875 research outputs found
Lo studio del tonno rosso a partire dalla collezione Sella
No full textIl tonno rosso Thunnus thynnus (Atlantic Bluefin tuna) è una specie che ha attirato l’interesse delle civiltà del Mediterraneo sin dalla loro nascita. Accanto ad un interesse di tipo economico si è da sempre posto un parallelo interesse scientifico e culturale. Oggi questa specie rappresenta per la comunità civile e scientifica una attualissima sfida-simbolo su cui tentare di riconciliare con successo pesca e conservazione. Da un lato i dati scientifici ottenuti dalla pesca indicano una situazione di forte rischio di sopravvivenza degli stock e declino delle popolazioni. Dall’altro la pesca del tonno rosso è rilevante e prioritaria per la socioeconomia dei paesi del Mediterraneo e dell’Atlantico centro settentrionale. Ai fini di ottenere una conoscenza scientifica sempre più approfondita della complessa ecologia di questo grande predatore e migratore, all’approccio investigativo di tipo monodisciplinare basato sulle analisi dei dati pesca si stanno affiancando ricerche interdisciplinari condotte con approcci indipendenti dai dati di pesca. Il preziosissimo lavoro di raccolta dati di pesca e campioni delle popolazioni di tonno rosso del Mediterraneo svolto dal Massimo Sella nei primi decenni del secolo scorso ha prodotto una collezione di circa 7000 reperti scheletrici (colonne vertebrali, pinne caudali e crani), la quale per consistenza e natura appare unica per la specie, per la datazione storica e per la consistenza. La buona qualità di conservazione dei reperti scheletrici e la loro consistenza numerica per differenti aree geografiche di pesca rappresenta un materiale di enorme potenzialità per lo studio dei cambiamenti che queste popolazioni hanno subito in rapporto ai cambiamenti ambientali, incluso la differente pressione antropica sugli stock da pesca. Un esempio di sfruttamento scientifico di questa potenzialità è venuta dall’utilizzo del DNA antico e dallo studio comparativo delle caratteristiche genetiche delle popolazioni storiche e contemporanee al fine di evidenziare segnali di erosione e strutturazione genetica svolta da ricercatori delle Università di Bologna, Ferrara e Padova con il supporto finanziario di due PRIN (2005: TUNING, TUNa’s changING; 2008: BFTbySNP). Tuttavia questa enorme potenzialità di fruibilità da parte dei ricercatori è fortemente limitata dall’assenza di una musealizzazione scientifica adeguata della collezione e dalla mancanza di risorse per realizzarla
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
Influenze ambientali sulla struttura genetica del tonno rosso nel Mediterraneo
No full textIl tonno rosso mostra una complessa demografia nel Mediterraneo a livello locale, nonostante possa compiere migrazioni transatlantiche. Dal punto di vista genetico il debole segnale di struttura individuato tramite
statistiche riassuntive (FST), sebbene significativo, non è stato confermato con metodi più sofisticati (Riccioni et al.
2010). Campioni di tonno rosso del Mediterraneo sono stati analizzati con una versione aggiornata del
programma di clustering Bayesiano STRUCTURE (Pritchard et al. 2000, Falush et al. 2003; Hubisz et al. 2009) che consente di utilizzare nell’analisi l’informazione sul sito di campionamento. Per confermare il segnale di struttura rilevato, sono stati implementati metodi di ordinamento vincolato (Constrained Correspondence Analysis, CCA) e test classico e parziale di Mantel che consentono di valutare anche l’ influenza che variabili spaziali e ambientali possono aver avuto sulla struttura genetica identificata. Queste indagini mostrano la presenza di un gradiente di differenziamento nord-sud nel Mediterraneo, inoltre le analisi multivariate suggeriscono che due fattori ambientali (temperatura e salinità), piuttosto che le variabili spaziali, possano essere coinvolti nella generazione del gradiente di diversità genetica identificato. Il nostro studio conferma il segnale di struttura del tonno rosso nel Mediterraneo e suggerisce un adattamento a variabili ambientali locali come fattore responsabile del differenziamento genetico. Riuscire a chiarire i meccanismi ecologici ed evolutivi di flusso genico e di adattamento ambientale è fondamentale per un’ efficace gestione degli stock marini
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
Metabarcoding analysis of European hake diet in the Mediterranean Sea.
