Phylogenetic relationships among Thunnus species inferred from rDNA ITS1 sequence

Abstract

Intra and interspecific nucleotide sequence variation of rDNA first internal transcribed spacer (ITS1) was analysed using all eight species of the genus Thunnus plus two out-group species within the same family, skipjack tuna Katsuwonus pelamis and striped bonito Sarda orientalis. Intraspecific nucleotide sequence variation in ITS1, including intra-genomic variation, was low, ranging from 0Á003 to 0Á014 [Kimura's two parameter distance (K2P)], whereas variation between species within the genus Thunnus ranged from 0Á009 to 0Á05. The Atlantic and Pacific northern bluefin tunas Thunnus thynnus thynnus and Thunnus thynnus orientalis, recently proposed to be distinct species, were found to share nearly identical ITS1 sequences (mean K2P ¼ 0Á006) well within the range of intraspecific variation. The northern bluefin tuna appeared to be a sister group to albacore Thunnus alalunga, with all other Thunnus species in a distinct clade. The ITS1 phylogeny was consistent with mtDNA phylogeny in clustering the three tropical Thunnus species (T. albacares, T. atlanticus and T. tonggol). Southern bluefin Thunnus maccoyii and bigeye Thunnus obesus tunas showed a closer affinity to this tropical tuna group than to the northern bluefin tuna and albacore. The molecular data supported mitochondrial introgression between species and contradicted morphological subdivision of the genus into two subgenera Neothunnus and Thunnus.

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

“…Some authors have hypothesized mitochondrial introgression events between different Thunnus species as the main reason for discordances between mtDNA and nuclear DNA-based inferred relationships (Chow et al, 2006;Viñas and Tudela, 2009). This is supported by our analyses as the comparative study of the COI sequences revealed two T. thynnus individuals with introgressed mitochondrial DNA (Supplementary Figure 1) that had no phylogenetic relationships with T. alalunga or T. orientalis in the nuclear DNA-based phylogenetic trees.…”

“…This is supported by our analyses as the comparative study of the COI sequences revealed two T. thynnus individuals with introgressed mitochondrial DNA (Supplementary Figure 1) that had no phylogenetic relationships with T. alalunga or T. orientalis in the nuclear DNA-based phylogenetic trees. Attending to morphological features (Gibbs Jr and Collette, 1967) and allozyme and mitochondrial molecular markers (Collette et al, 2001), the Atlantic and Pacific bluefin tunas have been considered as two different subspecies; yet, this has been questioned after their ITS1 nuclear marker sequences were found nearly identical (Chow et al, 2006). In our study, most analyses support the respective monophylies of T. thynnus and T. orientalis, with only some trees based on the smallest matrices not providing support for either of the two monophylies (Table 1).…”

“…Most of molecular phylogenies aimed at solving the relationships among tuna species are based on mitochondrial markers (Alvarado Bremer et al, 1997;Chow and Kishino, 1995;Chow et al, 2006;Tseng et al, 2012;Viñas and Tudela, 2009) and/or do not include all the species of the genus Thunnus (Miya et al, 2013;Orrell et al, 2006;Santini et al, 2013). These studies consistently recover the Neothunnus subgenus and a close relationship between the albacore and the Pacific bluefin tuna.…”

“…These studies consistently recover the Neothunnus subgenus and a close relationship between the albacore and the Pacific bluefin tuna. Yet, evidence of mitochondrial introgression in T. orientalis with T. thynnus or T. alalunga (Chow and Inoue, 1993;Chow and Kishino, 1995;Chow et al, 2006), and in T. thynnus with T. alalunga or T. orientalis (Bremer et al, 2005;Chow et al, 2006;Pla et al, 2003;Takeyama et al, 2001;Viñas and Tudela, 2009) makes mitochondrial-based inferences of the relationships between these three species ambiguous. The only nuclear based phylogenetic studies that include all eight species of Thunnus (Chow et al, 2006;Viñas and Tudela, 2009) resolution is translated into a lack of suitable DNA-based tools for tuna species discrimination.…”

“…The few genetic markers in use for this purpose (e.g. Bartlett and Davidson, 1991;Chow et al, 2003;Pardo and Pérez-Villareal, 2004;Takeyama et al, 2001;Tseng et al, 2011;Viñas and Tudela, 2009) are mitochondrial, and the sole contrasted nuclear marker, the ribosomal internal transcribed spacer (ITS1), can only be used as a complement to mitochondrial markers when introgression is suspected (Viñas and Tudela, 2009), as it does not discriminate between all eight Thunnus species (Chow et al, 2006;Viñas and Tudela, 2009). Thus, overcoming the lack of congruence and/or resolution associated to the published Thunnus evolutionary relationships requires evolutionary inferences based on genome-wide phylogenetically informative positions of nuclear origin.…”