNA in some areas. Of H. akiensis sensu lato, each of the two contains the type locality of two species recently reported (H. sumidai and H. geiyoensis), and the use of these names has been previously advocated. However, their sympatric distribution was rejected based on nuclear DNA data, which we consider is more reliable than mtDNA. We thus clarify geographic boundary of these two species and revise the species delimitations.
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Affiliation(s)
- Yusuke Tomimori
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu-cho; Sakyo-ku; Kyoto 606-8501; JAPAN; Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN.
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu-cho; Sakyo-ku; Kyoto 606-8501; JAPAN.
| | | | - Kanto Nishikawa
- Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN.
| | - Shingo Tanabe
- Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN.
| | - Ryo Kamasaka
- Kuta 435-19-103; Izuhara-Machi; Tsushima; Nagasaki 817-0032; JAPAN.
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Sakaba T, Soejima A, Fujii S, Ikeda H, Iwasaki T, Saito H, Suyama Y, Matsuo A, Kozhevnikov AE, Kozhevnikova ZV, Wang H, Wang S, Pak JH, Fujii N. Phylogeography of the temperate grassland plant Tephroseris kirilowii (Asteraceae) inferred from multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) data. JOURNAL OF PLANT RESEARCH 2023:10.1007/s10265-023-01452-w. [PMID: 37148377 DOI: 10.1007/s10265-023-01452-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/12/2023] [Indexed: 05/08/2023]
Abstract
A group of temperate grassland plant species termed the "Mansen elements" occurs in Japan and is widely distributed in the grasslands of continental East Asia. It has been hypothesized that these species are continental grassland relicts in Japan that stretch back to a colder age, but their migration history has not been elucidated. To assess the migration history of the Mansen elements, we performed phylogeographic analyses of Tephroseris kirilowii, a member of this group, using single-nucleotide polymorphisms (SNPs) obtained from multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq). It was estimated that the Japanese populations of T. kirilowii were divided from those of continental East Asia at 25.2 thousand years ago (ka) with 95% highest probability density interval (HPD) of 15.3-40.0 ka and that Japanese clades first diverged at 20.2 ka with 95% HPD of 10.4-30.1 ka. As the climatically suitable range during the last glacial maximum (LGM) estimated using ecological niche modeling (ENM) was limited in Japan and there was a slight genetic differentiation among Japanese populations, a post-glacial expansion of T. kirilowii in the Japanese Archipelago was indicated.
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Affiliation(s)
- Tomoka Sakaba
- Graduate School of Science and Technology, Kumamoto University, Kurokami 2-39-1, Chuo-Ku, Kumamoto, 860-8555, Japan
| | - Akiko Soejima
- Department of Biological Science, Faculty of Advanced Science and Technology, Kumamoto University, Kurokami 2-39-1, Chuo-Ku, Kumamoto, 860-8555, Japan.
| | - Shinji Fujii
- Department of Field Ecology, University of Human Environments, 6-2 Kamisanbonmatsu, Okazaki, 444-3505, Japan
| | - Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Takaya Iwasaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-Ku, Tokyo, 112-8610, Japan
| | - Hiroaki Saito
- Graduate School of Science and Technology, Kumamoto University, Kurokami 2-39-1, Chuo-Ku, Kumamoto, 860-8555, Japan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Kawatabi Field Science Center, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Ayumi Matsuo
- Graduate School of Agricultural Science, Kawatabi Field Science Center, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Andrey E Kozhevnikov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Zoya V Kozhevnikova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Hongfeng Wang
- Department of Forestry, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Siqi Wang
- Department of Forestry, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Jae-Hong Pak
- East Coast Research Institute of Life Science, Gangneung-wonju National University, Jukheon-gil 7, Gangneung city, Gangwon-do, 25457, South Korea
| | - Noriyuki Fujii
- Department of Biological Science, Faculty of Advanced Science and Technology, Kumamoto University, Kurokami 2-39-1, Chuo-Ku, Kumamoto, 860-8555, Japan
