Genetic identification of native populations of Mediterranean brown troutSalmo truttaL. complex (Osteichthyes: Salmonidae) in central Italy

Abstract

Italian native populations of Mediterranean brown trout belong to the Salmo trutta complex. This species complex includes many mitochondrial lineages and phenotypes that have caused taxonomic controversies over time. The spatial distribution and the genetic diversity of these fishes are threatened by habitat destruction, global warming and, mainly, by the introduction of domestic trout of Atlantic origin. Indeed allochthonous trouts were massively restocked in Italian rivers for a century and they admixed with native populations. In order to identify residual native populations of Mediterranean brown trout, a genetic analysis of specimens collected within Latium region, on the Tyrrhenian slope of central Italy, was undertaken. To this purpose, 210 trout specimens were collected from six different rivers and analyzed for the identification of their nuclear (LDH-C1* RFLP) and mitochondrial (Control Region sequences) genotypes. Genetic characterization with these molecular markers allowed a quantitative estimate of allochthonous genotypes, which are present in all brown trout populations of the six sites, even if not equally distributed across the sampling area. At least three populations, inhabiting diverse lotic ecosystems (mountain, hilly and coastal streams respectively), are characterized by a high percentage of native nuclear allele *100 at locus LDH-C1* and typical Mediterranean haplotypes (of AD and ME lineages), which can be considered as different management units (MUs). This finding highlighted the aquatic ecosystems of the Latium Region as an important hotspot of salmonid biodiversity within the Italian peninsula, with important implications from a conservation perspective.

Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

“…In Italy, although the taxonomy is still controversial, the Mediterranean trout is referred to as Salmo cettii syn. Salmo macrostigma [ 3 , 4 , 5 , 6 , 7 , 8 ] and, unfortunately, it is one of the most highly threatened freshwater fish at risk of extinction [ 3 , 7 , 9 ]. Its biodiversity is declining rapidly due to a complex pattern of climatic and anthropogenic pressures [ 10 , 11 ], and it is currently listed in the Italian IUCN Red List as ‘critically endangered’ ( , accessed on: 31 March 2021).…”

Balancing selection, genetic drift, and human‐mediated introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout

“…Moreover, the retention of MHC polymorphism predating speciation is frequently reported (Těšický & Vinkler, 2015), thus MHC allele sharing among recently diverged TA B L E 2 Results of linear models with MHC diversity (MHC-DAB richness) and functional diversity (MHC-ST richness) as the dependent variable, and microsatellite diversity (STR richness) and admixture between native and domestic brown trout lineages (LDHadmixture) as predictors Cortázar-Chinarro et al, 2017;. Therefore, it is possible that Italy-a well-known hot spot of brown trout genetic diversity (Lobón-Cerviá & Sanz, 2018)-and the study area in particular (Rossi et al, 2019), may harbor remarkably high levels of diversity even for MHC genes. However, we cannot entirely rule out that high levels of MHC diversity revealed in our study may be partially due to the increased accuracy of the high-throughput sequencing to detect rare and/or poorly amplified MHC variants, compared to traditional approaches adopted in previous studies (Campos et al, 2006;Monzón-Argüello et al, 2014;Schenekar & Weiss, 2017).…”

“…Here, we characterize putative adaptive (MHC) and neutral (microsatellite loci) variation in genetically unrelated wild populations of brown trout from central Italy. The study area was previously recognized as a hotspot of genetic diversity for native brown trout lineages, although almost all populations were variously subject to stocking with domestic brown trout (Fabiani et al, 2018;Rossi et al, 2019). Such activities may ultimately favor introgressionwhich refers to the consequence of hybridization between lineages rather than distinct species in this case-and maintenance of novel genetic variation into wild native populations through balancing selection mechanisms, especially at putatively adaptive genes such as MHC.…”

“…Artificial and/or natural barriers (e.g., dams, waterfalls, fluctuations of water flow) interrupt hydrological connectivity giving rise to genetically structured wild populations with low effective sizes, moreover frequently biased by restocking with domestic trout (Berrebi et al, 2019;Fabiani et al, 2018;Rossi et al, 2019;Splendiani et al, 2019). (Forsberg et al, 2007;Jacob et al, 2010).…”

Multi-Parametric Portfolio to Assess the Fitness and Gonadal Maturation in Four Key Reproductive Phases of Brown Trout

“…Brown trout has a very high genetic variation and a wide range of morpho-phenotypes. Specific populations may differ from each other in molecular genetic markers, color, size, and seasonality [ 14 , 15 ]. For instance, specimens from an Iberian Peninsula wild population reached 39.5 cm in length and around 1 kg in weight [ 16 ], while sexual maturity occurred at any age between 1 and 10 years [ 13 ].…”