Reticulate evolution: ancient introgression of the Adriatic brown trout mtDNA in softmouth trout Salmo obtusirostris (Teleostei: Salmonidae)

Two populations of softmouth trout ( Salmo obtusirostris ) from the rivers Neretva (Bosnia and Herzegovina) and Jadro (Croatia), along with two neighbouring populations of brown trout ( Salmo trutta ) were analysed with a suite of genetic markers (two mtDNA genes, two nuclear genes, and nine microsatellites) as well as morphological characters. The Jadro softmouth trout were fixed for a brown trout mtDNA haplotype of the Adriatic lineage, which is 1.7% divergent from a previously described haplotype characteristic for the Neretva softmouth trout. All other genetic markers, as well as morphological analysis, supported the clear distinction of softmouth trout from the rivers Neretva and Jadro from brown trout in neighbouring populations, and thus a mtDNA capture event is assumed. Population specific microsatellite allele profiles, as well as a high number of private alleles for both populations of softmouth trout, support the hybridization between brown trout and the Jadro softmouth trout most likely being of ancient origin, thus leading to a reticulate evolutionary pattern of mtDNA in this taxon.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 139–152.     

Genetic variation among trout in the River Neretva basin, Bosnia and Herzegovina

Mitochondrial DNA haplotypes, characteristic of the Adriatic, Danubian and Atlantic lineages of brown trout Salmo trutta and of Salmo obtusirostris were found in trout inhabiting the River Neretva basin. With the exception of the one associated with softmouth trout, haplotypes were not correlated with operational taxonomic units based on phenotype. Nuclear DNA analysis identified four genetic assemblages corresponding to S. obtusirostris , different geographically confined autochthonous S. trutta populations, introduced S. trutta and a genetically heterogeneous group located between S. obtusirostris and S. trutta in the dendrogram of individuals, indicating the existence of hybrid swarms in the Neretva basin. Genetic assemblages corresponding to Salmo marmoratus and the recently proposed Salmo cf. montenigrinus were not detected. The presence of genetic intermediates indicates that the studied taxa are not completely reproductively isolated and that genetic stability has been either anthropogenically interrupted or not yet achieved among Neretva trout. This finding should be considered in management decisions since such an unstable community must be particularly susceptible to breakdown in genetic population structure as a result of hybridization between native and non-native introduced trout stocks.     

DNA phylogeny supports revised classification of Salmothymus obtusirostris

Salmothymus obtusirostris (soft-muzzled trout) is endemic to the South Adriatic drainage. Owing to its unusual appearance, which resembles both trout and grayling, it has been initially classified as a separate genus. However, this classification is ambiguous and has never been firmly established. We have studied mtDNA (control region and cytochrome b gene) and nuclear DNA (a part of LDH C*1 gene) variation between soft-muzzled trout from the upper part of the River Neretva, Bosnia and Herzegovina, and other salmonid representatives in order to examine how the current classification is congruent with molecular data. On the basis of sequence identity of mtDNA control region among several genera (i.e. Salmo , Oncorhynchus , Salvelinus , Acantholingua , Brachymystax , Thymallus and Coregonus ) a close relationship between Salmothymus , Salmo and Acantholingua was established. Phylogenetic analysis on a combined data set of mitochondrial and nuclear DNA, supported by 100% bootstraping, indicated that S. obtusirostris and A. ohridana are sister taxa which exhibit a closer relationship to S. trutta than to S. salar . This finding refutes the current classification, which recognizes S. obtusirostris as separate genus, and instead suggests its reclassification on the species level as Salmo obtusirostris .  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 399–411.     

Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia

Populations of the marble trout (Salmo marmoratus) have declined critically due to introgression by brown trout (Salmo trutta) strains. In order to define strategies for long-term conservation, we examined the genetic structure of the 8 known pure populations using 15 microsatellite loci. The analyses reveal extraordinarily strong genetic differentiation among populations separated by < 15 km, and extremely low levels of intrapopulation genetic variability. As natural recolonization seems highly unlikely, appropriate management and conservation strategies should comprise the reintroduction of pure populations from mixed stocks (translocation) to avoid further loss of genetic diversity.     

