Mitochondrial DNA sequence variation and phylogeography among Salmo trutta L. (Greek brown trout) populations

To investigate the phylogenetic relationships and geographical structure among brown trout S. trutta L. populations from the South Adriatic-Ionian and Aegean sea basins, mitochondrial DNA nucleotide sequence comparisons were used. A 310-base-pair (bp) segment of the control region (D-loop), and an additional 280-bp segment of the cytochrome b gene were sequenced from representatives of 13 brown trout populations. Phylogenetic analyses, conducted after combining the data presented with published data from other Eurasian brown trout, revealed four major phylogenetic groups, three of which were found widely distributed within the southern Balkan region. The phylogeographical patterns revealed by mtDNA represent one of the few cases where phylogenetic discontinuity in a gene tree exists without obvious geographical localization within a species' range and has most likely resulted from the differentiation of the major mtDNA clades during Messinian or early Pleistocene times. Finally, the genetic relationships among the populations suggested by mtDNA were generally not in accordance with either allozyme or morphological data.     

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.     

A rapid method for detecting mitochondrial DNA variation in the brown trout, Salmo trutta

A method is described for the amplification and restriction digestion of two variable regions of mitochondrial DNA (mtDNA) in the brown trout ( Salmo trutta ) as a non-invasive sampling and rapid screening technique for measuring genetic variation in populations.     

DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Saltno trutta populations

Throughout its natural range, the brown trout Salmo trutta L. exhibits a complex pattern of morphological and life-history variation. This has led to considerable taxonomic confusion, hampering the understanding of the evolutionary history of the species. To document the phylogenetic relationships among morphologically and geographically remote brown trout populations across western Europe, we determined the DNA sequence variation in segments of the mitochondrial control region for 151 individuals representing 24 populations. DNA was prepared for double-stranded sequencing by the polymerase chain reaction (PCR). Twenty-one variable nucleotide positions within a 640-bp fragment surveyed defined 12 genotypes differing by a mean of 7 nucleotide substitutions (range 1-12). Five major phylogenetic assemblages differing by mean sequence divergence estimates of 0.96 to 1.44% were identified. These groupings exhibited a strong spatial partitioning but lacked congruence with either ecological or morphological differentiation. Complete mitochondrial DNA (mtDNA) monomorphism across all Atlantic basin populations contrasted with the high interdrainage genetic diversity observed in more southerly populations. This study exemplified the usefulness of mitochondrial DNA sequence analysis for estimating phylogenetic relationships within S. trutta populations.     

Genetic diversity of trout (genus Salmo) from its most eastern native range based on mitochondrial DNA and nuclear gene variation

Russia and western Asia harbour trout populations that have been classified as distinct species and subspecies, most often on the basis of morphological and ecological variation. In order to assess their origins and to verify whether traditional taxonomy reflects their evolutionary distinctiveness, we documented their genetic relationships on the basis of mitochondrial DNA (mtDNA) RFLP, mtDNA sequence analysis, and allozyme variation. Both mtDNA and nuclear gene variation defined two ancient phylogenetic assemblages of populations distributed among northern (Baltic, White, Barents), and southern (Black, Caspian, Aral) sea basins, between which gene flow has been possible but limited in postglacial times. These results supported the traditional taxonomic differentiation between populations of these two regions. They provided weak support for the taxonomic distinction of southern brown trout (Salmo trutta) populations based on their basin of origin. They also refuted the hypothesis that L. Sevan trout (Salmo ischchan) diverged from a primitive brown trout ancestor. Nevertheless, all trout populations from southern sea basins possessed private alleles or mtDNA genotypes and were genetically distinct Therefore, they represent unique gene pools that warrant individual recognition for conservation and management.     

