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.     

Phylogeography of the Turkish brown trout Salmo trutta L.: mitochondrial DNA PCR‐RFLP variation

In the present study, mitochondrial DNA polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) assay was used to assess the phylogenetic and phylogeographic relationships among 27 brown trout Salmo trutta populations from Turkey. The complete NADH 5/6 region and a second segment comprising the cytochrome b gene and D‐loop of mtDNA amplified by PCR were digested with six and five restriction enzymes, respectively. A total of 27 haplotypes were observed and divided into three major phylogenetic assemblages, namely Danubian (DA), Adriatic (AD) and a newly proposed Tigris (TI) lineage. The timing of the net nucleotide divergence between the major lineages along with the geological history of Turkey suggested pre‐Pleistocene isolation of the Turkish brown trout and provided evidence that Turkey could be considered as a centre of diversification for these lineages. The average haplotype diversity (0·1397) and the nucleotide diversity (0·000416) within populations were low in comparison to the observed interpopulation nucleotide diversity (0·021266). PCR‐RFLP analysis showed that most of the mtDNA sequence variation found in the Turkish brown trout populations was imputable to differences among lineages. On the other hand, there was also an obvious relationship between geographical distribution of the populations and their clustering. The present study showed that brown trout populations from Turkey are highly divergent and mainly have a unique genetic profile that could be used for conservation and management purposes.     

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.     

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.     

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.     

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.     

Variation in mitochondrial DNA and post-glacial colonization of north western Europe by brown trout

A purified mitochondrial DNA (mtDNA) probe was used to examine restriction fragment length polymorphisms produced by six restriction enzymes ( Xba I, Eco RV, Ava II, Hinf I, Hae III, Mbo I) in 915 brown trout from western Europe. A total of 20 composite haplotypes were found with one to seven haplotypes in individual populations. Icelandic trout samples from north, south, east, and west coast drainages showed only a single common haplotype in contrast to the high level of polymorphism found in Irish and Scottish populations. The phylogeny of mtDNA haplotypes and the pattern of haplotype distribution suggests that post-glacial colonization of brown trout in NW Europe was more complex than the dual colonization model which has been proposed on the basis of differential LDH-5* allele distribution. For example, Lough Melvin (Ireland) appears to have been independently     

A pyrosequencing assay for the rapid discrimination of mitochondrial lineages in the Salmo trutta species complex

The European trout (Salmo trutta species complex) is genetically very diverse consisting of five distinct mitochondrial lineages that probably originated in the Pleistocene. Here, we describe a novel pyrosequencing protocol to generate two short sequence reads from the mitochondrial control region, which allow the unambiguous identification of all five lineages. The approach was found to be easily transferable between laboratories and should be a valuable tool for the assessment of genetic diversity in trout. Pyrosequencing-based assays for molecular species identification are expected to be generally useful whenever multiple positions in a short DNA sequence need to be assessed.     

Maintenance of an endemic lineage of brown trout (Salmo trutta) within the Duero river basin

The Iberian Peninsula contains diverse populations of freshwater fish, with major river basins comprising differentiated biogeographic units. The Duero River flows through the North‐Western Iberian Peninsula and is one of the most important rivers within the Iberian glacial refuge. Brown trout (Salmo trutta) populate this whole basin, and studies using both allozyme and microsatellite loci have detected a geographically sorted distribution of genetic variation in this species. In this work, sequences of the mitochondrial control region obtained from 299 brown trout from the Duero River were compared with other Iberian and European datasets. Two differentiated haplotype groups were detected inside the Duero River basin. One of them was related to the Atlantic (AT) lineage that is present in Northern European populations, whereas the other comprised an unique group that was restricted to the inner region of the basin. The amount of divergence of this Duero group from the other brown trout populations studied is consistent with a new trout lineage (Duero, DU) that is endemic to this river basin and that diverged from other Atlantic populations during the Pleistocene. The distribution of the DU and AT quaternary lineages in the Duero River was consistent with the ichthyological pattern described in the basin that originated during the Miocene–Pliocene. Evidence of selective processes that favour the haplotypes of the DU lineage may explain this discrepancy.     