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Hirano T, Saito T, Ito S, Ye B, Linscott TM, Do VT, Dong Z, Chiba S. Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia. Mol Phylogenet Evol 2023; 182:107728. [PMID: 36804427 DOI: 10.1016/j.ympev.2023.107728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Fossils provide important insight into our understanding of phylogenetic history by serving as calibration points for divergence time estimation. However, uncertainties in the fossil record due to parallel evolution and convergent evolution can critically affect estimates of node ages. Here, we compare and contrast estimates of phylogenetic divergence with geologic and fossil history for two freshwater snail genera of the family Viviparidae in East Asia (Cipangopaludina and Margarya). Cipangopaludina species are commonly widely distributed species in East Asia, but extant Margarya species are endemic to the ancient lakes in Yunnan, China. According to some previous studies, parallel evolution or convergent evolution of shell morphology has occurred in the family several times which may affect divergence time estimation using fossil records. In this study, we used SNP data derived from ddRAD-seq loci to investigate population demographic history of both genera. Our results show a common pattern of lake endemic lineages diversifying from widely distributed lineages in the Miocene, and multiple colonization to a single ancient lake occurred in the Pleistocene. Our results indicate substantial incongruence among estimated phylogenomic divergence times, some fossil records, and formation ages of ancient lakes. These findings suggest some fossil records may be misidentified in these groups and highlight the need to carefully evaluate geological evidence and fossil records when using these for divergence time estimation.
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Affiliation(s)
- Takahiro Hirano
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan; Biology Program, Faculty of Science, University of the Ryukyus, Okinawa, Japan.
| | - Takumi Saito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Shun Ito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
| | - Bin Ye
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - T Mason Linscott
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, USA
| | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | - Zhengzhong Dong
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Satoshi Chiba
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
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38
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Croce ME, Hoshino M, Gauna MC, Parodi ER, Kogame K. Taxonomic study of Scytosiphon (Phaeophyceae) from temperate coasts of Argentina. JOURNAL OF PHYCOLOGY 2023; 59:383-401. [PMID: 36680561 DOI: 10.1111/jpy.13315] [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: 07/23/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 05/28/2023]
Abstract
Scytosiphon is a common intertidal genus widely distributed on temperate coasts worldwide. Recently, eight species have been delimited with molecular tools. Although S. lomentaria is the only species that predominates in the macroalgal literature of the Southwestern Atlantic Ocean (SwAO), unpublished molecular data obtained for a population study of S. lomentaria revealed hidden species diversity of Scytosiphon among the individuals collected from four localities at the SwAO. The aim of this study was to revise the identity and phylogenetic relationships of Scytosiphon from temperate coasts of the SwAO using DNA data. Thalli were collected from the Argentinean coast between 39° S and 43° S, from which cox1 and rbcL gene sequences were obtained. Phylogenies and haplotype networks were inferred and morphology of gametophytes was studied. Four species were recognized, S. lomentaria, S. promiscuus, S. shibazakiorum, and one species that belongs to a complex of species known as "Scytosiphon Atlantic complex." This complex was known to occur only in the North Atlantic, however, the results found in this study revealed that it has an extended distribution range that includes the southern hemisphere, where its populations have high genetic diversity and unique haplotypes. The morphological differences among the four species were subtle; denoting that previous Scytosiphon records from the SwAO attributed to the renowned S. lomentaria could represent different species. In addition, sex ratio and genome-wide single nucleotide polymorphisms (SNPs) analyses were done for populations of S. promiscuus presumably introduced to the SwAO, and the results indicated that they included female-dominant parthenogenetic populations, which were probably introduced from Japan.
