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

Identification of Ancestry Informative Markers in Mediterranean Trout Populations of Molise (Italy): A Multi-Methodological Approach with Machine Learning

Brown trout (Salmo trutta), like many other freshwater species, is threated by the release in its natural environment of alien species and the restocking with allochthonous conspecific stocks. Many conservation projects are ongoing and several morphological and genetic tools have been proposed to support activities aimed to restore genetic integrity status of native populations. Nevertheless, due to the complexity of degree of introgression reached up after many generations of crossing, the use of dichotomous key and molecular markers, such as mtDNA, LDH-C1* and microsatellites, are often not sufficient to discriminate native and admixed specimens at individual level. Here we propose a reduced panel of ancestry-informative SNP markers (AIMs) to support on field activities for Mediterranean trout management and conservation purpose. Starting from the genotypes data obtained on specimens sampled in the main two Molise’s rivers (Central-Southern Italy), a 47 AIMs panel was identified and validated on simulated and real hybrid population datasets, mainly through a Machine Learning approach based on Random Forest classifier. The AIMs panel proposed may represent an interesting and cost-effective tool for monitoring the level of introgression between native and allochthonous trout population for conservation purpose and this methodology could be also applied in other species.

The Italian Alpine and Subalpine trouts: Taxonomy, Evolution, and Conservation

Simple Summary

In a great part of the world, trout fishing has long inspired human spiritual ideals of immersion into nature and recreation, far removed from the fast-encroaching urbanization. Concurrently, these values and emotions fueled a white-hot business, establishing a florid market of outdoor recreation. Since the 20th century, the trout-culture industry strived to provide anglers with fishing entertainment by stocking massive amounts of non-native trouts in dozens of countries, irrespective of the lakes’ and rivers’ carrying capacity. This had dire consequences on the structural and functional diversity of these ecosystems. “Trout wars” sparked throughout the world between the promoters of stocking activities and the promoters of “wild trout management” and ethics. The “Italian trout war” has been fought on the harsh battleground of trout taxonomy, ecology, distribution, and native vs. non-native interfertile species. Northern Italy, home to the Italian Alpine and subalpine trouts and economic center of the national trout-culture and stocking industry, was particularly affected by this clash. We review here the state of art of this ongoing debate, outlining our scientific view of the taxonomy, evolution, distribution, and sustainable management of the native Italian trouts of northern Italy.

Abstract

During the last 150 years, the trout-culture industry focused on enhancing trout populations by stocking, in response to the growing anglers’ demand and the habitat degradation associated to the rapid urbanization and hydropower development. The industrialized north of Italy, home to the Italian Alpine and subalpine trout populations, is the source of most of the revenues of the national trout-culture industry. Its rapid growth, and the massive introduction of non-native interfertile trouts eroded the genetic diversity of native lineages, leading to harsh confrontations between scientists, institutions, and sportfishing associations. We review here the state of the art of the taxonomy and distribution of the northern Italian native trouts, presenting both scientific results and historical documentation. We think the only native trouts in this region are Salmo marmoratus, widespread in this region, plus small and fragmented populations of S. ghigii, present only in the South-western Alps. We strongly recommend the interruption of stocking of domesticated interfertile non-native trouts in this area, and recommend the adoption of Evolutionary Significant Units for salmonid fishery management. We further propose future research directions for a sustainable approach to the conservation and ecosystem management of the fishery resources and inland waters of northern Italy.

Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy

Salmonid fish have become ecological and research models of study in the field of conservation genetics and genomics. Over the last decade, brown trout have received a high level of interest in research and publications. The term Salmo trutta complex is used to indicate the large number of geographic forms present in the species Salmo trutta. In Europe, the S. trutta complex consists (based on mitochondrial DNA control region analysis) of seven major evolutionary lineages: Atlantic (AT), Mediterranean (ME), Adriatic (AD), Danubian (DA), Marmoratus (MA), Duero (DU) and Tigris (TI). In several nations, the difficulty of identifying some lineages derives from their wide phenotypic and geographic plasticity and the presence of mixed lineages (due to introgressive hybridization with domestic AT populations). In Italy, the S. trutta complex populations living in the Tyrrhenian area and on the main islands (Sicily, Sardinia and Corsica) showed high genetic diversity. Currently, on the Italian Red List, the protected (near threatened) populations are the AD and ME lineages. Recent studies based on traditional (mitochondrial and nuclear markers) and NGS (next-generation sequencing) analyses have clarified some genetic differences between the populations of the Tyrrhenian region, Sicily, Sardinia and Corsica. Native populations in Sardinia belong to the AD lineage, while those living in Corsica are mainly characterized by the AD, MA and ME haplotypes. In Sicily, in the area of the Iblei mountains, an AT lineage (North African) exists. According to some authors, the term Salmo macrostigma should only be used for populations in North Africa. The use of genotyping methods based on mtDNA and nuclear markers and the latest generation sequencing techniques can improve the study of populations and evolutionary lineages in areas where there are overlaps and hybridization phenomena.

Conservation Genetics of Mediterranean Brown Trout in Central Italy (Latium): A Multi-Marker Approach

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.