Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation
The Japanese eel (Anguilla japonica), European eel (Anguilla anguilla), and American eel (Anguilla rostrata) are migratory, catadromous, temperate zone fish sharing several common life cycle features. The population genetics of panmixia in these eel species has already been investigated. Our extensi...
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2018-09-01
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Online Access: | http://www.mdpi.com/2073-4425/9/10/474 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yoji Igarashi Hong Zhang Engkong Tan Masashi Sekino Kazutoshi Yoshitake Shigeharu Kinoshita Susumu Mitsuyama Tatsuki Yoshinaga Seinen Chow Hiroaki Kurogi Akira Shinoda Yu-San Han Ryoshiro Wakiya Noritaka Mochioka Toshihiro Yamamoto Hiroshi Kuwada Yoshitsugu Kaji Yutaka Suzuki Takashi Gojobori Takanori Kobayashi Kenji Saitoh Shugo Watabe Shuichi Asakawa |
spellingShingle |
Yoji Igarashi Hong Zhang Engkong Tan Masashi Sekino Kazutoshi Yoshitake Shigeharu Kinoshita Susumu Mitsuyama Tatsuki Yoshinaga Seinen Chow Hiroaki Kurogi Akira Shinoda Yu-San Han Ryoshiro Wakiya Noritaka Mochioka Toshihiro Yamamoto Hiroshi Kuwada Yoshitsugu Kaji Yutaka Suzuki Takashi Gojobori Takanori Kobayashi Kenji Saitoh Shugo Watabe Shuichi Asakawa Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation Genes genome mapping genetic patchiness single nucleotide polymorphisms population genomics fixation index endangered species |
author_facet |
Yoji Igarashi Hong Zhang Engkong Tan Masashi Sekino Kazutoshi Yoshitake Shigeharu Kinoshita Susumu Mitsuyama Tatsuki Yoshinaga Seinen Chow Hiroaki Kurogi Akira Shinoda Yu-San Han Ryoshiro Wakiya Noritaka Mochioka Toshihiro Yamamoto Hiroshi Kuwada Yoshitsugu Kaji Yutaka Suzuki Takashi Gojobori Takanori Kobayashi Kenji Saitoh Shugo Watabe Shuichi Asakawa |
author_sort |
Yoji Igarashi |
title |
Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation |
title_short |
Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation |
title_full |
Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation |
title_fullStr |
Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation |
title_full_unstemmed |
Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation |
title_sort |
whole-genome sequencing of 84 japanese eels reveals evidence against panmixia and support for sympatric speciation |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2018-09-01 |
description |
The Japanese eel (Anguilla japonica), European eel (Anguilla anguilla), and American eel (Anguilla rostrata) are migratory, catadromous, temperate zone fish sharing several common life cycle features. The population genetics of panmixia in these eel species has already been investigated. Our extensive population genetics analysis was based on 1400 Gb of whole-genome sequence (WGS) data from 84 eels. It demonstrated that a Japanese eel group from the Kuma River differed from other populations of the same species. Even after removing the potential adapted/selected single nucleotide polymorphism (SNP) data, and with very small differences (fixation index [Fst] = 0.01), we obtained results consistently indicating that panmixia does not occur in Japanese eels. The life cycle of the Japanese eel is well-established and the Kuma River is in the center of its habitat. Nevertheless, simple reproductive isolation is not the probable cause of non-panmixia in this species. We propose that the combination of spawning area subdivision, philopatry, and habitat preference/avoidance accounts for the non-panmixia in the Japanese eel population. We named this hypothesis the “reproductive isolation like subset mapping” (RISM) model. This finding may be indicative of the initial stages of sympatric speciation in these eels. |
topic |
genome mapping genetic patchiness single nucleotide polymorphisms population genomics fixation index endangered species |
url |
http://www.mdpi.com/2073-4425/9/10/474 |
work_keys_str_mv |
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doaj-9dddcceb049644149e308ec09297027d2020-11-25T00:57:53ZengMDPI AGGenes2073-44252018-09-0191047410.3390/genes9100474genes9100474Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric SpeciationYoji Igarashi0Hong Zhang1Engkong Tan2Masashi Sekino3Kazutoshi Yoshitake4Shigeharu Kinoshita5Susumu Mitsuyama6Tatsuki Yoshinaga7Seinen Chow8Hiroaki Kurogi9Akira Shinoda10Yu-San Han11Ryoshiro Wakiya12Noritaka Mochioka13Toshihiro Yamamoto14Hiroshi Kuwada15Yoshitsugu Kaji16Yutaka Suzuki17Takashi Gojobori18Takanori Kobayashi19Kenji Saitoh20Shugo Watabe21Shuichi Asakawa22Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, JapanDepartment of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, JapanDepartment of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, JapanNational Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa 236-8648, JapanDepartment of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, JapanDepartment of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, JapanDepartment of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, JapanSchool of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, JapanNational Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa 236-8648, JapanYokosuka Laboratory, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Yokosuka, Kanagawa 238-0316, JapanDepartment of Biology, Tokyo Medical University, Tokyo 160-8402, JapanInstitute of Fishery Science, College of Life Science, National Taiwan University, Taipei 10617, TaiwanBioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka 812-0053, JapanBioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka 812-0053, JapanYokosuka Laboratory, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Yokosuka, Kanagawa 238-0316, JapanMinami-Izu Laboratory, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Kamo, Shizuoka 415-0156, JapanWakayama Prefectural Museum of Natural History, Kainan, Wakayama 642-0001, JapanDepartment of Medical Genome Science, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, JapanCenter for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, JapanNational Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa 236-8648, JapanNational Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa 236-8648, JapanSchool of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, JapanDepartment of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, JapanThe Japanese eel (Anguilla japonica), European eel (Anguilla anguilla), and American eel (Anguilla rostrata) are migratory, catadromous, temperate zone fish sharing several common life cycle features. The population genetics of panmixia in these eel species has already been investigated. Our extensive population genetics analysis was based on 1400 Gb of whole-genome sequence (WGS) data from 84 eels. It demonstrated that a Japanese eel group from the Kuma River differed from other populations of the same species. Even after removing the potential adapted/selected single nucleotide polymorphism (SNP) data, and with very small differences (fixation index [Fst] = 0.01), we obtained results consistently indicating that panmixia does not occur in Japanese eels. The life cycle of the Japanese eel is well-established and the Kuma River is in the center of its habitat. Nevertheless, simple reproductive isolation is not the probable cause of non-panmixia in this species. We propose that the combination of spawning area subdivision, philopatry, and habitat preference/avoidance accounts for the non-panmixia in the Japanese eel population. We named this hypothesis the “reproductive isolation like subset mapping” (RISM) model. This finding may be indicative of the initial stages of sympatric speciation in these eels.http://www.mdpi.com/2073-4425/9/10/474genome mappinggenetic patchinesssingle nucleotide polymorphismspopulation genomicsfixation indexendangered species |