Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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.

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Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy

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.

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

Intraspecific genetic diversity is heterogeneously distributed in natural landscapes and often forms repeatable spatial patterns. For instance, in rivers, genetic diversity increases towards downstream areas, whereas genetic differentiation increases in isolated upstream areas. Nonetheless, these patterns can be modified by human-induced perturbations, and documenting the extent to which human activities alter these natural patterns is important for conservation. Among the human pressures that affect freshwater biodiversity, stocking natural populations with captive-bred strains is a common practice worldwide that can strongly alter the genetic integrity of wild populations. The main objectives of this study were to document the spatial distribution of captive-bred ancestry in brown trout (Salmo trutta) populations from four French basins having been stocked according to different practices, and to quantify for each basin the effect of captive-bred ancestry on the spatial distribution of genetic diversity and differentiation. The four basins were sampled along their upstream–downstream gradient, and a total of 1,686 individuals were genotyped at 192 single nucleotide polymorphism loci. For all basins, individuals with a strong assignment to the captive strain were mostly found in upper reaches, although the average proportion of captive-bred ancestry varied strikingly among rivers (from 1.9 to 58.7%). Although spatial patterns of genetic differentiation were not affected by introgression and showed an expected increase with increasing distances from the river mouth in all basins, there was evidence that the classical pattern of downstream increase in genetic diversity was reversed when considering highly introgressed populations. These findings demonstrate that the stocking of captive-bred strains can strongly modify natural spatial patterns of diversity, even when stocking occurred many generations ago and has now ended. The study illustrates the major impacts of humans on intraspecific biodiversity patterns, and emphasizes the importance of conservation plans that take into account this artificial distribution of genetic diversity. 

Captive‐bred ancestry affects spatial patterns of genetic diversity and differentiation in brown trout (
 
 Salmo trutta
 
 ) populations

\n In the Neotropics, freshwater streams harbour high fish diversity and are constantly threatened by anthropogenic disturbance. However, there are few studies on the genetic diversity of fish populations inhabiting these streams. We aimed to assess, based on microsatellite and mitochondrial DNA markers, the population structure and genetic diversity of the suckermouth catfish, Hypostomus ancistroides, a Neotropical species widely distributed across the Upper Paraná River Basin in South America. Twenty-five locations were sampled, distributed across 18 sites in six tributary streams and another seven sites in the main river channel. Our analyses revealed a spatial heterogeneity in genetic diversity within the basin, indicating fine-scale genetic structuring. Samples from all streams showed exclusive haplotypes and private alleles, reinforcing the importance of preserving the tributaries for the conservation of the genetic diversity of the studied populations. The fine-scale genetic structuring of H. ancistroides is probably related to the limited displacement capacity of this species.

Fine-scale genetic structure of suckermouth Hypostomus ancistroides populations: the importance of Neotropical streams for fish conservation

The role of the south-western Alps as a corridor for Mediterranean trout (Salmo trutta complex Linnaeus, 1758) was evaluated in order to understand the influence of the last glacial events in shaping the spatial distribution of the genetic diversity of this salmonid. For this, the allochthonous hypothesis of a man-mediated French origin (19th century) of the Mediterranean trout inhabiting the Po tributaries in the Italian side of the south-western Alps was tested. A total of 412 individuals were analysed at the mitochondrial control region. The phylogenetic classification was carried out by using a Median-Joining Network analysis. Mismatch pair-wise analysis, molecular dating and Kernel density distribution analysis of the main mitochondrial lineages were evaluated to compare past demographic dynamics with the current spatial distribution of genetic diversity. The main outcomes resulted strongly in agreement with a biogeographic scenario where the south-western Alps acted as a unidirectional corridor that permitted the colonization of the upper Durance (Rhone River basin) by trout from the Po River basin. Therefore, the Mediterranean trout should be considered as native also along the Italian side of the south-western Alps and the allochthonous hypothesis should be rejected.

https://hal.umontpellier.fr/hal-03032062/document

Alessandro Candiotto

Papers

The role of the south-western Alps as a unidirectional corridor for Mediterranean brown trout (Salmo trutta complex) lineages