Mitogenome sequence comparison in the endangered congeneric Pinna nobilis and Pinna rudis bivalves

Identifying surviving Pinna nobilis after the Mass Mortality Event (MME) in the Mediterranean: Proposal of a low-risk methodology for collecting genetic samples

The critically endangered species, Pinna nobilis, has nearly disappeared from the Mediterranean Sea, primarily due to infection by the protozoan parasite Haplosporidium pinnae. However, some individuals survive in specific areas with favorable environmental conditions, such as water salinity and temperature. On the Spanish coast, the only two surviving populations are confined to the Ebro Delta and the Mar Menor coastal lagoon. Some resistant P. nobilis specimens have been found in the areas affected by mass mortality. It is sometimes difficult to distinguish between P. nobilis and P. rudis specimens by external morphological characteristics. Only genetic analysis allows unambiguous discrimination between the two species and even the detection of hybrid specimens. Biopsies, as a traditional sampling method for obtaining samples for genetic analysis, have proven to be an aggressive technique that causes high mortality rates among biopsied specimens, both in surviving specimens in natural environments and in stabled specimens kept in captivity ex situ. Therefore, it is important to look for sampling techniques that do not pose a risk to the health status of the specimens. This study focuses on the development of a novel methodology for obtaining samples for genetic studies. A survey of Pinna spp. individuals in open waters along the Mediterranean coast of spanish levantine area (western Mediterranean) was conducted. To identify the species of the individuals found and distinguish them from the closely related P. rudis, a new, less invasive methodology for genetic sampling was used. By collecting environmental DNA (eDNA) from the water inside the valves of 13 Pinna spp. individuals, a potential surviving specimen of Pinna nobilis was identified in the coast of Murcia (SE Spain).

Genetic analysis of Pinna rudis L 1758 (Mollusca, Bivalvia, Pinnidae) in the Northwest Cabo Verde Islands (Central-East Atlantic)

The rough pen shell Pinna rudis Linnaeus, 1758 (family Pinnidae) is a mollusc with an Atlantic-Mediterranean distribution, typically inhabiting coarse sandy substrates. Habitat degradation is considered the primary cause of population decline, leading to the designation 'Vulnerable' in certain regions. In this study, we conducted a genetic analysis of populations of P. rudis from Cabo Verde and compared them with populations from the Mediterranean and Macaronesia. We based our analysis on two mitochondrial DNA markers, cytochrome oxidase I (COI) and 16S rRNA, and one nuclear marker, 28S rRNA. The results showed a strong genetic structuring among Macaronesia populations, with each island tending to have unique or exclusive haplotypes, though some sharing occurred between islands. We found significant genetic divergence between the population from Cabo Verde and the other sampled population, suggesting that P. rudis is not monotypic, but may include several cryptic species. Bayesian and maximum-likelihood phylogenetic analysis, including all Pinnidae species, indicated that P. rudis from Gorée Island (Senegal) and Baía das Gatas (São Vicente Island) might be undergoing speciation. The high genetic structure found for P. rudis could be influenced by hydrodynamic barriers, local currents and hydrographic isolation, in association with the short larval duration (planktotrophic) reported for this species. Altogether, our findings highlight significant genetic divergence in P. rudis populations, possibly supporting speciation events in the Cabo Verde archipelago among widely distributed taxonomic groups.

The characterization of toll-like receptor repertoire in Pinna nobilis after mass mortality events suggests adaptive introgression

The fan mussel Pinna nobilis is currently on the brink of extinction due to a multifactorial disease mainly caused to the highly pathogenic parasite Haplosporidium pinnae, meaning that the selection pressure outweighs the adaptive potential of the species. Hopefully, rare individuals have been observed somehow resistant to the parasite, stretching the need to identify the traits underlying this better fitness. Among the candidate to explore at first intention are fast-evolving immune genes, of which toll-like receptor (TLR). In this study, we examined the genetic diversity at 14 TLR loci across P. nobilis, Pinna rudis and P. nobilis × P. rudis hybrid genomes, collected at four physically distant regions, that were found to be either resistant or sensitive to the parasite H. pinnae. We report a high genetic diversity, mainly observed at cell surface TLRs compared with that of endosomal TLRs. However, the endosomal TLR-7 exhibited unexpected level of diversity and haplotype phylogeny. The lack of population structure, associated with a high genetic diversity and elevated dN/dS ratio, was interpreted as balancing selection, though both directional and purifying selection were detected. Interestingly, roughly 40% of the P. nobilis identified as resistant to H. pinnae were introgressed with P. rudis TLR. Specifically, they all carried a TLR-7 of P. rudis origin, whereas sensitive P. nobilis were not introgressed, at least at TLR loci. Small contributions of TLR-6 and TLR-4 single-nucleotide polymorphisms to the clustering of resistant and susceptible individuals could be detected, but their specific role in resistance remains highly speculative. This study provides new information on the diversity of TLR genes within the P. nobilis species after MME and additional insights into adaptation to H. pinnae that should contribute to the conservation of this Mediterranean endemic species.

The Nursehound Scyliorhinus stellaris Mitochondrial Genome—Phylogeny, Relationships among Scyliorhinidae and Variability in Waters of the Balearic Islands

The complete mitochondrial DNA sequence of the Nursehound Scyliorhinus stellaris has been determined for the first time and compared with congeneric species. The mitogenome sequence was 16,684 bp in length. The mitogenome is composed of 13 PCGs, 2 rRNAs, 22 transfer RNA genes and non-coding regions. The gene order of the newly sequenced mitogenome is analogous to the organization described in other vertebrate genomes. The typical conservative blocks in the control region were indicated. The phylogenetic analysis revealed a monophyletic origin of the Scyliorhininae subfamily, and within it, two subclades were identified. A significant divergence of Scyliorhinus spp. together with Poroderna patherinum in relation to the group of Cephaloscyllium spp. was observed, except for Scyliorhinus torazame, more related to this last cited clade. A hypothesis of a divergent evolution consequent to a selective pressure in different geographic areas, which lead to a global latitudinal diversity gradient, has been suggested to explain this phylogenetic reconstruction. However, convergent evolution on mitochondrial genes could also involve different species in some areas of the world.

An incubation water eDNA method for a non-destructive rapid molecular identification of Pinna nobilis and Pinna rudis bivalve juveniles

The pen shell Pinna nobilis is critically endangered due to a disease that has affected all open water populations since late 2016. Collection of early spats is considered a fundamental step for pen shell conservation. However, the identification between P. nobilis and P. rudis juveniles by morphology is a very difficult task. Furthermore, due to the small size of juveniles and high sensitivity to handling, the sampling for this purpose must not damage individuals. As a consequence, the application of molecular techniques for conservation strategies to identify threatened and endangered bivalve species is every day more and more necessary.

In this study, we present the development of a multiplex-PCR procedure for the rapid identification of two Pinna species from eDNA water samples. Using species-specific primers, designed in the rRNA16S and rRNA12S mitochondrial genes, identification of species was obtained by cellular or extracellular DNA dissolved in water and differentiated based on the size of the amplified DNA fragments.

• Development of a molecular multiplex-PCR procedure for the rapid identification of two Pinna species from eDNA water samples

• Using specie-specific primers, the different species can be differentiated basing on the size of the amplified DNA fragments

• This technique removes many of the limitations commonly associated with sampling of threatened and endangered juvenile bivalves for conservation strategies (sampling does not damage individuals).