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

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.

Molecular phylogenetic relationships reveal contrasting evolutionary patterns in Gorgoniidae (Octocorallia) in the Eastern Pacific

“…colleagues (2011, 2014) showed that only ~70 % of species analysed could be discriminated using mtMutS and CoxII-Igr-CoxI (the "extended mitochondrial barcode"). Furthermore, it has been shown that if species delimitation estimates are based solely on mtDNA, boundaries between closely related octocoral species cannot be detected, and these groups would be consider identical (Vargas et al, 2014;Yasuda et al, 2015). Therefore, nuclear markers, such as 28SrRNA (28S) or internal transcribed spacers (ITS), are used to compensate for the low substitution rate of mitochondrial genes (Aguilar and Sánchez, 2007;McFadden et al, 2006McFadden et al, , 2014Sánchez et al, 2007).…”

Phylogeography of Orinus (Poaceae), a dominant grass genus on the Qinghai-Tibet Plateau

“…The plastid DNA data and the AFLPs are not in conflict with this hypothesis. Plastid DNA loci sort and become fixed more slowly than nuclear markers (Wolfe et al, 1987;de Villiers et al, 2013;Shaw et al, 2017), such as nrITS, and the shared haplotypes among all three species and between O. kokonoricus and O. intermedius may represent incomplete lineage sorting (Choleva et al, 2014;Yasuda et al, 2015;Kuritzin et al, 2016). Alternatively, the haplotype shared among all three species may represent an older secondary contact (Miraldo et al, 2011;Sardell & Uy, 2016), predating the S10 event and too old to be preserved in nrITS data.…”

“…AFLPs revealed that species and populations within species comprise clades. Therefore, most but not all lineage sorting among species is complete (Choleva et al, 2014;Yasuda et al, 2015;Kuritzin et al, 2016).…”

Foxed intra- and interspecific differentiation in <em>Leptogorgia</em> (Octocorallia: Gorgoniidae). A description of a new species based on multiple sources of evidence

“…unequally share a genetic polymorphism, may also explain the lack of congruence of the molecular nuclear data. This phenomenon has been observed between closely related species within other coral genera such as Heliopora (Yasuda et al 2015), Seriatopora (Flot et al 2008) and Acropora (Vollmer and Palumbi 2004), and in other invertebrates such as Cypraeidae marine gastropods (Meyer and Paulay 2005), Melanoplus grasshopper species (Carstens and Knowles 2007) and the butterfly family Lycaenidae (Wiemers and Fiedler 2007).…”

“…sp.) and outgroup, confirming the need to complement the use of these markers with nuclear ones in the study of close relationships (Yasuda et al 2015, McFadden et al 2010. Hybridization or incomplete lineage sorting, in which L. alba and L. manabiensis n. sp.…”