Genetic divergence and phylogenetic relationships among Salmo trutta L. (brown trout) populations from Greece and other European countries

Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.

A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.

Genetic divergence between morphological forms of brown trout Salmo trutta L. in the Balkan region of Macedonia

The objective of this study was to characterize the genetic structure of two Balkan brown trout morphotypes, Salmo macedonicus and Salmo pelagonicus, and to test whether molecular traits support the species' status proposed by traditional morphological identification. The mitochondrial DNA 12S-rDNA, cyt b and control region genes were sequenced in 15 specimens collected from three localities in the Former Yugoslav Republic of Macedonia. The results of these markers did not support the taxonomic category of species but confirmed the existence of two morphotypes, Salmo trutta macedonicus and Salmo trutta pelagonicus, in the Aegean-Adriatic lineages of the Salmo trutta species complex.

Genetic structure of northwestern Spanish brown trout (Salmo trutta L.) populations, differences between microsatellite and allozyme loci

Genetic variation in nine wild brown trout (Salmo trutta L.) populations was studied by means of allozyme and microsatellite markers. All brown trout populations were clearly separated into two clusters that represented the Sil and Duero basins. Although both markers revealed a strong genetic differentiation between basins, microsatellite loci resulted much more accurate when population structure at the intrabasin level was analysed. Also pairwise multilocus FST estimates and assignment tests of individual fish to the set of sampled populations demonstrated a much higher efficiency of microsatellites compared to allozymes. The analysis of both markers provides new insights in defining the conservation units at this local area and confirms the existence of a recognized sub-lineage in the Duero basin. The management implications of these findings are discussed and changes in trout release activity are recommended to avoid mixing of trout gene pools mainly in the Sil basin.

The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in the brown trout

Technical and biological hurdles have precluded the retrieval of nuclear gene genealogies within most species. Among these obstacles, the possibility of intragenic recombination is one of the most demanding challenges. We studied the utility of nuclear genes for intraspecific evolutionary inferences by selecting a nuclear gene that exhibits patterns of considerable geographic differentiation in the brown trout (Salmo trutta) species complex. Haplotype variation from a nucleotide sequence of approximately 3.7 kb encompassing a portion of the transferrin (TF) gene was surveyed in 31 brown trout individuals collected across the native Eurasian range. Statistically significant recombination and gene conversion events were detected. However, we showed that the substantial cladistic structure was not disrupted by recombination or gene conversion events and the additional structure was estimated to have emerged after those events. Because loci with unusually high levels of variation might indicate the presence of selection, we tested the hypothesis of neutrality and found some evidence for directional selection. The strong geographic signal observed in the TF genealogy, coupled with the current spatial distribution of electromorphs, gave us the ability to draw empirical phylogeographic inferences. We delineated the composition of current brown trout populations on the basis of 3,625 individuals electrophoretically scored for the TF locus. We hypothesized scenarios of historical radiation and dispersal events, thus providing new insights refining previous allozyme and mtDNA inferences. We infer that the most ancestral brown trout populations inhabited tributaries from the Black, Caspian, and Aral Sea drainages. An early radiation of the species occurred throughout the Mediterranean, followed by independent dispersal events from the Adriatic to the southernmost Iberian Atlantic and, more recently, a rapid expansion throughout most of the Atlantic drainages.

Allozymic evidence of parapatric differentiation of brown trout (Salmo trutta L.) within an Atlantic river basin of the Iberian Peninsula

The genetic variation of brown trout from Duero, one of the main Atlantic Iberian river basins, was assessed at 34 enzymatic loci in 62 native populations. A strong intrabasin differentiation was detected (G(ST) = 0.46; range D: 0-0.066), mainly attributable to the existence of two divergent groups of populations within Duero: southern and northern groups. This divergence was mainly a consequence of the unequal distribution of *75 and *100 alleles at sMDH-B1,2* isoloci, which were correlated with substantial differences in genetic diversity among regions. The Lower Course region (nearly fixed for the *100 allele) and Pisuerga River (nearly fixed for the *75 allele) showed lower heterozygosities (H approximately 0.8%) in contrast with adjacent areas, which evidenced intermediate frequencies for both alleles and higher heterozygosities (H: 2.2-3.1%). Vicariance appeared as the more probable explanation for the significant positive correlation detected between genetic and geographical distances in Duero Basin. Genetic relationships with adjacent Iberian drainages indicate a close similarity between the southern group and Cantabric trout, whereas the northern group constitutes an ancient form from this basin. This study confirmed complex genetic relationships in brown trout from northwest Iberia, reasserting the existence of clines at several loci and for genetic diversity. The interaction between Cantabric and Duero trout, as well as the location of the limit of the anadromous form around the 42 degrees N parallel, are both required to understand the genetic characteristics of brown trout from this area.

The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation

Phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA (mtDNA) variation were used to infer the temporal dynamics of distributional and demographic history of brown trout (Salmo trutta). Both new and previously published data were analyzed for 1,794 trout from 174 populations. This combined analysis improved our knowledge of the complex evolutionary history of brown trout throughout its native Eurasian and North African range of distribution in many ways. It confirmed the existence of five major evolutionary lineages that evolved in geographic isolation during the Pleistocene and have remained largely allopatric since then. These should be recognized as the basic evolutionarily significant units within brown trout. Finer phylogeographic structuring was also resolved within major lineages. Contrasting temporal juxtaposition of different evolutionary factors and timing of major demographic expansions were observed among lineages. These unique evolutionary histories have been shaped both by the differential latitudinal impact of glaciations on habitat loss and potential for dispersal, as well as climatic impacts and landscape heterogeneity that translated in a longitudinal pattern of genetic diversity and population structuring at more southern latitudes. This study also provided evidence for the role of biological factors in addition to that of physical isolation in limiting introgressive hybridization among major trout lineages.