An assessment of the spatial scale of local adaptation in brown trout (Salmo trutta L.): footprints of selection at microsatellite DNA loci

Local adaptation is considered a paradigm in studies of salmonid fish populations. Yet, little is known about the geographical scale of local adaptation. Is adaptive divergence primarily evident at the scale of regions or individual populations? Also, many salmonid populations are subject to spawning intrusion by farmed conspecifics that experience selection regimes fundamentally different from wild populations. This prompts the question if adaptive differences between wild populations and hatchery strains are more pronounced than between different wild populations? We addressed these issues by analyzing variation at 74 microsatellite loci (including anonymous and expressed sequence tag- and quantitative trait locus-linked markers) in 15 anadromous wild brown trout (Salmo trutta L.) populations, representing five geographical regions, along with two lake populations and two hatchery strains used for stocking some of the populations. F_ST-based outlier tests revealed more outlier loci between different geographical regions separated by 522±228 km (mean±s.d.) than between populations within regions separated by 117±79 km (mean±s.d.). A significant association between geographical distance and number of outliers between regions was evident. There was no evidence for more outliers in comparisons involving hatchery trout, but the loci under putative selection generally were not the same as those found to be outliers between wild populations. Our study supports the notion of local adaption being increasingly important at the scale of regions as compared with individual populations, and suggests that loci involved in adaptation to captive environments are not necessarily the same as those involved in adaptive divergence among wild populations.     

Evolutionary relationship between marble trout of the northern and the southern Adriatic basin

Marble trout (Salmo marmoratus) populate two geographically separated areas in the northern and southern parts of the Adriatic Sea drainage. Although morphologically similar, each population is distinguished by a different set of unrelated mitochondrial haplotypes, suggesting that they have evolved from different ancestors. Due to a possible discordance between mitochondrial and species phylogeny, we performed phylogenetic analysis based on 22 nuclear loci. The results inferred from Maximum-likelihood and Bayesian Inference analysis revealed that northern and southern populations are closely related, forming a monophyletic group. This observation is concordant with the present marble trout classification, which considers both populations as conspecific. On the other hand, our findings are in marked contrast to those of previous mtDNA-based studies and highlight potential dangers of making phylogenetic inferences from mtDNA alone. Reasons for discordance between mtDNA and nDNA phylogeny are discussed with incomplete lineage sorting proposed as the most parsimonious explanation for mtDNA divergence in marble trout.     

Recent status and life history traits of endangered soft‐mouth trout,Salmo obtusirostris in the River Neretva catchment (Bosnia and Herzegovina) as a consequence of river alteration

Soft‐mouth trout, Salmo obtusirostris has disappeared from most of its historical distribution range in the River Neretva catchment. Remnant groups are highly fragmented and distribution of the species is restricted to only 15% of it's historical area. The most abundant length range of remnant individuals is between 20 and 40 cm; with a significant decrease of the bigger individuals. Age population structure is dominated by younger fish aged 2, 3 and 4 years, however, age class 4⁺ and 6⁺ predominated in the lower river part. Specimens older than 8 years were not observed, and estimated fishing mortality (F) was high, particularly in the upper part of the river (0.786). The River Neretva soft‐mouth trout population is under heavy pressure including anthropogenic habitat changes and illegal fishery, leading to disappearance in number of formerly inhabited areas. The Upper and Lower Neretva are the only areas where the species is still abundant. However, the collapse of the number of old individuals increases the risk of extinction of the remaining wild subpopulations.     

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.     

Biochemical genetic variation in populations of golden trout, Salmo aguabonita: evidence of the threatened Little Kern River golden trout, S.a. whitei.