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Affiliation(s)
- Maria Emilia Croce
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Bahía Blanca, Argentina
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, CONICET-Bahía Blanca, Bahía Blanca, Argentina
| | - Masakazu Hoshino
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Maria Cecilia Gauna
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Bahía Blanca, Argentina
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, CONICET-Bahía Blanca, Bahía Blanca, Argentina
| | - Elisa R Parodi
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Bahía Blanca, Argentina
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, CONICET-Bahía Blanca, Bahía Blanca, Argentina
| | - Kazuhiro Kogame
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
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39
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Barrett CF, Corbett CW, Thixton-Nolan HL. A lack of population structure characterizes the invasive Lonicera japonica in West Virginia and across eastern North America. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530604. [PMID: 36909462 PMCID: PMC10002767 DOI: 10.1101/2023.03.01.530604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Invasive plant species cause massive ecosystem damage globally, yet represent powerful case studies in population genetics and rapid adaptation to new habitats. The availability of digitized herbarium collections data, and the ubiquity of invasive species across the landscape make them highly accessible for studies of invasion history and population dynamics associated with their introduction, establishment, spread, and ecological interactions. Here we focus on Lonicera japonica, one of the most damaging invasive vine species in North America. We leveraged digitized collections data and contemporary field collections to reconstruct the invasion history and characterize patterns of genomic variation in the eastern USA, using a straightforward method for generating nucleotide polymorphism data and a recently published, chromosome-level genome for the species. We found an overall lack of population structure among sites in northern West Virginia, USA, as well as across sites in the central and eastern USA. Heterozygosity and population differentiation were both low based on Fst, analysis of molecular variance, principal components analysis, and cluster-based analyses. We also found evidence of high inbreeding coefficients and significant linkage disequilibrium, in line with the ability of this otherwise outcrossing, perennial species to propagate vegetatively. Our findings corroborate earlier studies based on allozyme data, and suggest that intentional, human-assisted spread explains the lack of population structure, as this species was planted for erosion control and as an ornamental, escaping cultivation repeatedly across the USA. Finally, we discuss how plant invasion genomics can be incorporated into experiential undergraduate education as a way to integrate teaching and research.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 5209 Life Sciences Building, 53 Campus Drive, Morgantown, WV, USA 26506
| | - Cameron W. Corbett
- Department of Biology, West Virginia University, 5209 Life Sciences Building, 53 Campus Drive, Morgantown, WV, USA 26506
| | - Hana L. Thixton-Nolan
- Department of Biology, West Virginia University, 5209 Life Sciences Building, 53 Campus Drive, Morgantown, WV, USA 26506
| | - Biology 320 Class
- Department of Biology, West Virginia University, 5209 Life Sciences Building, 53 Campus Drive, Morgantown, WV, USA 26506
- Biology 320 Capstone Students, “Total Science Experience: Genomics” [Appendix 1]
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40
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GRAS-Di SNP-based molecular characterization and fingerprinting of a Turkish Corylus avellana core set provide insights into the cultivation and breeding of hazelnut in Turkey. Mol Genet Genomics 2023; 298:413-426. [PMID: 36595074 DOI: 10.1007/s00438-022-01990-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Hazelnut (Corylus avellana L.) is an economically and socially important product for Turkey, the country that leads global production of this crop. The preservation of Turkish hazelnut genetic diversity and informed breeding of new cultivars are crucial for maintaining quality and crop yield stability. In this study, genotyping by random amplicon sequencing (GRAS-Di) was used to identify single-nucleotide polymorphisms (SNPs) in a panel of 96 individuals representing the Turkish national hazelnut collection. The resulting 7609 high-quality SNPs were physically mapped to the Tombul cultivar reference genome and used for population structure and diversity analyses. These analyses revealed that cultivars are not less diverse than wild accessions and that 44% of the panel had admixed ancestry. The results also indicated that recently released Turkish cultivars are highly similar to each other, suggesting that diversity analysis is an important tool that should be employed to prevent future genetic bottlenecks in this crop. A minimal marker algorithm was used to select a set of seven SNP markers that were capable of differentiating the panel accessions. These fingerprinting markers should be useful for the propagation of true-to-type elite cultivars that can be used to renew Turkey's aging hazelnut orchards.