Effects of low pH on the chorion of rainbow trout, Oncorhynchus mykiss, and brown trout, Salmo trutta f. fario

Morphological studies on the effect of low pH on egg shells (chorion) of rainbow trout, Oncorhynrhus mykiss Walbaum (formerly Salmo gairdneri ), and brown trout, Salmo trutta f. fario L., showed that the plugs of the outer layer of the chorion, which block the channels of the underlying layer, developed distinctive vacuolization at low pH exposure. This may lead to loss of chorional semi-permeability. Chorions were incompletely degraded at low pH inducing hatching problems. Partially hatched alevins showed only a small local zone of dissolution of the chorion around the head of the embryo preventing the larvae from being freed.     

Morphological variability among seven populations of brown trout, Salmo trutta L., in Greece

Morphological variation in five meristic and 21 morphometric characters was examined in the brown trout, Salmo trutta L., from seven distinct streams and rivers from N and NW Greece. Variation within each sample, estimated as the multivariate generalization of the coefficient of variation, did not vary substantially among the populations. The phenetic relationships of these populations were examined using the stepwise discriminant analysis. The taxonomic implications of these results are discussed.     

Catecholamine release and interrenal response of brown trout, Salmo trutta, exposed to aluminium in acidic water

Cannulated brown trout, Salmo trutta , were exposed for 36 h to synthetic water with a low calcium content of pH 5 and similar synthetic water dosed with aluminium to raise the filterable A1 from 5 to 290 μg 1⁻¹ over the 36-h period. There were no significant disturbances of plasma concentrations of glucose, cortisol or catecholamine (adrenaline and noradrenaline) in fish held in water of pH 5. The addition of aluminium to this acidic synthetic water resulted in a generalized endocrine stress response with a four-fold increase in plasma glucose concentration after 18 h and a significant increase in plasma cortisol concentration from 24 h onwards when filterable A1 exceeded 200 μg 1⁻¹. Plasma catecholamine concentration indicated an adrenergic stress response in aluminium-exposed brown trout. A transient doubling in noradrenaline after 6 h in A1 was followed by a larger increase in both plasma adrenaline and noradrenaline concentrations in fish surviving the 36-h exposure to A1.     

An intensive study of allozyme variation in freshwater resident and anadromous trout,Salmo trutta L., in western Ireland*

Ten polymorphic enzyme coding loci were assayed using starch gel electrophoresis in anadromous (sea trout) and freshwater-resident trout, Salmo trutta, from two neighbouring river systems draining into Clew Bay in western Ireland. Samples were collected from the Burrishoole and from the neighbouring Newport river system. In the Burrishoole system, two samples were from above waterfalls impassable to migratory trout, two consisted of anadromous smolts or post-smolts and the remainder were freshwater-resident trout from freely accessible areas. There were large differences in gene frequency between trout from above impassable barriers and all others sampled, and these two groups also differed substantially from each other. More minor differences were evident between some other samples, particularly between trout from the upper lake and streams entering it and a stream associated with the lower lake. Two anadromous populations therefore occur in the Burrishoole system. In contrast, no differences were evident in two sampling years between anadromous trout and cohabiting freshwater-resident trout from the upper part of the Burrishoole system. Thus, in the upper part of this system, anadromous trout do not appear to comprise a separate population from non-migratory trout and interbreeding may occur.     

Seasonal and spatial microhabitat selection and segregation in young Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L., in a Norwegian river

Seasonal microhabitat selection by sympatric young Atlantic salmon and brown trout was studied by diving. Both species, especially Atlantic salmon, showed seasonal variation with respect to surface and mean water velocities and depth. This variation is partly attributed to varying water flows and water temperatures. In winter the fish sought shelter in the substratum. A spatial variation in habitat use along the river due to different habitat availabilities was observed. Both species occupied habitats within the ranges of the microhabitat variables, rather than selecting narrow optima. It is hypothesized that the genetic basis allows a certain range to the behavioural response. Microhabitat segregation between the two species was pronounced, with brown trout inhabiting the more slow-flowing and partly more shallow stream areas. Atlantic salmon tolerated a wider range of water velocities and depths. Habitat suitability curves were produced from both species. It is suggested that habitat suitability curves that are based on observations of fish occupancy of habitat at median or base flow may not be suitable in habitat simulation models, where available habitat is projected at substantially greater water flows.     

Cortisol and thyroid hormone responses to acid stress in the brown trout, Salmo trutta L.

