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Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus

Publication . Cunha, Regina L.; Nicastro, Katy; Zardi, Gerardo I.; Madeira, Celine; McQuaid, Christopher D.; J. Cox, Cymon; Castilho, Rita

Background: The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods: To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the "primer-walking" method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. Results: The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.

2022-09Journal article

Open access

Hidden diversity of the olive ridley sea turtle (Lepidochelys olivacea) from Angola, West Africa

Publication . Cunha, Regina L.; Costa, Adjany; Godinho, Filipa; Santos, Carmen; Castilho, Rita

The olive ridley sea turtle (Lepidochelys olivacea) occupies a wide range within the tropical and subtropical areas of the Pacific, Indian, and Southern Atlantic Oceans. Although occurring in large numbers, the IUCN status for this species is "vulnerable" due to existing threats in their nesting sites. We report the first genetic data on L. olivacea from Palmeirinhas-Onca beach, Angola, West Africa. Genetic diversity based on a 400 bp-fragment of the mitochondrial control region of 39 individuals indicated low nucleotide and haplotype diversities compared to other Atlantic populations. We detected a new haplotype present in two individuals from Angola, while the remaining specimens shared a haplotype that is distributed in both sides of the Atlantic and in the Mediterranean, suggesting connectivity between these populations. The baseline data we are generating have a broader significance for characterizing intraspecific biodiversity in the olive ridley sea turtle, which is vital for developing effective conservation policies.

2022-01Journal article

Restricted access

Three mitochondrial lineages and no Atlantic-Mediterranean barrier for the bogue Boops boops across its widespread distribution

Publication . Cunha, Regina L.; Faleh, Abderraouf Ben; Francisco, Sara; Šanda, Radek; Vukić, Jasna; Corona, Luana; Dia, Mamadou; Glavičić, Igor; Kassar, Abderrahmane; Castilho, Rita; Robalo, Joana I.

Marine species exhibiting wide distributional ranges are frequently subdivided into discrete genetic units over limited spatial scales. This is often due to specific life-history traits or oceanographic barriers that prevent gene flow. Fine-scale sampling studies revealed distinct phylogeographic patterns in the northeastern Atlantic and the Mediterranean, ranging from panmixia to noticeable population genetic structure. Here, we used mitochondrial sequence data to analyse connectivity in the bogue Boops boops throughout most of its widespread distribution. Our results identified the existence of three clades, one comprising specimens from the Azores and eastern Atlantic/Mediterranean, another with individuals from the Canary Islands, Madeira and Cape Verde archipelagos, and the third with samples from Mauritania only. One of the branches of the northern subtropical gyre (Azores Current) that drifts towards the Gulf of Cadiz promotes a closer connection between the Azores, southern Portugal and the Mediterranean B. boops populations. The Almeria-Oran Front, widely recognised as an oceanographic barrier for many organisms to cross the Atlantic-Mediterranean divide, does not seem to affect the dispersal of this benthopelagic species. The southward movement of the Cape Verde Frontal Zone during the winter, combined with the relatively short duration of the pelagic larval stage of B. boops, may be potential factors for preventing the connectivity between the Atlantic oceanic archipelagos and Mauritania shaping the genetic signature of this species.

2022-12Journal article

Open access