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Conservation and management of chondrichthyans are becoming increasingly important, as many species are particularly vulnerable to fishing activities, primarily as bycatch, which leads to incomplete catch reporting, potentially hiding the impact on these organisms. Here, we aimed at implementing an eDNA metabarcoding approach to reconstruct shark and ray bycatch composition from 24 hauls of a bottom trawl fishing vessel in the central Mediterranean. eDNA samples were collected through the passive filtration of seawater by simple gauze rolls encapsulated in a probe (the “metaprobe”), which already showed great efficiency in detecting marine species from trace DNA in the environment. To improve molecular taxonomic detection, we enhanced the 12S target marker reference library by generating sequences for 14 Mediterranean chondrichthyans previously unrepresented in public repositories. DNA metabarcoding data correctly identifies almost all bycaught species and detected five additional species not present in the net, highlighting the potential of this method to detect rare species. Chondrichthyan diversity showed significant association with some key environmental variables (depth and distance from the coast) and the fishing effort, which are known to influence demersal communities. As DNA metabarcoding progressively positions itself as a staple tool for biodiversity monitoring, we expect that its melding with opportunistic, fishery-dependent surveys could reveal additional distribution features of threatened and elusive megafauna.

The extraordinary polymorphism of major histocompatibility complex (MHC) genes is considered a paradigm of pathogen‐mediated balancing selection, although empirical evidence is still scarce. Furthermore, the relative contribution of balancing selection to shape MHC population structure and diversity, compared to that of neutral forces, as well as its interaction with other evolutionary processes such as hybridization, remains largely unclear. To investigate these issues, we analyzed adaptive (MHC‐DAB gene) and neutral (11 microsatellite loci) variation in 156 brown trout (Salmo trutta complex) from six wild populations in central Italy exposed to introgression from domestic hatchery lineages (assessed with the LDH gene). MHC diversity and structuring correlated with those at microsatellites, indicating the substantial role of neutral forces. However, individuals carrying locally rare MHC alleles/supertypes were in better body condition (a proxy of individual fitness/parasite load) regardless of the zygosity status and degree of sequence dissimilarity of MHC, hence supporting balancing selection under rare allele advantage, but not heterozygote advantage or divergent allele advantage. The association between specific MHC supertypes and body condition confirmed in part this finding. Across populations, MHC allelic richness increased with increasing admixture between native and domestic lineages, indicating introgression as a source of MHC variation. Furthermore, introgression across populations appeared more pronounced for MHC than microsatellites, possibly because initially rare MHC variants are expected to introgress more readily under rare allele advantage. Providing evidence for the complex interplay among neutral evolutionary forces, balancing selection, and human‐mediated introgression in shaping the pattern of MHC (functional) variation, our findings contribute to a deeper understanding of the evolution of MHC genes in wild populations exposed to anthropogenic disturbance., We investigate evolutionary mechanisms shaping genetic structure and diversity at the major histocompatibility complex class II gene (MHC‐DAB) in wild populations of Mediterranean brown trout (Salmo trutta L. complex) exposed to introgression from domestic (hatchery) lineages. We reveal the role of historical positive selection and current balancing selection (rare‐allele advantage, but not heterozygote advantage or divergent allele advantage) to mantaining high MHC (functional) polymorhism. Also, we provide evidence for the interplay between genetic drift and human‐mediated introgression to shape MHC diversity and population structure.

Amphibians are experiencing an ascertained global decline, which causes include the introduction of alien species and the (anthropogenic) hybridization between native and exotic taxa. Detecting introductions and assessing their impact on populations of native species is crucial for amphibian conservation. We used mitochondrial and nuclear markers to reveal introgressive hybridization between the native Bombina pachypus and the exotic B. variegata (probably introduced from Albania) in a population from a protected area of central Italy. Almost all genotyped individuals were genetically admixed, showing a larger proportion of the allochthonous genome. To our knowledge, this study provides the first evidence of successful hybridization between the two species (we found both putative F1 and backcrosses), hence representing a new threat to the conservation of the endangered, Italian-endemic B. pachypus.

The global need to monitor the status of marine resources is a priority task in marine management, but most ocean surveys still rely on costly and time-consuming capture-based techniques. Here we test a novel, easy-to use device to collect eDNA on board of bottom trawl fishing vessels, during normal fishing operations, quickly and easily: custom-made rolls of gauze tied to a hollow perforated spherical probe (the ‘metaprobe’) that placed inside the fishing net aims to gather traces of genetic material from the surrounding environment. We collected six samples from three central Tyrrhenian sites. Using an established fish-specific metabarcoding marker, we recovered over 70% of the caught species and accurately reconstructed fish assemblages typical of the different bathymetric layers considered. eDNA metabarcoding data also returned a biodiversity ‘bonus’ of mostly mesopelagic species, not catchable by bottom trawls. Further investigation is needed to upscale this promising approach as a powerful tool to monitor catch composition, assess the distribution of stocks, and generally record changes in fish communities across the oceans.