Assessment of the stocked or wild origin of anadromous brown trout (Salmo trutta L.) in a Danish river system, using mitochondrial DNA RFLP analysis

Declines in the number of anadromous brown trout in the Karup River in Denmark, due to environmental degradation, led to the stocking of large numbers of hatchery trout during the 1980s. This practice was gradually replaced by stocking with the offspring of electrofished local trout The genetic contribution of the hatchery fish to the current population of anadromous trout in the river was estimated by restriction fragment length polymorphism analysis of mitochondrial DNA, using seven restriction endonucleases. Fish from the hatchery strain as well as from five locations in the river system, and from a further unstocked river were screened. Eight haplotypes were observed. The distribution and frequencies of the observed haplotypes revealed little genetic differentiation among stocked populations. The hatchery strain differed significantly from the stocked populations. One haplotype which was found at a high frequency in the hatchery strain was almost absent from the stocked populations. This suggests that the genetic contribution of the hatchery trout to the current population is much less than would be expected from the number of stocked fish. The possible reasons for the failure of the hatchery trout to contribute to the gene pool, and also the implications for conservation biology, are discussed.     

Mitochondrial DNA variation in River Usk brown trout, Salmo trutta

Mitochondrial DNA (mtDNA) polymorphism in the essentially non-anadromous River Usk brown trout Salmo trutta population was investigated by restriction analysis. Following mtDNA extraction and purification on caesium chloride density gradients, monomorphic restriction profiles were obtained with Hae III , Hind III , Sau 3AI and Xbal . However, the restriction endonucleases Ava II and HinfIl proved informative. The distribution of four composite genotypes found within the Usk system was heterogeneous, and a fifth genotype appeared exclusively in an outgroup sample from the adjacent River Wye drainage. The source of the observed genetic variation is discussed in relation to estimated divergence times for Usk mtDNA genotypes and the stocking history of the catchment.     

The post‐spawning movements of migratory brown trout Salmo trutta L.

The post spawning behaviour of sea trout Salmo trutta was studied over a 2 year period in the river and estuary of the River Fowey, south‐west England. Forty‐five sea trout kelts were trapped immediately after spawning in December and intraperitoneally tagged with miniature acoustic transmitters. The subsequent emigration into coastal waters was monitored using acoustic receivers deployed throughout the river catchment. The levels of gill Na⁺K⁺ATPase activity in sea trout kelts sampled at the same time as the tagged fish were within the range of 2·5 to 4·5 μmol Pi per mg protein per h indicating that the post‐spawning fish were not physiologically adapted to salt water. The tagged kelts were resident in fresh water between 4 and 70 days before entering the estuary. Sixty two per cent of the tagged kelts subsequently migrated successfully into coastal waters, with a higher success rate for male fish (75%) than females (58%). There was a significant size related difference in the run‐timing of the kelts with the larger fish moving more quickly into coastal waters after spawning than smaller fish. Seaward migration within fresh water was predominantly nocturnal and generally occurred in conjunction with increasing river discharge and rising water temperature. Migration through the estuary continued to be predominantly nocturnal and occurred during an ebbing tide. Residency within the estuary varied amongst individuals although it was invariably short, with most fish moving out into coastal waters within one to two tidal cycles. Five tagged kelts returned from the coastal zone and re‐entered fresh water during April and June. Marine residence time varied between 89 and 145 days (mean 118 days) and the minimum estimated marine survival was c. 18%. One of these sea trout was subsequently recaptured after successfully spawning in the vicinity where it had been previously tagged demonstrating a degree of spawning site fidelity.     

Microsatellite and mitochondrial DNA polymorphism reveals life-history dependent interbreeding between hatchery and wild brown trout (Salmo trutta L.)

