Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs

Abstract

Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes.

Molecular Taxonomy and Diversification of Atlantic Skates (Chondrichthyes, Rajiformes): Adding More Pieces to the Puzzle of Their Evolutionary History

“…Moreover, the morphologically-based reallocation of Dipturus linteus within the genus Rajella [ 104 ] was supported by both ML and BI phylogenies, although the genus Rajella remains poorly supported in the ML tree (BS < 0.50; Figure S4 ), but highly supported in the BI reconstruction (prob = 0.99; Figure S4 ). The phylogenetic position of Raja undulata as the basal taxon of Raja in the ML tree was consistent with the recent molecular phylogeny inferred by Kousteni et al [ 100 ].…”

“…Most phylogenetic relationships among skate taxa were strongly supported by both ML and BI analyses and are concordant with those obtained by previous studies based on mtDNA [10,34,36], combined mtDNA and nuclear DNA markers [28,35], and mitogenomes [99,100]. Phylogenetic trees clustered skate taxa into seven main lineages corresponding to the tribes Rajini (e.g., Raja and Dipturus), Amblyrajini (e.g., Amblyraja, Leucoraja and Rajella), Rostrorajini (e.g., Rostroraja), Crurirajini (e.g., Cruriraja), Arhynchobatini (e.g., Psammobatis), Bathyrajini (e.g., Bathyraja) and Riorajini (e.g., Rioraja and Atlantoraja).…”

Mitochondrial genome of ‘numbfish’ Narcine timlei (Bloch &amp; Schneider, 1801) and phylogenetic relationships among order Torpediniformes

“…The mitogenome was deposited in the NCBI GenBank under the accession number OM404361. The size of the assembled mitogenome was 17,964 bp, which is the expected size range for Batoids (Kousteni et al 2021). However, the size is slightly longer than previously published mitogenome of other Narcine spp.…”

First genetically confirmed records of the little gulper shark Centrophorus uyato (Squaliformes: Centrophoridae) from Cypriot waters

“…Following Compagno (1984) and White et al (2013) , the macroscopic characteristics of all specimens resembled those of C. uyato (Figs 2 , 3 ). Molecular methods were used as a complementary tool for species identification as commonly applied in elasmobranch research ( Ward et al 2005 , Kousteni et al 2016 , Kousteni et al 2021 ). For this purpose, individual fin clips were obtained from all 13 individuals, preserved in 95% ethanol and stored at -20°C.…”