Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses

Handle URI:
http://hdl.handle.net/10754/582756
Title:
Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses
Authors:
Akihito; Akishinonomiya, Fumihito; Ikeda, Yuji; Aizawa, Masahiro; Nakagawa, So; Umehara, Yumi; Yonezawa, Takahiro; Mano, Shuhei; Hasegawa, Masami; Nakabo, Tetsuji; Gojobori, Takashi ( 0000-0001-7850-1743 )
Abstract:
To understand how geographical differentiation of gobioid fish species led to speciation, two populations of the Pacific Ocean and the Sea of Japan for each of the two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus, were studied in both morphological and molecular features. Analyzing mitochondrial genes, Akihito et al. (2008) suggested that P. zonoleucus does not form a monophyletic clade relative to P. elapoides, indicating that “Sea of Japan P. zonoleucus” and P. elapoides form a clade excluding “Pacific P. zonoleucus” as an outgroup. Because morphological classification clearly distinguish these two species and a gene tree may differ from a population tree, we examined three nuclear genes, S7RP, RAG1, and TBR1, in this work, in order to determine whether nuclear and mitochondrial trees are concordant, thus shedding light on the evolutionary history of this group of fishes. Importantly, nuclear trees were based on exactly the same individuals that were used for the previously published mtDNA trees. The tree based on RAG1 exon sequences suggested a closer relationship of P. elapoides with “Sea of Japan P. zonoleucus”, which was in agreement with the mitochondrial tree. In contrast, S7RP and TBR1 introns recovered a monophyletic P. zonoleucus. If the mitochondrial tree represents the population tree in which P. elapoides evolved from “Sea of Japan P. zonoleucus”, the population size of P. elapoides is expected to be smaller than that of “Sea of Japan P. zonoleucus”. This is because a smaller population of the new species is usually differentiated from a larger population of the ancestral species when the speciation occurred. However, we found no evidence of such a small population size during the evolution of P. elapoides. Therefore, we conclude that the monophyletic P. zonoleucus as suggested by S7RP and TBR1 most likely represents the population tree, which is consistent with the morphological classification. In this case, it is possible that the incongruent mitochondrial and RAG1 trees are either due to incomplete lineage sorting of ancestral polymorphisms or to introgression by hybridization. Because of a smaller effective population size of mitochondria compared with nuclear genes, the introgression might be a more likely scenario in explaining the incongruent mitochondrial tree than the incomplete lineage sorting. Because of smaller effective population size of “Sea of Japan P. zonoleucus” than that of P. elapoides, the direction of the introgression was likely to be from the latter to the former. This evolutionary work of the two gobioid species highlights the need of analyzing multiple gene trees for both nuclear and mitochondrial genes as well as scrutinization of morphological characteristics to obtain a population tree representing the organismal evolutionary history.
KAUST Department:
Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses 2015 Gene
Publisher:
Elsevier BV
Journal:
Gene
Issue Date:
28-Oct-2015
DOI:
10.1016/j.gene.2015.10.014
Type:
Article
ISSN:
03781119
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S0378111915012226
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorAkihitoen
dc.contributor.authorAkishinonomiya, Fumihitoen
dc.contributor.authorIkeda, Yujien
dc.contributor.authorAizawa, Masahiroen
dc.contributor.authorNakagawa, Soen
dc.contributor.authorUmehara, Yumien
dc.contributor.authorYonezawa, Takahiroen
dc.contributor.authorMano, Shuheien
dc.contributor.authorHasegawa, Masamien
dc.contributor.authorNakabo, Tetsujien
dc.contributor.authorGojobori, Takashien
dc.date.accessioned2015-11-26T06:29:37Zen
dc.date.available2015-11-26T06:29:37Zen
dc.date.issued2015-10-28en
dc.identifier.citationSpeciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses 2015 Geneen
dc.identifier.issn03781119en
dc.identifier.doi10.1016/j.gene.2015.10.014en
dc.identifier.urihttp://hdl.handle.net/10754/582756en
dc.description.abstractTo understand how geographical differentiation of gobioid fish species led to speciation, two populations of the Pacific Ocean and the Sea of Japan for each of the two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus, were studied in both morphological and molecular features. Analyzing mitochondrial genes, Akihito et al. (2008) suggested that P. zonoleucus does not form a monophyletic clade relative to P. elapoides, indicating that “Sea of Japan P. zonoleucus” and P. elapoides form a clade excluding “Pacific P. zonoleucus” as an outgroup. Because morphological classification clearly distinguish these two species and a gene tree may differ from a population tree, we examined three nuclear genes, S7RP, RAG1, and TBR1, in this work, in order to determine whether nuclear and mitochondrial trees are concordant, thus shedding light on the evolutionary history of this group of fishes. Importantly, nuclear trees were based on exactly the same individuals that were used for the previously published mtDNA trees. The tree based on RAG1 exon sequences suggested a closer relationship of P. elapoides with “Sea of Japan P. zonoleucus”, which was in agreement with the mitochondrial tree. In contrast, S7RP and TBR1 introns recovered a monophyletic P. zonoleucus. If the mitochondrial tree represents the population tree in which P. elapoides evolved from “Sea of Japan P. zonoleucus”, the population size of P. elapoides is expected to be smaller than that of “Sea of Japan P. zonoleucus”. This is because a smaller population of the new species is usually differentiated from a larger population of the ancestral species when the speciation occurred. However, we found no evidence of such a small population size during the evolution of P. elapoides. Therefore, we conclude that the monophyletic P. zonoleucus as suggested by S7RP and TBR1 most likely represents the population tree, which is consistent with the morphological classification. In this case, it is possible that the incongruent mitochondrial and RAG1 trees are either due to incomplete lineage sorting of ancestral polymorphisms or to introgression by hybridization. Because of a smaller effective population size of mitochondria compared with nuclear genes, the introgression might be a more likely scenario in explaining the incongruent mitochondrial tree than the incomplete lineage sorting. Because of smaller effective population size of “Sea of Japan P. zonoleucus” than that of P. elapoides, the direction of the introgression was likely to be from the latter to the former. This evolutionary work of the two gobioid species highlights the need of analyzing multiple gene trees for both nuclear and mitochondrial genes as well as scrutinization of morphological characteristics to obtain a population tree representing the organismal evolutionary history.en
dc.language.isoenen
dc.publisherElsevier BVen
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S0378111915012226en
dc.rightsNOTICE: this is the author’s version of a work that was accepted for publication in Gene. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Gene, 28 October 2015. DOI: 10.1016/j.gene.2015.10.014en
dc.titleSpeciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analysesen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalGeneen
dc.eprint.versionPost-printen
dc.contributor.institutionThe Imperial Residence, 1-1 Chiyoda, Chiyoda-ku, Tokyo 100-0001, Japanen
dc.contributor.institutionThe University Museum, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japanen
dc.contributor.institutionTokyo University of Agriculture, 1737 Funako, Atsugi-shi, Kanagawa 243-0034, Japanen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorGojobori, Takashien
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