The effects of stocking hatchery trout into wild populations were studied in a Danish river, using microsatellite and mitochondrial DNA (mtDNA) markers. Baseline samples were taken from hatchery trout and wild trout assumed to be unaffected by previous stocking. Also, samples were taken from resident and sea trout from a stocked section of the river. Genetic differentiation between the hatchery strain and the local wild population was modest (microsatellite FST = 0.06). Using assignment tests, more than 90% of individuals from the baseline samples were classified correctly. Assignment tests involving samples from the stocked river section suggested that the contribution by hatchery trout was low among sea trout (< 7%), but high (46%) among resident trout. Hybrid index analysis and a high percentage of mtDNA haplotypes specific to indigenous trout observed among resident trout that were assigned to the hatchery strain suggested that interbreeding took place between hatchery and wild trout. The latter result also indicated that male hatchery trout contributed more to interbreeding than females. We suggest that stronger selection acts against stocked hatchery trout that become anadromous compared to hatchery trout that become resident. As most resident trout are males this could also explain why gene flow from hatchery to wild trout appeared to be male biased. The results show that even despite modest differentiation at neutral loci domesticated trout may still perform worse than local populations and it is important to be aware of differential survival and reproductive success both between life-history types and between sexes.     

Genetic structure of brown trout (Salmo trutta, L.) populations from south-western France: data from mitochondrial control region variability

The genetic relationships between several French Atlantic populations of brown trout were analysed using polymerase chain reaction-single-strand conformation polymorphism and sequencing of two parts of the mitochondrial control region. Ten mitochondrial haplotypes were identified, separated by a small number of mutations. The distribution of these haplotypes confirmed our hypothesis of the existence of two genetically well-differentiated groups of populations in this area, which has already been suggested using nuclear markers. Nuclear and mitochondrial markers, however, show different patterns of genetic differentiation: some populations which belong to one group according to allozyme results appear to be part of the other when using mitochondrial DNA. The origin of these different forms is discussed; they seem to belong to the Atlantic grouping. Nevertheless, the hypothesis of an ancestral and a modern form suggested for northern populations does not appear valid in this particular case.     

Genetic variation in skipjack tuna Katsuwonus pelamis(L.) using PCR‐RFLP analysis of the mitochondrial DNA D‐loop region

A high level of genetic diversity was observed in Katsuwonus pelamis populations from India ( h  = 0·952, ne  = 14·3) and Japan ( h  = 0·897, ne  = 8·9). The log‐likelihood ( G )‐based exact test revealed significant heterogeneity in the distribution of haplotypes between the two populations ( P  < 0·01, s . e . = 0·001). This result suggests that the two populations should now be treated as demographically independent and managed separately.     

Mitochondrial DNA as a genetic marker for brown trout, Salmo trutta L., populations

Mitochondrial DNA was examined in natural and hatchery-reared stocks of brown trout, using different methods of restriction analysis. The methods included the development of a brown trout mt DNA hybridization probe through cloning part of the brown trout mitochondrial genome. In addition, fragments were analysed by ethidium bromide staining and end-labelling. The relative merits of each of these methods in assessing levels of genetic relatedness between the natural and hatchery-reared brown trout stocks were evaluated. In addition, the study revealed a diagnostic mtDNA restriction pattern which could be used as a genetic marker for the discrimination of these two groups of brown trout.     

Complete mitochondrial control region sequences indicate a distinct variety of brown trout Salmo trutta in the Aral Sea

Complete sequencing of the mtDNA control region (CR) from five specimens of brown trout Salmo trutta from the Amu Darya River identified two novel haplotypes belonging to the Danubian lineage. This finding supports the long-standing hypothesis that brown trout in the Aral Sea represent a distinct genetic stock and also illustrates the benefits that complete sequencing of the CR can provide for elucidating phylogeographic relationships.     

The problem of sampling families rather than populations: relatedness among individuals in samples of juvenile brown trout Salmo trutta L.

In species exhibiting a nonrandom distribution of closely related individuals, sampling of a few families may lead to biased estimates of allele frequencies in populations. This problem was studied in two brown trout populations, based on analysis of mtDNA and microsatellites. In both samples mtDNA haplotype frequencies differed significantly between age classes, and in one sample 17 out of 18 individuals less than 1 year of age shared one particular mtDNA haplotype. Estimates of relatedness showed that these individuals most likely represented only three full-sib families. Older trout exhibiting the same haplotypes generally were not closely related.     