Polymorphism of the major histocompatibility complex (MHC), DAB1 gene was characterized for the first time in the European bitterling (Rhodeus amarus), a freshwater fish employed in studies of host-parasite coevolution and mate choice, taking advantage of newly designed primers coupled with high-throughput amplicon sequencing. Across 221 genotyped individuals, we detected 1–4 variants per fish, with 28% individuals possessing 3–4 variants. We identified 36 DAB1 variants, and they showed high sequence diversity mostly located within predicted antigen-binding sites, and both global and codon-specific excess of non-synonymous mutations. Despite deep divergence between two major allelic lineages, functional diversity was surprisingly low (3 supertypes). Overall, these findings suggest the role of positive and balancing selection in promotion and long-time maintenance of DAB1 polymorphism. Further investigations will clarify the role of pathogen-mediated selection to drive the evolution of DAB1 variation.

Proteins encoded by extraordinarily polymorphic major histocompatibility complex (MHC) genes are involved in the adaptive immune response. Balancing selection is believed to maintain MHC polymorphism in the long term, although neutral processes also play a role in shaping MHC diversity. However, the relative contribution of these processes is poorly understood. Here we characterized MHC class II variation of a low-dispersal, pond-breeding newt (Triturus carnifex) over a restricted, geographically structured area. We aimed to (1) evaluate the contribution of selection and neutral processes to shaping MHC diversity at two geographic scales, and (2) test for signatures of divergent allele advantage (DAA), which is a potentially important mechanism of balancing selection. The dominant role of selection in shaping MHC variation was suggested by the lack of correlation between MHC and neutral (microsatellite) variation. Although most variation occurred within populations for both types of markers, they differed in the extent of structuring at the two spatial scales. MHC structuring was more pronounced at local scales, suggesting the role of local selection, while structuring was not detectable at a larger scale, possibly due to the effect of balancing selection. Microsatellites showed the opposite pattern. As expected under DAA, the observed genotypes combined more sequence diversity than expected under a random association of alleles. Thus, DAA may contribute to maintaining MHC polymorphism, which is ancient, as supported by signatures of historical positive selection and trans-species polymorphism. Our results point to the importance of a multi-scale approach in studying MHC variation, especially in low-dispersal taxa, which are genetically structured at fine spatial scales.

Monitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time consuming and costly, fishery-dependent data (i.e., derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of assessing catch composition of single hauls carried out by trawlers by applying DNA metabarcoding to the dense water draining from fishing nets just after the end of hauling operations (hereafter "slush"). We assess the performance of this approach in portraying β-diversity and examining the quantitative relationship between species abundances in the catch and DNA amount in the slush (read counts generated by amplicon sequencing). We demonstrate that the assemblages identified using DNA in the slush satisfactorily mirror those returned by visual inspection of net content (about 71% of species and 86% of families of fish) and detect a strong relationship between read counts and species abundances in the catch. We therefore argue that this approach could be upscaled to serve as a powerful source of information on the structure of demersal assemblages and the impact of fisheries.

The brook chub (Squalius lucumonis) is a freshwater fish, endemic of Central Italy, which is experiencing a rapid range decline so that it is presently listed as Critically Endangered in the Italian IUCN Red List. For effective conservation, information about the spatial pattern of genetic diversity is crucial. Therefore, we analysed the mitochondrial Control Region and nuclear (microsatellites) markers to investigate population genetic structure, demography and spatial diversity over the whole species distribution range. We revealed significant divergence among populations, even at the local spatial scale, according to the isolation by distance model. At the biogeographic spatial scale, genetic diversity was shaped by past hydrogeological and climatic events that isolated the principal drainage basins (Vara, Tiber and Arno) from each other. On the other hand, strong genetic differentiation within the Tiber drainage basin could be due to local factors that acted at single-stream scale, as recent barriers to fish dispersal and irregular seasonal flow rates typical of small Mediterranean streams. Our findings contribute to the basal data collection on S. lucumonis required by European Habitats Directive and necessary for planning protection actions. We recommend that the three river drainages and most of the sampling sites should be regarded as different Management Units (MUs) to preserve their genetic distinctiveness. A recovery plan for the brook chub should consider environmental intervention and creation of protected areas, as well as in situ/ex situ restocking activities with juveniles produced by breeders from the same MU, to preserve local (adaptive) diversity.