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41
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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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Multiplexed ISSR Genotyping by Sequencing (MIG-Seq). Methods Mol Biol 2023; 2638:403-414. [PMID: 36781659 DOI: 10.1007/978-1-0716-3024-2_29] [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: 02/15/2023]
Abstract
Multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) is a simple, rapid, and inexpensive method for detecting single-nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS). The advantages of MIG-seq include easy application to various species without prior genetic information. In addition, this method opens the door to genome-wide nucleotide sequence analyses of low-quality and trace-level deoxyribonucleic acid (DNA) samples, which have previously been difficult to analyze. Another advantage is that the procedure is simple, time-saving, and inexpensive. Recently, MIG-seq has been applied to wild and cultivated plants and has produced novel results. Using invisible DNA information, questions related to gene flow through pollination and seed dispersal, the genetic structure and diversity of populations, clonality, and the hybridization of wild and cultivated plants are being rapidly answered. In this chapter, I present the results of plant research based on MIG-seq and describe the procedure for this method as a user of MIG-seq.
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Genetic population structures of common scavenging species near hydrothermal vents in the Okinawa Trough. Sci Rep 2023; 13:2348. [PMID: 36759539 PMCID: PMC9911719 DOI: 10.1038/s41598-022-14100-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/01/2022] [Indexed: 02/11/2023] Open
Abstract
Deep-sea mining of hydrothermal deposits off the coast of Japan is currently under consideration, and environmental baseline studies of the area are required to understand possible impacts. The aim of this study is to clarify population structures of dominant benthic megafaunal species near hydrothermal vent fields in the Okinawa Trough, using a population genetics approach. We examined dominant deep-sea scavenging species including eels, several amphipods, and a decapod and performed population genetic analyses based on the mitochondrial cytochrome c oxidase subunit I region. Several sites were sampled within Okinawa Trough to examine intra-population diversity while two other locations 1400-2400 km away were chosen for inter-population comparisons. For synaphobranchid eels Simenchelys parasitica and Synaphobranchus kaupii, our results showed significant intra-population diversity but no inter-population genetic differentiation, suggesting strong genetic connectivity and/or large population sizes. In addition, single nucleotide polymorphism analysis also confirmed strong genetic connectivity for Simenchelys parasitica. Among scavenging amphipods, we detected seven putative species using molecular phylogenetic analysis. We evaluated population structures of the most abundant species of amphipods and a decapod species (Nematocarcinus lanceopes). Our results provide basic information on the genetic population structures of benthic megafaunal species near hydrothermal vent fields, which can be used to select candidate species for future connectivity analysis with high-resolution genetic markers and aid understanding of the potential population impacts of environmental disturbances.
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Suzuki M, Ohno K, Sawayama E, Morinaga SI, Kishida T, Matsumoto T, Kato H. Genomics reveals a genetically isolated population of the Pacific white-sided dolphin (Lagenorhynchus obliquidens) distributed in the Sea of Japan. Mol Ecol 2023; 32:881-891. [PMID: 36440502 DOI: 10.1111/mec.16797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
The processes by which animals become genetically isolated in an open environment such as the ocean have not yet been fully elucidated. Morphologically different populations of Pacific white-sided dolphin Lagenorhynchus obliquidens are observed sympatrically in the Sea of Japan. However, genetic studies that exclusively used limited mitochondrial loci or microsatellite DNA have failed to demonstrate the existence of genetically distinct populations. Here, to reveal the population structure, we analysed genome-wide population genetic data using single nucleotide polymorphisms (SNPs) gathered in 2018-2021 from all domestic captive individuals in aquaria, the majority of which originated from the wild, as well as from some stranded individuals, together covering a wide area of coastal water around Japan (n = 123). Multiplexed intersimple sequence repeat genotyping-by-sequencing analysis was performed to obtain the SNP data. Principal coordinate analysis and the clustering method structure indicated that two genetically-distinct populations exist, with little interpopulation gene flow revealed. In addition, the genotypic segregation was reflected in differences in external morphotype. Furthermore, a population demographic analysis based on the whole-genome sequences of an individual from each population indicated that sea-level changes during the Last Glacial Period probably led to allopatric divergence of this species in a limited area of the Sea of Japan, with that group subsequently sharing a distribution area with the other population. These findings yield insights into the formation of genetically isolated sympatric populations in the ocean.
