226 research outputs found
Genomic analysis of population structure of yellowfin tuna (Thunnus albacares) at the global scale
No full textA mosaic of cryptic species among the family Rajidae: moving from phylogenetics to phylo-transcriptomics
No full textNowadays, the cliché depicting speciation as synonym of change seems to be outdated, since more and more marine species reveal, besides analogous ecological traits, also similar morphological patterns. This condition appears to be particularly widespread among elasmobranchs (Quattro et al., 2006; Griffiths et al., 2010), especially within the monophyletic Raja cluster. The peculiar feature that make this group so interesting is the presence of a remarkable number of cryptic and few non-cryptic species. The evolutionary maintenance of a stable architecture between recently diverged clusters could be ascribed to a paleo-hydrogeographical isolation (Valsecchi et al., 2005; Pasolini et al., 2011; Messinetti, 2013) coupled with the preferential use of the electric sense for communication and camouflage as anti-predatory mechanism. For instance, the siblings Raja polystigma and R. montagui have been taxonomically misidentified for a long time (Frodella et al., submitted). The most striking case is the R. miraletus complex, where a significant variation in mtDNA led to recognize at least three parapatric clades in the Mediterranean, Eastern Atlantic and South African waters (McEachran et al., 1989; Ferrari et al., in preparation). DNA barcoding was a trigger for the identification of cryptic species but, currently, shading light on Rajids’ evolution and understanding the morphological cladogenesis have become a challenge. A first attempt of transcriptome profiling of different skin tissues of these non-model organisms will be carried out in order to investigate which loci are linked to skates patterning and establish how they diverge between cryptic and non-cryptic species. To date, a sampling protocol for downstream RNA analyses was established and applied on nine species collected in the Mediterranean Sea, Eastern Atlantic and South African waters. After RNA libraries construction and sequencing, data analysis will target the identification of a pool of loci likely related to coloration differing between cryptic and non-cryptic taxa
Stock boundaries of Mullus barbatus (Mullidae) and Parapenaeus longirostris (Penaeidae) populations in the Italian seas: development of genomic 2b-RAD markers
No full textOver-fishing is one of the most complex and argued issue among the human impacts affecting the marine environment. The development of integrated policies for fish stock conservation and its responsible use are essential. Nowadays, genomics is considered an ultimate tool to define stock boundaries and population structure as it expands the focus on the entire organism’s genetic makeup and its interaction with the environment. An example of effort and capitalization on genomics is shown by the Italian RITMARE Flagship Project, which aims to create a genomic mapping for stocks of two commercially important species, the red mullet (Mullus barbatus L.) and the deep-water rose shrimp (Parapenaeus longirostris Lucas, 1847), through the use of 2b-RAD technology, based on sequencing the uniform fragments produced by type IIB restriction endonucleases. A sampling design covering 8 Geographical Sub-Areas was defined on the basis of nursery areas, abundance and importance in local fishery and it was completed during the MEDITS 2013 survey. After the extraction of high quality genomic DNA from 7 individuals for each species, the 2b-RAD protocol was tested for the first time. Thereafter, a high-throughput sequencing of libraries was accomplished through Illumina® platform and the software STACKS was used to analyze the sequences. Several millions of high quality reads per individual were obtained and approximately from 1.0 to 2.0x10e3 candidate SNP markers were identified. These preliminary results confirm the successful application of 2b-RAD technology on both non model species and, above all, its effective extendibility to larger number of individuals and population samples, necessary to assess stock boundaries and stock units in the Italian Seas
Another piece of the evolutionary history of Atlantic skates (Chondrichthyes, Rajiformes ): integrating DNA barcoding approach and phylogenetic inferences
No full textConservation and long-term management plans of marine species need to be conceived upon a universally recognised key-feature: species identity. This important assignment resulted particularly arduous among skates (order Rajiformes), in which the phenotypic similarity between some taxa and the individual variability in others, entangled accurate species identification.
This study confirms the power of DNA barcoding for the discrimination between skate species across the Atlantic Ocean and for its use as effective tool to minimize the risk of species misidentification and to elucidate species boundaries. In this perspective, this work compiles and establish a new fully available and well-curated barcode library, the ELASMO-ATL project, which gathered biological and molecular information of 432 skate specimens and covered coastal waters of four FAO Major Fishing Areas (27, 34, 47, 41) of the Atlantic Ocean.
