Genetic identification of native populations of Mediterranean brown trout Salmo trutta L. complex (Osteichthyes: Salmonidae) in central Italy

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.

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.

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.

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

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.

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

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations' abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted F_ST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.

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

Simple Summary

Brown trout is a freshwater fish with economic importance and with a great potential to be used as an environmental biosensor species. Despite being selected as a model species in distinct scientific contexts, in cultured specimens, there is a surprising lack of works investigating the morpho-physiological changes associated with the reproductive cycle; particularly concerning the gonads. In this study, a multi-parameter portfolio of biometric, biochemical, hormonal, and morphological analysis was established, which allowed a seasonal and sex characterization of the gonad status of adult brown trout males and females. Sampling included four reproductive phases: spawning capable (December), regressing (March), regenerating (July), and developing (November). Sex- and season-specific changes were described. The discriminative parameters characterized here stand now as normal baseline values against which abnormal patterns can be compared with. These parameters have the potential to be used as tools for the environmental monitoring of the reproductive status of wild populations and for the control of breeding stocks in aquaculture.

Abstract

Brown trout is an environmental freshwater sentinel species and is economically important for recreational fishing and aquaculture. Despite that, there is limited knowledge regarding morpho-physiological variations in adults throughout the reproductive cycle. Thus, this study aimed to analyze the fitness and gonadal maturation of cultured adult brown trout in four reproductive phases (spawning capable—December, regressing—March, regenerating—July, and developing—November). The systematic evaluation of males and females was based on biometric, biochemical, and hormonal parameters, along with a histomorphological grading of gonads and the immunophenotype location of key steroidogenic enzymes. The total weight and lengths reached the lowest levels in December. Gonad weights were higher in December and November, while the opposite pattern was found for liver weights. The lowest levels of cholesterol and total protein were also noted during those stages. The 11-ketotestosterone (11-KT) and testosterone (T) for males, and estradiol (E2) and T for females, mostly explained the hormonal variations. The immunohistochemistry of cytochrome P450c17 (CYP17-I), aromatase (CYP19), and 17β-hydroxysteroid dehydrogenase (17β-HSD) showed sex and site-specific patterns in the distinct reproductive phases. The sex- and season-specific changes generated discriminative multi-parameter profiles, serving as a tool for environmental and aquaculture surveys.

Population status and ecology of the Salmo trutta complex in an Italian river basin under multiple anthropogenic pressures

Salmonids inhabiting Mediterranean rivers are of particular concern for biodiversity conservation, as they are threatened by various stressors, including habitat alterations, overfishing, climate change, and introgressive hybridization with alien species. In the Tiber River basin (Central Italy), genetic introgression phenomena of the native Salmo cettii with the non-native Salmo trutta hinder the separate analysis of the two species, which are both included in the S. trutta complex. Little is known about the factors currently limiting the trout populations in this area, particularly with respect to climate change. With the intention of filling this gap, the aims of the current study were to (a) quantify changes in the climate and (b) analyze the distribution, status, and ecology of trout populations, in the context of changing abiotic conditions over the last decades. Fish stock assessments were carried out by electrofishing during three census periods (1998-2004, 2005-2011, and 2012-2018) at 129 sites. The trend over time of meteorological parameters provided evidence for increased air temperature and decreased rainfall. Multivariate analysis of trout densities and environmental data highlighted the close direct correlation of trout abundance with water quality, altitude, and current speed. Climate-induced effects observed over time in the sites where trout were sampled have not yet led to local extinctions or distribution shifts, indicating a marked resilience of trout, probably due to the buffering effect of intrinsic population dynamics. Decreasing body conditions over time and unbalanced age structures support the hypothesis that variations in hydraulic regime and water temperature could overcome these compensatory effects, which may lead to a severe decline in trout populations in the near future. In a climate change context, habitat availability plays a key role in the distribution of cold-water species, which often do not have the possibility to move upstream to reach their thermal optimum because of water scarcity in the upper river stretches.