Research Article: Mitocondrial COI and 16S rDNA sequences support morphological identification and biogeography of deep-sea red crabs of the genus Chaceon (Crustacea, Decapoda, Geryonidae) in the Eastern Central and South Atlantic Ocean

Date Published: February 11, 2019

Publisher: Public Library of Science

Author(s): Mariano Hernández, M. Virginia Martín, Pedro M. Herrador-Gómez, Sebastián Jiménez, Carlos Hernández-González, Santiago Barreiro, Roberto Sarralde, Barend Johannes van Zyl, Johny Charles Gamatham, Teresa Almeida, Luis J. López-Abellán, Tomoo Sawabe.

http://doi.org/10.1371/journal.pone.0211717

Abstract

The geographical spreading of new fishing activities and the increasingly deeper locations of these activities have shown the worldwide distribution of gerionid crabs and new descriptions of Chaceon taxa. However, incomplete penetrance, variable expressivity, and phenotypic overlap make the morphometric identification of these species difficult. In this study, partial sequences of the cytochrome c oxidase subunit 1 (COI) and 16S mitochondrial ribosomal RNA (16S rRNA) genes have been analyzed in Chaceon species from the Eastern Central and South Atlantic and compared with sequences of species from Western Atlantic. Our results corroborate the proposed morphological species and highlight the significant separation of the Eastern Atlantic species and those from Atlantic coasts of South America for both markers (97% Bayesian posterior probability, BPP / 83% Bootstrap replicates, BT). Interestingly, Chaceon sanctaehelenae shows a closer relationship with the species of the American coast than with those from the Eastern Atlantic. On the other hand, while COI marker clearly separates Chaceon atopus and Chaceon erytheiae species (99 BPP / 91% BT), these species share haplotypes for the 16S rRNA marker, pointing to a recent speciation process. Moreover, a close relationship was observed between Chaceon maritae and Chaceon affinis (94% BPP / 77% BT). The topologies of the trees obtained indicate that the ancestor of this genus was closer related to those species from South America than to those from the Eastern Atlantic.

Partial Text

Morphological identification of species belonging to the Geryonidae family has been a difficult task in the past for people studying deep-sea resources and marine biodiversity. Interspecific similarities and intraspecific morphological variability have contributed to former and potential current misclassification [1]. Thus, other considerations such as the geographical site of collections have also been an element used in the species identification, regarding previous species citations in the same geographic zone [1, 2, 3].

Forty-three samples of muscle tissue from individuals of deep-sea red crabs (Chaceon spp.) were collected from different places in the Eastern Central and South Atlantic (Fig 1). Species names assigned on morphological basis [1, 3, 10] and sampling areas are reported in Table 1. The presence and potential geographic distribution of species of Chaceon genus in the Central East and South Atlantic is shown in Fig 1. Five species of Chaceon were morphologically identified. C. erytheiae from Valdivia Bank was identified following Macpherson [10]. C. atopus [1] and C. sanctaehelenae [1] specimens collected in the Vavilov Ridge (Gulf of Guinea) were identified using Manning and Holthuis [1] description. Finally C. affinis [11] from the Canary Islands and Fantasma Bank (north Canary Islands) and C. maritae [2] from Western Sahara waters were identified through Manning and Holthuis [2]. Also, nine samples of unidentified specimens from Namibian Exclusive Economic Zone (EEZ) and the Walvis Ridge (Valdivia Bank) were incorporated to the analysis (Table 1; Figs 1 and 2). Table 1 also includes the serial code; the ID Code used on labelling the samples; name of research cruises or fishing trips in which samples were obtained; collectors; places of harvesting and depths; and measurements of individuals and sex. All collected specimens belonged to commercial exploited species so there is no prohibition for their fishing. The fishing vessels and fishing research vessels where they were captured have the legal permits to carry out their fishing and research activities. This study did not involve endangered or protected species.

From all 43 samples of deep-sea red crabs (Chaceon spp.), a fragment of 468 base pairs (bp) of mtDNA COI gene was amplified and sequenced from 38 samples. The absence of stop codons seems to discard the presence of nuclear mitochondrial insertions (Numts) in the sequences. Among the 468 nucleotide sites, 142 sites were variable and 87 were phylogenetically informative. From 42 samples, the amplification of the corresponding fragment of 16S rRNA resulted in a single band of 429–430 bp. The alignment of the sequences generated a 432 bp matrix because of the need to include “gaps” (variants insertion / deletion, “indels”) for optimal alignment. Of the 432 sites, 104 showed variation and of these, 47 were informative. Indels were discarded in subsequent analyses. The absence of double bands in PCR and double peaks in the electropherogram of the sequences as well as the similarity among them and with those originals deposited in Genbank seems to discard the presence of nuclear mitochondrial DNA sequences (Numts) in these sequences too.

Mitochondrial DNA (mtDNA) is the marker commonly used for genetic reconstruction of the history of populations, population demography, biogeography and speciation, and recommended for taxonomic studies [25]. Despite the fact that mtDNA is not exempt from some disadvantages as the presence of Numts or pseudogenes [26], the presence of nuclear sequences is highly unlikely in our data.

 

Source:

http://doi.org/10.1371/journal.pone.0211717

 

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