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Affiliation(s)
- Miwa Suzuki
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Kaho Ohno
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Eitaro Sawayama
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Shin-Ichi Morinaga
- Department of Natural & Environmental Science, Teikyo University of Science, Tokyo, Japan
| | - Takushi Kishida
- Museum of Natural and Environmental History, Shizuoka, Japan
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Shibabayashi M, Shimizu T, Tokuhiro C, Suyama Y, Sakaguchi S, Ito T, Yu CC, Chung KF, Nagasawa J, Shiuchi T, Kokubugata G, Abe A, Naiki A, Nagano AJ, Isagi Y. The contrary conservation situations of two local critically endangered species, Vaccinium emarginatum (Ericaceae) and Elatostema platyphyllum (Urticaceae), growing on the eastern edge of the distribution. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1093321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
As biodiversity loss continues, there is an urgent need to develop efficient conservation measures to protect diversity with limited conservation resources. Conservation targets have generally been selected based on their population size, but more detailed assessments clarifying the phylogenetic genetic status, history, and phylogenetic uniqueness of rare species is crucial to set more appropriate and effective conservation measures. In Japan, the Act on Conservation of Endangered Species of Wild Fauna and Flora designated endangered plants with high conservation priority, but >40% of these species also grow overseas. We conducted comparative analyses based on ddRADseq and MIG-seq to evaluate the population conservation status and value of Vaccinium emarginatum and Elatostema platyphyllum which are growing across national borders at the eastern edge of their species distribution range. The analyses revealed contrasting conservation status between the two species; the Japanese population of V. emarginatum had lower genetic diversity at the individual level and phylogenetically differentiated from Taiwanese populations, while that of E. platyphyllum had higher diversity at the individual level and is a relatively recent migrant with little phylogenetical differentiation from Taiwanese populations. The two species, which share the common feature of being critically rare in Japan, showed contrasting genetic/phylogenetic characteristics. This study provided useful information for appropriate conservation measures based on species’ phylogenetic traits and genetic diversity.
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46
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Putri D, Cronin AL. Widespread and ongoing invasion by the ant
Technomyrmex brunneus
Forel in eastern Asia as elucidated by molecular data. Ecol Res 2023. [DOI: 10.1111/1440-1703.12383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Diyona Putri
- Department of Biological Sciences Tokyo Metropolitan University Tokyo Japan
| | - Adam L. Cronin
- Department of Biological Sciences Tokyo Metropolitan University Tokyo Japan
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47
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Yamazaki Y, Kajita T, Takayama K. Spatiotemporal process of long-distance seed dispersal in a pantropically distributed sea hibiscus group. Mol Ecol 2023; 32:1726-1738. [PMID: 36635976 DOI: 10.1111/mec.16836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/25/2022] [Accepted: 12/20/2022] [Indexed: 01/14/2023]
Abstract
Long-distance dispersal (LDD) of seeds plays an essential role in the migration of plants to a new habitat and maintaining gene flow among geographically isolated populations. Pantropical plants with sea-drifted seeds, which have one of the largest distributions in all flowering plants, have achieved their global distribution by LDD. However, the spatiotemporal processes to achieve the wide distribution and the role of LDD in it have not yet been elucidated. In this study, we conducted phylogenomic analyses on the plastome, genome-wide nuclear SNP, and low-copy gene data of Hibiscus tiliaceus and its relatives. The dated phylogeny suggested that global expansion started approximately 4 million years ago (Ma), and species diversification occurred 1 Ma. Plastome phylogeny confirmed the nonmonophyly of the haplotypes in the two widely distributed coastal species, H. tiliaceus and H. pernambucensis. In contrast, genome-wide nuclear SNP phylogenies demonstrated clear genetic segregation among species and/or geographical regions. Ancestral polymorphisms in chloroplast genomes shared among widely distributed species have remained below the range of rapid expansion and speciation of marginal populations. This study demonstrated that the LDD of sea-drifted seeds contributed to the rapid expansion and pantropical distribution of sea hibiscus in the last few million years, and adaptation to local environment or isolation by regional effect after LDD promoted speciation, suppressing gene flow.
