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AbstractThe Salmo trutta species complex includes threatened or intensively managed taxa. Domestic-Atlantic strains are widely farmed and massively introduced into the wild to support fisheries, although such practices seriously threaten native populations of Mediterranean brown trout through anthropogenic hybridization. Characterizing the distribution and genetic composition of wild populations across river catchments is crucial to identify conservation priorities and define appropriate management strategies. Here, we genotyped 586 brown trout at the diagnostic nuclear LDH-C1 gene and the mitochondrial D-loop fragment, to assess the conservation status of 33 sites in a protected area spanning river catchments from both the Adriatic and Tyrrhenian slopes in the northern Apennines (Italy). The results indicated a critical situation of widespread domestic-Atlantic introgression. Further analyses at 15 microsatellite loci on 159 individuals from 12 natural sites (along with 113 references from hatcheries) revealed similarity to hatchery stocks, higher genetic diversity and bottleneck signals in introgressed/exotic populations, consistently with relatively recent introductions of domestic-Atlantic individuals into wild sites. Conversely, the only native sites from a single river catchment on the Adriatic slope showed genetic distinctiveness, reduced diversity and demographic stability. We also found genetic evidence of a human-mediated introduction of allochthonous Mediterranean trout in a single wild site, as well as of a putative between-slopes translocation. We provide further insight into the occurrence and consequences of human manipulations on wild Mediterranean brown trout populations, contextually offering a reliable baseline for an ongoing conservation project aiming at preserving native populations of this endangered taxon.

The Salmo trutta species complex includes threatened or intensively managed taxa. Domestic-Atlantic strains are widely farmed and massively introduced into the wild to support fisheries, although such practices seriously threaten native populations of Mediterranean brown trout through anthropogenic hybridization. Characterizing the distribution and genetic composition of wild populations across river catchments is crucial to identify conservation priorities and define appropriate management strategies. Here, we genotyped 586 brown trout at the diagnostic nuclear LDH-C1 gene and the mitochondrial D-loop fragment, to assess the conservation status of 33 sites in a protected area spanning river catchments from both the Adriatic and Tyrrhenian slopes in the northern Apennines (Italy). The results indicated a critical situation of widespread domestic-Atlantic introgression. Further analyses at 15 microsatellite loci on 159 individuals from 12 natural sites (along with 113 references from hatcheries) revealed similarity to hatchery stocks, higher genetic diversity and bottleneck signals in introgressed/exotic populations, consistently with relatively recent introductions of domestic-Atlantic individuals into wild sites. Conversely, the only native sites from a single river catchment on the Adriatic slope showed genetic distinctiveness, reduced diversity and demographic stability. We also found genetic evidence of a human-mediated introduction of allochthonous Mediterranean trout in a single wild site, as well as of a putative between-slopes translocation. We provide further insight into the occurrence and consequences of human manipulations on wild Mediterranean brown trout populations, contextually offering a reliable baseline for an ongoing conservation project aiming at preserving native populations of this endangered taxon. [ABSTRACT FROM AUTHOR]

Brown trout is considered a complex of incipient species, including several phylogenetic lineages, whose natural distribution in the Mediterranean area has been altered, since the beginning of the 1900s, by massive introductions of domestic strains of Atlantic origin to support fisheries. Introduced trout naturalize in new suitable environments and extensively hybridize with native populations. Here, we characterized putatively neutral and adaptive genetic variability and population structure of Mediterranean brown trout from six river catchments in central peninsular Italy, as revealed by both mitochondrial (Control Region) and nuclear (microsatellites, LDH-C1, major histocompatibility complex) markers. We quantified the admixture of wild populations with hatchery strains and evaluated the effects of domestic trout introductions on shaping population genetics. Our analyses indicated: (1) a composite picture of genetic variability in the area, with the presence of all native Mediterranean trout mitochondrial lineages ("Adriatic", "Mediterranean", "marmoratus"), various frequencies of allochthonous genotypes and different rates of introgression among sampling sites; (2) asymmetric mito-nuclear introgression; (3) increasing nuclear marker diversity with increasing levels of admixture across populations; (4) strong population structure coupled with relatively low effective population size. Data allowed the identification of five management units and we propose specific actions to support ongoing and future conservation strategies within the examined area. [ABSTRACT FROM AUTHOR]

Background: Brown trout Salmo trutta have been described in terms of five major mtDNA lineages, four of which correspond to major ocean basins, and one, according to some authors, to a distinct taxon, marbled trout Salmo marmoratus. The Atlantic and Danubian lineages of brown trout meet in a poorly documented contact zone in Central Europe. The natural versus human mediated origin of the Atlantic lineage in the upper Danube is a question of both theoretical and practical importance with respect to conservation management. We provide a comprehensive population genetic analysis of brown trout in the region with the aim of evaluating the geographic distribution and genetic integrity of these two lineages in and around their contact zone. Results: Genetic screening of 114 populations of brown trout across the Danube/Rhine/Elbe catchments revealed a counter-intuitive phylogeographic structure with near fixation of the Atlantic lineage in the sampled portions of the Bavarian Danube. Along the Austrian Danube, phylogeographic informative markers revealed increasing percentages of Danube-specific alleles with downstream distance. Pure Danube lineage populations were restricted to peri-alpine isolates within previously glaciated regions. Both empirical data and simulated hybrid comparisons support that trout in non-glaciated regions north and northeast of the Alps have an admixed origin largely based on natural colonization. In contrast, the presence of Atlantic basin alleles south and southeast of the Alps stems from hatchery introductions and subsequent introgression. Despite extensive stocking of the Atlantic lineage, little evidence of first generation stocked fish or F1 hybrids were found implying that admixture has been established over time. Conclusions: A purely phylogeographic paradigm fails to describe the distribution of genetic lineages of Salmo in Central Europe. The distribution pattern of the Atlantic and Danube lineages is extremely difficult to explain without invoking very strong biological mechanisms. The peri-alpine distribution of relict populations of pure Danubian lineage brown trout implies that they colonized headwater river courses post-glacially ahead of the expansion of the Atlantic lineage. The recognition of natural as opposed to anthropogenic introgression of the Atlantic lineage into Danubian gene pools is of fundamental importance to management strategies. [ABSTRACT FROM AUTHOR]

Genetic diversity was analysed in a putative autochthonous brown trout ( Salmo trutta fario L.) population (Monterivoso Stream, Tyrrhenian Apennine Slope) by means of seven microsatellite loci and PCR‐RFLP of two mitochondrial (ND1 and ND5/6) and one nuclear (LDH‐C1*) locus. Monterivoso data were compared to those obtained analysing populations of the same basin (Nera River) and of the Po basin; Irish populations were used as a source of Atlantic strain brown trout. Haplotypes distributions, heterozygosity, F‐statistic and UPGMA analyses indicated a genetic diversification between these populations, suggesting a widespread alteration of the genetic structure due to repeated stocking with allochthonous material, mainly of Atlantic origin, that has partially polluted the Monterivoso population. This population appeared to be constituted of Mediterranean strain samples and might represent a residue of an indigenous pool: it shows high specificity characteristics and it is genetically separate from the others observed and from populations of the Adriatic slope of the Apennines. This population should be employed in managing and breeding programmes finalised to an eco‐sustainable restocking of brown trout in the Nera River Basin, with periodic monitoring by genetic analyses. [ABSTRACT FROM AUTHOR]