The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA

Mitochondrial DNA of Sardinian and North-West Italian Populations Revealed a New Piece in the Mosaic of Phylogeography and Phylogeny of Salariopsis fluviatilis (Blenniidae)

The genus Salariopsis (Blenniidae) comprises freshwater blenny fish that inhabits Mediterranean Sea, Black Sea, and north-east Atlantic areas. Three species were formally described to date: Salariopsis fluviatilis. S. economidisi, and S. atlantica. In this study, 103 individuals were collected from different Italian regions (Sardinia, Liguria, Piedmont, Lombardy) and analyzed using the mtDNA Control Region and the ribosomal 16s gene. We aimed (i) to depict the phylogeographic patterns of S. fluviatilis in northern Italy and Sardinia and (ii) to compare the genetic structure of Italian samples with those from other Mediterranean regions. Results obtained showed the presence of a well-supported genetic structuring among Italian S. fluviatilis populations, shedding new light on the phylogeographic patterns of northern Italian populations of S. fluviatilis sensu stricto across the Ligurian Alpine ridge and the Sardinia Island-mainland dispersal patterns. Furthermore, our species delimitation analysis was consistent in supporting results of previous research about the presence of genetic differentiation among S. fluviatilis, evidencing: (i) a large group of S. fluviatilis sensu stricto that includes two sub-groups (Occidental and Oriental), (ii) one group comprising populations from the Middle East of a taxonomic entity corresponding to Salariopsis cf. fluviatilis, and (iii) one group of Iberian individuals from the Guadiana River.

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.

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

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 (Rhône 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.

Unlocking the potential of ancient fish DNA in the genomic era

Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.

Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha

The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed "the four H's": habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have divergent demographic histories.

Museum samples could help to reconstruct the original distribution of Salmo trutta complex in Italy

Partial D-loop sequences of museum specimens of brown trout and marble trout (Salmo trutta species complex) collected from Mediterranean rivers in the late 19th century were analysed to help to describe the native distribution of these species. All the individuals studied carried native haplotypes, the geographic distribution of which is consistent with published data. These results indicate that museum specimens from the 19th century could represent an opportunity to get a picture of the original genetic diversity distribution of this species complex.