Genetic diversity, paraphyly and incomplete lineage sorting of mtDNA, ITS2 and microsatellite flanking region in closely related Heliopora species (Octocorallia)

Type Article
Date 2015-12
Language English
Author(s) Yasuda NinaORCID1, 7, Taquet Coralie2, Nagai Satoshi3, Fortes Miguel4, Fan Tung-Yung5, Harii Saki6, Yoshida Terutoyo7, Sito Yuta7, Nadaoka KazuoORCID8
Affiliation(s) 1 : Miyazaki Univ, Org Promot Tenure Track, Miyazaki 8892192, Japan.
2 : Univ Polynesie Francaise, UMR Ecosyst Insulaires Oceaniens 241, F-98702 Faaa Aeroport, Tahiti, France.
3 : Natl Res Inst Fisheries Sci, Aquat Genom Res Ctr, Yokohama, Kanagawa 2368648, Japan.
4 : Univ Philippines, Marine Sci Inst CS, Quezon City 1101, Philippines.
5 : Natl Museum Marine Biol & Aquarium, Pingtung, Taiwan.
6 : Univ Ryukyus, Trop Biosphere Res Ctr, Okinawa 9050227, Japan.
7 : Miyazaki Univ, Fac Agr, Dept Marine Biol & Environm Sci, Gakuen Kibanadainishi 1-1, Miyazaki 8892192, Japan.
8 : Tokyo Inst Technol, Grad Sch Informat Sci & Engn, Meguro Ku, Tokyo 1528552, Japan.
Source Molecular Phylogenetics And Evolution (1055-7903) (Academic Press Inc Elsevier Science), 2015-12 , Vol. 93 , P. 161-171
DOI 10.1016/j.ympev.2015.07.009
WOS© Times Cited 11
Keyword(s) ITS2, Concerted evolution, mtMutS, Secondary structure, Species identification, Speciation
Abstract

Examining genetic diversity and lineage sorting of different genes in closely related species provide useful information for phylogenetic analyses and ultimately for understanding the origins of biodiversity. In this study, we examined inter- and intraspecific genetic variation in internal transcribed spacer 2 (ITS2), partial mitochondrial gene (mtMutS), and nuclear microsatellite flanking region in two closely related octocoral species (Heliopora coerulea, HC-A and HC-B). These species were recently identified in a population genetic study using microsatellite markers. The two species have different reproductive timing, which ecologically promotes lineage sorting. In this study, we examined whether species boundaries could be detected by the commonly used nuclear ITS2 and mtMutS, as well as by possibly neutral microsatellite flanking sequences. Haplotype network analysis of microsatellite flanking region revealed that a possible ancestral haplotype was still shared between the two species, indicating on-going lineage sorting. Haplotype network analysis of ITS2 and microsatellite flanking region revealed shared haplotypes between the two lineages. The two species shared fewer ITS2 sequences than microsatellite flanking region sequences. The almost fixed point mutation at the tip of helix 3 of ITS2 was not associated with the secondary structure or compensatory base changes (CBCs). The phylogenetic tree of ITS2 showed paraphyly and that of the microsatellite flanking region indicated that lineage sorting for the two species may be incomplete. Much higher intra-and inter-individual variation of ITS2 was observed in HC-B than that in HC-A, highlighting the importance of examining ITS2 from multiple individuals to estimate genetic diversity. The mitochondrial mtMutS gene sequences from 39 individuals, including both species collected from Japan and Taiwan, showed no variation because of slow rates of mitochondrial nucleotide substitution. This study suggests caution is warranted when reciprocal monophyly in a phylogenetic tree is used as the criterion for delimiting closely related octocoral species based on ITS2 or mtMtuS sequences. Detection of boundaries between closely related species requires multi-locus analysis, such as genetic admixture analysis using multiple individuals.

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Yasuda Nina, Taquet Coralie, Nagai Satoshi, Fortes Miguel, Fan Tung-Yung, Harii Saki, Yoshida Terutoyo, Sito Yuta, Nadaoka Kazuo (2015). Genetic diversity, paraphyly and incomplete lineage sorting of mtDNA, ITS2 and microsatellite flanking region in closely related Heliopora species (Octocorallia). Molecular Phylogenetics And Evolution, 93, 161-171. Publisher's official version : https://doi.org/10.1016/j.ympev.2015.07.009 , Open Access version : https://archimer.ifremer.fr/doc/00667/77932/