No full textEuropean hake (EH), Merluccius merluccius, is a demersal fish distributed from the North Sea and Atlantic to the Levantine Sea in the Mediterranean. EH is an important predator of deep Mediterranean upper shelf slope communities and it is currently characterised by growth overexploitation. EH adults feed mainly on fish and squids whereas the young (<16 cm) feed on crustaceans. All current EH diet studies relied on the morphological identification of prey remains in stomach content, however this method is labour intensive and it precludes the identification of strongly digested food. The development of High-Throughput Sequencing (HTS) approaches provide more accurate methods for dietary studies revealing many consumed species simultaneously (DNA metabarcoding). The aim of this study is to use a HTS approach based on COI amplification, contextually to classic microscopic morphological identification, to analyse EH stomach content and to evaluate the efficiency of the molecular method. HTS sequencing has been carried out on the amplicons obtained by PCR amplification (Leray et al. 2013) of stomach remains and all the Miseq Illumina paired-end reads have been analysed by using bioinformatic tools (Boyer et al. 2015) for taxonomic assignment. The selected sequences clustered in OCTUs (Operational Clustered Taxonomic Units) and taxonomically assigned, will be used in diversity analyses to compute distance matrices among samples, to compare taxa summaries from different samples, to create networks and perform PCA and PcoA analysis. Classic microscopic morphological analyses on stomach content remains have been carried out contextually to compare the results of the two methods. The molecular approach has proven a promising method to study marine fish dietary habits. All the data will be summarized to reconstruct EH trophic dynamics in the Mediterranean Sea
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
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
First microsatellite loci of red mullet (Mullus barbatus) and their application to genetic structure analysis in transboundaries Adriatic shared stock
No full textIn order to study the genetic structure of the Adriatic shared stock of red mullet (Mullus barbatus), we developed a set of dinucleotide microsatellite markers. A dinucleotide-enriched genomic library was obtained, and 6 polymorphic dinucleotide loci were successfully optimized. The markers showed high expected heterozygosity (from 0.68 to 0.92) and allele number (from 12 to 33); thus they appear to be suitable for detecting genetic differences in the population of red mullet. Four Adriatic samples were subsequently analyzed for microsatellite variation, and the results showed subtle but statistically significant genetic differentiation, indicating that the Adriatic red mullet may group into local, genetically isolated populations. No correlation between geographic distance and genetic differentiation was observed. In addition, the evidence of recent bottlenecks in the Adriatic samples indicates that the observed population subdivision might reflect random local allelic variations, generated by reproductive success, survival rates, or fishing pressure
Tassonomia integrata morfologica e molecolare di leptocefali del mare Adriatico.
No full textLa campagna scientifica di pesca profonda svolta dalla m/n Andrea dell’Università di Bologna nel 2010 nell’Adriatico meridionale ha permesso di collezionare un elevato numero di leptocefali di Anguilliformi. Il “leptocefalo” è una peculiare forma larvale dei Teleostei del superordine Elopomorpha, la cui caratterizzazione bio-ecologica risulta ancora oggi incompleta (Miller 2009). In particolare, la mancanza di chiavi dicotomiche esaustive limita la conoscenza tassonomica specifica dei leptocefali del Mediterraneo.
Questo lavoro ha l’obiettivo di aggiornare la descrizione tassonomica di leptocefali pescati in Adriatico integrando la tradizionale analisi morfologica con quella genetica eseguita mediante DNA barcoding.
Il DNA barcoding è una metodica molecolare basata sull’analisi della variabilità di un marcatore di sequenza universale (COI) che consente di ottenere una identificazione tassonomica a livello specifico in modo univoco (Hebert 2003 a,b; Ward 2005)
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