Individual cannulated brown trout monitored during exposure to acidic water showed increased plasma cortisol after 3 h at pH 4.0 with low (0.05 mm) or high (2.8 mm) calcium (Ca) content, and after 2 days in acidic water with a high Ca content. Most fish did not survive for 2 days in acidic water with a low Ca content. Non-cannulated fish showed a similar increase in mean plasma cortisol after 2 days in high-Ca acidic water (pH 4.0–4.6), but not in acidic water of a low Ca content. After 7 days of exposure to acidic water, plasma cortisol appeared to recover when there was a high Ca content but increased 20-fold when Ca content was low. In cannulated fish severe acid stress resulted in a marked and rapid thyroid response. Plasma thyroxine (T₄) was elevated after 3 h exposure to acidic water of both low and high Ca content and remained elevated for 2 days of acid exposure with high Ca. In non-cannulated fish an increase in mean T₄ was apparent only after 7 days in low-Ca acidic water. Plasma triiodothyronine (T₃) levels were not significantly altered by any of the acid regimes. Plasma glucose of cannulated fish was elevated within 3 h of acid-exposure and remained elevated after 2 days in high-Ca acidic water.     

Reproductive isolation and genetic differentiation of ferox trout from sympatric brown trout in Loch Awe and Loch Laggan, Scotland

Molecular marker studies reported here, involving allozymes, mitochondrial DNA and microsatellites, demonstrate that ferox brown trout Salmo trutta in Lochs Awe and Laggan, Scotland, are reproductively isolated and genetically distinct from co-occurring brown trout. Ferox were shown to spawn primarily, and possibly solely, in a single large river in each lake system making them particularly vulnerable to environmental changes. Although a low level of introgression seems to have occurred with sympatric brown trout, possibly as a result of human-induced habitat alterations and stocking, ferox trout in these two lakes meet the requirements for classification as a distinct biological, phylogenetic and morphological species. It is proposed that the scientific name Salmo ferox Jardine, 1835 , as already applied to Lough Melvin (Ireland) ferox, should be extended to Awe and Laggan ferox.     

Comparative Analysis of Mitochondrial DNA Diversity in Smelts

The polymerase chain reaction (PCR) was used to amplify a segment of the mitochondrial DNA coding for NADH-dehydrogenase subunits ND5/ND6 in five smelt species (family Osmeridae). Amplified DNA was screened for restriction fragment length polymorphism (RFLP). Nucleotide sequence divergence of mitochondrial DNA between species ranges from 11.9 (between Hypomesus nipponensis and H. japonicus) to 24.7% (between Osmerus mordax dentex and Mallotus villosus catervarius). The genetic divergence between populations of H. nipponensis, H. japonicus, and Osmerus mordax dentex was 0.32, 0.08 to 0.15, and 0.025%, respectively. The absence of common haplotypes enables differentiation of closely related smelt species and, therefore, can be used for solving current problems in the taxonomy and biogeography of this family.     

Endocrine responses of brown trout, Salmo trutta L., to acid, aluminium and lime dosing in a Welsh hill stream

Brown trout caged in an acidic, softwater, Welsh hill stream running through close-canopy conifer forest and in an adjacent, circumneutral, moorland stream were studied after a natural rainfall event and after experimental acid and aluminium dosing of the forest stream. Endocrine (cortisol and thyroxine) and metabolic (glucose) stress responses occurred in fish held in the forest stream. Liming downstream of the acid zones mitigated these responses.     

A comparison of AFLPs and microsatellites to identify the population structure of brown trout (Salmo trutta L.) populations from Hardangervidda, Norway

A total of 495 fish from 11 Hardangervidda lakes were genotyped in order to compare amplified fragment length polymorphisms (AFLP) and microsatellites in terms of their capacity to infer population genetic structure. The 11 microsatellites used in this study gave a greater polymorphism information content and greater gene diversity, with an average of 14.8 alleles per locus, than the six AFLP primer combinations used. However, the AFLPs resulted in 178 polymorphic loci and a 3.1 times larger marker index (effective multiplex ratio multiplied with the gene diversity). Comparable population structuring, for example in terms of distinguishing fish from the different river systems, was obtained with both marker systems. An AFLP and microsatellite multilocus Bayesian assignment test with the structure program divided the fish into six groups largely concurrent with main branches on a population neighbour-joining tree. Yet, the admixture status of individuals is mostly contradictory in the AFLP and the microsatellite analyses. The results are discussed concerning migration between lake populations.