The evolutionary histories of 34 skate species were estimated with two concatenated mitochondrial markers (COI and NADH2) through Bayesian and species level phylogeny analyses. It was possible to discover a new evolutionary lineage within the genus Raja in the southern-most part of its distribution area and to enable deepening the relationship between South-African endemic species of Rajella. Once again, Western South African coasts and oceanographic fronts may play a fundamental role among skates’ speciation events in which the paleoclimatic and paleogeographic history joined to hydrography events could have contributed to the formation of refugial areas, characterised by geographical isolation. Subsequent contact zones in these areas between Senegal and Angola seems to constitute a continuum/cline of genetic change among some Raja species.
These data successfully resolved many taxonomic ambiguities and demonstrated a highly cohesive monophyletic clustering among the order laying the foundations for further inference of evolutionary patterns suitable for addressing management and conservation issue
EDNA-ENABLED MONITORING OFFERS BOTH OPPORTUNITIES AND CHALLENGES FOR THE CONSERVATION OF MEDITERRANEAN ELASMOBRANCHS
No full textMonitoring marine biodiversity is essential for ecosystems conservation and fisheries management. Traditional methods based on visual surveys and capture techniques are invasive, costly, and labour-intensive. Advances in molecular detection from water samples allow for identifying organisms that inhabit, pass through, or interact with the surrounding environment. The environmental DNA (eDNA) currently emerged as an important source of biodiversity information across different ecosystems. Here, we present four case-studies applying different eDNA sampling and screening methods to assess their effectiveness in monitoring Mediterranean elasmobranchs: 1) we tested five eDNA sampling systems, both active and passive, in a controlled mesocosm. Active samplers recovered more DNA and detected all elasmobranchs, whereas passive tools showed lower efficiency; 2) we tested passive tools associated to deep-sea longlines, detecting 78% of captured species and revealing additional biodiversity, including pelagic and mesopelagic taxa not identified by traditional methods; 3) active filtration was applied on 75 samples from 25 sites in the Central Mediterranean, collected at three depths with Niskin bottles, allowing a fine-scale assessment of depth-driven species distribution; 4) over 500 samples were collected along the Italian coasts throughout 2024 using both active and passive tools, expanding spatial coverage and providing comprehensive data on elasmobranch biodiversity shifts.
All samples were analysed using eDNA metabarcoding techniques with an elasmobranch-specific marker (elas02-12S), and taxonomic assignments was performed against an improved custom 12S vertebrate reference database. Our findings confirm that eDNA can detect a broader spectrum of marine biodiversity, including elusive taxa not recovered by conventional methods. While eDNA offers insights into marine biodiversity, challenges remain in standardizing methodologies and interpreting abundance data, particularly for passive samplers in fisheries applications. Addressing these gaps will enhance eDNA’s role as cost effective marine monitoring tool in both conservation and management scenarios
The cradle of diversity: Central Atlantic Ocean hides a mosaic of skate species (Rajiformes)
No full textSkates (Rajiformes) represent one of the most intriguing cases of high species richness coupled with extremely conservative morphological and ecological traits. Small differences are described within and between species and increasing cases of cryptic speciation have been recorded among sister and non-sister taxa. More interestingly, this condition has been frequently observed in Central Atlantic Ocean (CAO), along the coasts of Western Africa, between Angola and Senegal, where oceanographic heterogeneities such as current systems, may play a key role for ecological speciation in skates. The use of multiple mtDNA loci and its integration with nuDNA microsatellite has been successfully applied to estimate the genetic variation in skate species inhabiting the CAO. Phylogenetic reconstructions, phylogeographic patterns and genetic connectivity estimates were applied to test the hypothesis that restricted gene flow and genetic divergence within Raja species reflect known climate and bio-oceanographic discontinuities. The widely distributed Raja miraletus species complex counts five deeply distinct lineages three of which co-occur in CAO: the Angolan Raja cf. miraletus, the Senegalese and sympatric R. parva and Raja cf. miraletus. In addition, an ancient, hidden lineage nesting in the clade Raja straeleni/R. clavata/R. maderensis was identified in Angola. The complexity of oceanographic system acting in the CAO (i.e., the Benguela Current region and the intertropical Canary current inflowing from the northeast) may have influenced the diversification of the Angolan and Senegalese taxa, boosting the biodiversity of the area, in an unprecedented anthology of species-specific evolutionary histories
Genetics of local adaptation of Atlantic Bluefin Tuna from the Mediterranean Sea.