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Affiliation(s)
- Yuri Yamazaki
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Kyoto, Japan.,Railway Systems Business Unit, Hitachi, Ltd., Ibaraki, Japan
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,United Graduate School of Agricultural Science, Kagoshima University, Kagoshima, Japan
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Kyoto, Japan
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48
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Suetsugu K, Hirota SK, Hsu TC, Kurogi S, Imamura A, Suyama Y. Monotropastrum kirishimense (Ericaceae), a new mycoheterotrophic plant from Japan based on multifaceted evidence. JOURNAL OF PLANT RESEARCH 2023; 136:3-18. [PMID: 36445504 PMCID: PMC9832082 DOI: 10.1007/s10265-022-01422-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/26/2022] [Indexed: 05/10/2023]
Abstract
Due to their reduced morphology, non-photosynthetic plants have been one of the most challenging groups to delimit to species level. The mycoheterotrophic genus Monotropastrum, with the monotypic species M. humile, has been a particularly taxonomically challenging group, owing to its highly reduced vegetative and root morphology. Using integrative species delimitation, we have focused on Japanese Monotropastrum, with a special focus on an unknown taxon with rosy pink petals and sepals. We investigated its flowering phenology, morphology, molecular identity, and associated fungi. Detailed morphological investigation has indicated that it can be distinguished from M. humile by its rosy pink tepals and sepals that are generally more numerous, elliptic, and constantly appressed to the petals throughout its flowering period, and by its obscure root balls that are unified with the surrounding soil, with root tips that hardly protrude. Based on genome-wide single-nucleotide polymorphisms, molecular data has provided clear genetic differentiation between this unknown taxon and M. humile. Monotropastrum humile and this taxon are associated with different Russula lineages, even when they are sympatric. Based on this multifaceted evidence, we describe this unknown taxon as the new species M. kirishimense. Assortative mating resulting from phenological differences has likely contributed to the persistent sympatry between these two species, with distinct mycorrhizal specificity.
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Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan.
- The Institute for Advanced Research, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Tian-Chuan Hsu
- Botanical Garden Division, Taiwan Forestry Research Institute, No. 53, Nanhai Rd., Taipei, 100, Taiwan
| | - Shuichi Kurogi
- Miyazaki Prefectural Museum of Nature and History, 2-4-4, Jingû, Miyazaki, 880-0053, Japan
| | - Akio Imamura
- Hokkaido University of Education, Sapporo, 002-8501, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
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49
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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Zeng Q, Sun Y, Zhong H, Yang C, Qin Q, Gu Q. Population Genomic Evidence for the Diversification of Bellamya aeruginosa in Different River Systems in China. BIOLOGY 2022; 12:biology12010029. [PMID: 36671722 PMCID: PMC9855799 DOI: 10.3390/biology12010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
Clarifying the genetic structure can facilitate the understanding of a species evolution history. It is crucial for the management of germplasm resources and providing useful guidance for effective selective breeding. Bellamya is an economically and ecologically important freshwater snail for fish, birds and even humans. Population genetic structures of the Bellamya species, however, were unknown in previous studies. Population genomics approaches with tens to hundreds of thousands of single nucleotide polymorphisms (SNPs) make it possible to detect previously unidentified structures. The population genomic study of seven populations of B. aeruginosa across three river systems (Yellow River, Yangtze River and Pearl River) in China was conducted by SLAF-seq. SLAF-seq obtained a total of 4737 polymorphisms SLAF-tags and 25,999 high-consistency genome-wide SNPs. The population genetic structure showed a clear division among populations from the Yellow River basin (YH and WL) and the Pearl River basin (QSH and LB), as well as population YC from the Yangtze River basin using the SNPs data. However, there existed no distinct population structure using the mitochondrial DNA (mtDNA). The anthropogenic translocation from the Yangtze River basin to the Pearl River basin and the passive dispersion from the Yangtze River basin to the Yellow River basin by flooding have weakened the phylogeographic pattern of B. aeruginosa. The divergence of B. aeruginosa in the three river systems suggests that the anthropogenic dispersal for aquaculture and breeding requires serious consideration of the population structure for the preservation of genetic diversity and effective utilization of germplasm resources.
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