Mitochondrial haplotype diversity among Portuguese brown trout Salmo trutta L. populations: relevance to the post-pleistocene recolonization of northern Europe

Mitochondrial haplotype diversity in seven Portuguese populations of brown trout, Salmo trutta L., was investigated by sequencing the 5' end of the mitochondrial DNA (mtDNA) control region. Five new haplotypes were described for this species, each two to three mutational steps distant from the common north Atlantic haplotype. Significant population subdivision of mtDNA haplotypes was also apparent. Based on these results, as well as on published data describing the distribution of both mtDNA haplotypes and allozyme alleles throughout Europe, the postglacial recolonization of northern Europe was re-evaluated. It is argued that the available data do not support the contribution of two major glacial refugia (southwest Atlantic and Ponto-Caspian Basin) to this postglacial recolonization, as proposed in a recently published model. The unique genetic architecture of Portuguese brown trout within the Atlantic-basin clade of this species represents a highly valuable genetic resource that should be protected from introgression with nonendemic strains of hatchery fish.

Genetic structure of brown trout, salmo trutta l., at the southern limit of the distribution range of the anadromous form

Genetic variation at 33 protein loci was investigated in 41 wild brown trout populations from four river basins in Galicia (northwest Spain) to analyse the amount and distribution of genetic diversity in a marginal area, located in the distribution limit of the anadromous form of this species. The genetic diversity detected within populations (H between 0 and 6%) lies within the range quoted for this species in previous reports. The Mino, the most southern river basin analysed, showed a significantly lower genetic diversity and the highest genetic differentiation among the river basins studied. The hierarchical gene diversity analysis showed high population differentiation in a restricted area (GST = 27%), mostly due to differences among populations within basins (GSC = 22%). The reduction of GST observed when the isolated samples were excluded from the analysis (GST = 17%) showed the importance of habitat fragmentation on the heterogeneity detected. Gene flow among populations was comparatively evaluated by three indirect methods, which in general revealed low figures of absolute number of migrants per generation, slightly higher than 1. The gene flow among basins reflected a positive relationship with geographical distance. This trend was confirmed by the significant correlation observed between geographical and genetic distances, including all population pairs, which suggests a component of isolation by distance in brown trout genetic structure. Nevertheless, the nonsignificant intrabasin correlation demonstrates the complexity of genetic relationships among populations in this species. The model of genetic structure in brown trout is discussed in the light of the results obtained.

Microsatellite polymorphism and genetic impact of restocking in mediterranean brown trout (Salmo trutta L.)

The genetic impact of restocking Mediterranean brown trout populations with hatchery stocks was investigated in the Orb River drainage (France), using genetic data from three microsatellite loci. We sampled two wild populations, the main river which is restocked each year and one of its tributaries which has not been restocked for 6 years. Each sample was divided into two age groups (juveniles/adults). Introgression of each native population by hatchery stocks was previously estimated using allele frequencies from two diagnostic protein-coding loci and one mtDNA haplotype. The genetic structure and allelic frequency at three microsatellite loci in native populations were compared with two hatchery samples belonging to stocks usually used for restocking this drainage. High levels of polymorphism (23-27 alleles per locus) were detected for two loci, whereas the third was less polymorphic. Polymorphism was significantly higher in the restocked population than in the now undisturbed population. Significant differences between age groups were observed in the main river, but not in its tributary. The introgression estimates using microsatellites were compared to those obtained from proteins and mtDNA. The different possible origins of alleles common to hatcheries and wild populations (homoplasy, ancestral polymorphism or introgression) are discussed.

Genetic differentiation and phylogenetic relationships among Greek Salmo trutta L. (brown trout) populations as revealed by RFLP analysis of PCR amplified mitochondrial DNA segments

The genetic differentiation and phylogenetic relationships of 13 populations (11 from Greece, one from Albania and one from France) of brown trout (Salmo trutta L.) were investigated at the mtDNA level. RFLP analysis of four segments of mitochondrial DNA (D-loop, cytochrome b and ND-5/6) amplified by PCR was used. Seven of 14 restriction endonucleases were found to detect variability in the ND-5/6 regions, whereas four and two out of 17 and 16 were polymorphic in the D-loop and cytochrome b, respectively. Eleven different haplotypes were observed. The observed interpopulation diversity was very high (mean = 1.65 per cent), whereas the intrapopulation diversity was low in most cases (mean = 0.063 per cent). Five phylogenetic assemblages were identified. The results demonstrate that Greece is one of the regions where brown trout display very high levels of genetic diversity. Most populations were genetically very distinct, possessing private mtDNA genotypes. Therefore, they represent unique gene pools which may warrant individual recognition for conservation and management. The genetic relationships among populations suggested by mtDNA data were not in accordance with allozyme data. This study illustrates the importance of considering the historical biogeography of a species in order to understand its population genetic structure. It also reinforces the view that mtDNA analysis represents a powerful tool to study past and present demographic phenomena.