Barcoding deep-water chondrichthyans from mainland Portugal

Abstract

Most deep-water chondrichthyans occurring off mainland Portugal are distributed worldwide. There are many closely related species with similar morphology, and the lack of diagnostic characters that unambiguously allow species discrimination has led to extensive identification problems. Here, DNA barcodes were used to evaluate the suitability of cytochrome c oxidase I (COI) to identify deep-water chondrichthyans and to further contribute to the worldwide molecular databases currently in use. The sample was composed of 40 individuals from the families Chimaeridae, Centrophoridae, Somniosidae, Etmopteridae, Oxynotidae, Dalatiidae, Scyliorhinidae, Mitsukurinidae, Chlamydoselachidae and Hexanchidae. COI proved to be adequate for species identification, with almost all putative species recovered as well supported monophyletic clades, with low intraspecific variation. Sequence matches against the BOLD database provided evidence for the existence of identification problems particularly within the genera Hydrolagus, Galeus and Centrophorus. Present results suggest that three different Centrophorus species occur off the Portuguese mainland, C. squamosus, C. granulosus and C. uyato. The sample also included an albino Deania calcea and a C. squamosus specimen without dermal denticles. This study updates the current knowledge on diversity and distribution of deep-water chondrichthyans occurring along the Portuguese coast, and provides an essential tool for species identification and consistency of taxonomic designations worldwide.

Initiating DNA barcoding of Eastern Mediterranean deep-sea biota

“…This high incongruence for COI sequences, that are below the accepted threshold for defining natural variation within a species (set up at 2-3%; Hebert et al, 2003a), further indicates the urgent needs for taxonomic validations of COI sequences, for quality checks of the chromatograms, for possible mitochondrial introgression between closely related species, the appearance of cryptic species and for possible contaminations. The above conclusion is further supported by studies on fish from the eastern Mediterranean Sea (Karahan et al, 2017), on fish from the central Mediterranean basin (Landi et al, 2014), on deep water sharks off Portugal (Moura et al, 2015), macroinvertebrates (Shackleton & Rees, 2016) and various other groups (e.g., Shen et al, 2013;Sonet et al, 2013).…”

New records and range extension of the Portuguese dogfish Centroscymnus coelolepis in the south‐western Atlantic Ocean, with comments on its morphology

“…Based on molecular data, size and shape of the first dorsal fin, as well as denticle morphology, the small juvenile female here reported can be undoubtedly identified as C. coelolepis . The COI sequence is considered a reliable barcode marker in fish (Ward et al ., ) and has been successfully used in the past for the identification of deep‐water chondrichthyans ( e.g ., Moura et al ., ; Bineesh et al ., ; Daly‐Engel et al ., ), including both Centroscymnus species (Moura et al ., ).…”

“…has been successfully used in the past for the identification of deepwater chondrichthyans (e.g., Moura et al, 2015;Bineesh et al, 2016;Daly-Engel et al, 2019), including both Centroscymnus species .…”

Assessing ecological and molecular divergence between the closely related species Hydrolagus pallidus and H. affinis (Chimaeridae)

“…In accord with our findings, Moura et al . () found coI divergence between H. lusitanicus and H. affinis of c . 1·16%.…”