No full textThe Atlantic Bluefin tuna (ABFT, Thunnus thynnus), one of the largest top-predator fish inhabiting the pelagic ecosystems of the North Atlantic Ocean and Mediterranean Sea, has been extensively overexploited in recent decades. However, in the Mediterranean Sea, the mixing rates between the eastern, central and western basins have not yet been resolved. Both electronic tagging, otolith and genetic markers cannot still depict a clear scenario of tuna movements and structuring, essential requirement for a proper management of ABFT fisheries. Here we used Expressed Sequence Tag-linked (EST-linked) microsatellites to explore the patterns of adaptive evolution of T. thynnus population and of its population dynamics in the Mediterranean Sea. For this purpose 16 EST-linked microsatellites were genotyped in 177 tuna individuals from the Mediterranean and several methods were used to explore population genetic structuring and estimate/detect signals of local adaptation. Bayesian clustering results indicated the presence of a single cluster, corroborated also by the Correspondence Analysis and pairwise FSTs. Similarly the two methods, used for the detection of FST outliers, did not reveal any pattern suggesting the presence of selective pressure. Our results advise that the low level of polymorphism detected in EST-SSR loci used in this study could be ascribed to the presence of relatively conserved regions flanking these microsatellites. These genomic regions are probably not involved in physiological responses to local adaptation and we were able to rule out action of divergent or balancing selection on EST-SSR polymorphism
First assessment of the genetic structure of deepwater blackmouth catshark (G. melastomus Rafinesque, 1810) in Atlantic and Mediterranean populations
No full textThe worldwide abundance of Galeus melastomus in the biological composition of fishery bycatch led to consider this species as a key-taxon for understanding the mysterious biology and ecology of sharks living in deep ecosystems. With the present work, we aim to unravel the population structure of the blackmouth catshark in the Mediterranean Sea and adjacent North-Eastern Atlantic with the use of nuclear molecular markers (simple sequence repeats, SSRs) and compare our results with recent findings based on mitochondrial DNA supporting total panmixia in the species. Given the absence of species-specific microsatellite markers we attempted the cross-amplification of a panel of 129 SSRs developed for Centroselachus crepidater, Galeorhinus galeus, Hexanchus griseus, Mustelus antarcticus, M. canis, M. henlei, M. mustelus, Negaprion brevirostris, Scyliorhinus canicula, Squalus acanthias and S. mitsukurii on blackmouth catsharks collected during scientific surveys undertaken in different years. The rationale of the chosen methodology was based on the calculation of genetic distances between NADH2 sequences (1044bp long) derived from 595 species of elasmobranchs. Our strategy focused on testing first SSRs markers developed on closely-related species. Then, we assessed highly polymorphic markers developed on non-closely-related species. After a pilot gradient amplification on few individuals from three different geographic macro-areas, we screened a total of 24 samples at the established conditions. To date, 16 microsatellite loci have been classified as potential candidates for the succesful cross-amplification on Atlantic and Mediterranean samples of G. melastomus. These candidate loci will be applied in the population genetic analysis delineated in the Atlantic Ocean (two sites) and in the Mediterranean Sea (five sites). Hopefully, the higher resolution power of the markers chosen for this study will be able to disclose any signal of genetic structure of the blackmouth catsharks and will contribute to improve the knowledge on deep-sharks
Evolutionary constraints limiting the variation of Expressed Sequence Tag-linked microsatellite loci, prevent the detection of local adaptation in Mediterranean Bluefin tuna
No full textThe Atlantic Bluefin tuna (BFT, Thunnus thynnus), one of the largest top-predator fish inhabiting the pelagic ecosystems of the North Atlantic Ocean and Mediterranean Sea, has been extensively overex- ploited in recent decades. However, in the Mediterranean Sea, the mixing rates between the eastern, central and western basins have not yet been fully and finally resolved. To date electronic tagging, otolith and genetic markers cannot still disentangle the pattern of tuna movements and population structuring in the basin, essential background for a proper management of BFT fisheries. Here, we used Expressed Sequence Tag-linked (EST-linked) microsatellites to explore population dynamics and adaptive evolution of Mediterranean T. thynnus. For this purpose, 16 EST-linked microsatellites were genotyped in 177 tuna individuals from the Mediterranean Sea and several methods were used to explore population genetic structuring and estimate/detect signals of local adaptation. Bayesian clustering results indicated the pres- ence of a single cluster, corroborated also by the Correspondence Analysis and pairwise FSTs. Similarly, the two methods used for the detection of outlier loci (LOSITAN and BayeScan), did not reveal any pattern suggesting the presence of selective pressure on the EST Simple Sequence Repeat (SSR) used. Our results suggest that the low level of polymorphism detected in this study could be ascribed to the presence of relatively conserved regions flanking these microsatellites. These genomic regions are probably not involved in physiological responses to local adaptation
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