Interpopulation variation in reproductive traits of anadromous female brown trout, Salmo trutta L.

We studied reproductive traits in nine anadromous brown trout, Salmo trutta L., populations in seven Norwegian rivers. Within populations we found a positive significant correlation between fish length and fecundity in all populations, and between fish length and egg diameter in five populations. There were significant differences in these relationships between populations from different rivers, and between populations from different locations within rivers. When adjusted for variation in fish length, mean fecundity and mean egg diameter showed a negative significant correlation among populations. The ratio of gonadal weight to somatic weight (gonadosomatic index) varied significantly among populations but was not associated with variation in fish length. Comparatively few large eggs were found in brown trout populations co-existing with several other fish species.     

Initial feeding in migratory brown trout (Salmo trutta L.) alevins

Initial feeding of brown trout was investigated under laboratory conditions. Fifty per cent feeding occurred when yolk constituted approximately 31% of total alevin dry weight, and feeding rate was positively correlated to developmental stage. The possible ecological implications of initial feeding are discussed.     

Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the Pleistocene

The phylogeography of Atlantic brown trout ( Salmo trutta ) was analysed using mitochondrial DNA control region complete sequences of 774 individuals from 57 locations. Additionally, the available haplotype information from 100 published populations was incorporated in the analysis. Combined information from nested clade analysis, haplotype trees, mismatch distributions, and coalescent simulations was used to characterize population groups in the Atlantic basin. A major clade involved haplotypes assigned to the Atlantic (AT) lineage, but another major clade should be considered as a distinct endemic lineage restricted to the Iberian Peninsula. The phylogeography of the Atlantic populations showed the mixed distribution of several Atlantic clades in glaciated areas of Northern Europe, whereas diverged haplotypes dominated the coastal Iberian rivers. Populations inhabiting the Atlantic rivers of southern France apparently contributed to postglacial colonization of northern basins, but also comprised the source of southern expansions during the Pleistocene.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 904–917.     

Evidence for phylogeographically informative sequence variation in the mitochondrial control region of Atlantic brown trout

Complete sequencing of the mitochondrial control region was undertaken among brown trout Salmo trutta from North Atlantic areas where previous studies, based on smaller mtDNA fragments, failed to detect any phylogeographic signal. Comparison of sequences suggests that brown trout in the Iberian Peninsula and Scandinavia belong to largely divergent evolutionary units.     

Phylogeographic study of brown trout from Serbia,based on mitochondrial DNA control region analysis

In order to illuminate the phylogeography of brown trout (Salmo trutta) populations in the Balkan state of Serbia, the 561 bp 5''-end of mtDNA control region of 101 individuals originating from upland tributaries of the Danubian, Aegean and Adriatic drainages were sequenced and compared to corresponding brown trout sequences obtained in previous studies. Among 15 haplotypes found, 14 were considered native, representing the Danubian and Adriatic lineages of the brown trout, while one haplotype (ATcs1), found only in two individuals originating from two stocked rivers, corresponded to the Atlantic lineage and was considered introduced. Native haplotypes exhibited a strong geographic pattern of distribution: the Danubian haplotypes were strictly confined to the Danubian drainage, while the Adriatic haplotypes dominated in the Aegean and Adriatic drainages; most of the total molecular variance (69%) was attributed to differences among the drainages. Phylogenetic reconstruction, supplemented with seven haplotypes newly described in this study, suggested a sister position of the Atlantic-Danubian and Adriatic-Mediterranean-marmoratus ("southern") phylogenetic group, and pointed to the existence of a distinct clade, detected within the "southern" group. The data obtained confirmed our expectation of the existence of high genetic diversity in Balkan trout populations, and we recommend more widespread surveys covering trout stocks from the region.