Eight wild populations of the High Sierra golden trout, Salmo aguabonita, and one domestic stock of rainbow trout, Salmo gairdneri, were examined for biochemical-genetic variation in eight protein systems. Variation within the eight systems was determined by at least 10 loci in both golden and rainbow trout and all the alleles identified in rainbow trout were observed as electro-phoretically identical phenotypes in golden trout. Variation was observed at an average of 51 percent of the loci in the golden trout samples and for five of the 10 loci in the rainbow trout. Average heterozygosity ranged from 12.6 to 13.9 percent for seven of the golden trout populations with one showing a low value of 5.4 percent. A comparable estimate of 12.1 percent was found for the rainbow stock. On the basis of genetic variation and allele frequencies at three loci, the eight golden trout populations were divided into two distinct groups. Three populations sampled from the Little Kern River basin tended to be genetically distinct from two additional Little Kern River basin populations and from three geographically distinct populations sampled from the eastern Kern River area. The former three populations were hypothesized to be of a recent rainbow-golden hybrid origin. Trout in the other two Little Kern River basin populations, sampled in head-waters of a stream tributary to the Little Kern River, were considered to be the threatened Little Kern golden trout, S. a. whitei Evermann, due to their high degree of genetic similarity to the geographically distinct subspecies S. a. aguabonita sampled from the eastern Kern River area. The finding of substantial genetic variation in the wild golden trout populations indicates that this threatened species is not at present genetically impoverished and thus does not appear to be in immediate danger of extinction through lack of adaptive capability.     

Effects of stocking on the genetic diversity of brown trout populations of the Adriatic and Danubian drainages in Switzerland

This study focuses on genetic variation of brown trout Salmo trutta populations of the Adriatic and Danubian drainages in Switzerland. The allozyme and other protein loci data show a major replacement of native stocks from the Adriatic drainages by introduced hatchery trout of Atlantic basin origin. In most samples, diagnostic alleles for the Adriatic form of Salmo trutta f. fario and for the marbled trout Salmo trutta marmoratus are found at very low frequencies (f<0.15). Taking into account previous genetic studies on brown trout of this basin, the Danubian samples are not heavily contaminated with foreign alleles. The results are consistent with records of local stocking activities which account in part for the high introgression rates of Atlantic alleles into local populations of the Adriatic drainages. In addition, introgression is enhanced by a decrease of natural reproduction which is caused by a deterioration of trout habitats through human activities. Furthermore, a third mechanism is proposed that may contribute to the high introgression rates observed: if Atlantic trout are introduced, the reproductive barriers between the two native forms, marbled trout and Adriatic fario respectively, break down. Atlantic trout apparently hybridize with both native forms and generate gene flow between them. In some parts of Adriatic drainages in Switzerland, the patterns of introgression and hybridization are further complicated by introduction of trout from the Danubian system. Alleles of the marbled trout are also found in the samples of the Danubian drainage system. These are due to stocking activities across the watershed.     

Phylogeographic structure and demographic patterns of brown trout in North-West Africa

The objectives of the study were to determine the phylogeographic structure of brown trout (Salmo trutta) in Morocco, elucidate their colonization patterns in North-West Africa and identify the mtDNA lineages involved in this process. We also aimed to resolve whether certain brown trout entities are also genetically distinct. Sixty-two brown trout from eleven locations across the Mediterranean and the Atlantic drainages in Morocco were surveyed using sequence analysis of the mtDNA control region and nuclear gene LDH, and by genotyping twelve microsatellite loci. Our study confirms that in Morocco both the Atlantic and Mediterranean basins are populated by Atlantic mtDNA lineage brown trout only, demonstrating that the Atlantic lineage (especially its southern clade) invaded initially not only the western part of the Mediterranean basin in Morocco but also expanded deep into the central area. Atlantic haplotypes identified here sort into three distinct groups suggesting Morocco was colonized in at least three successive waves (1.2, 0.4 and 0.2-0.1 MY ago). This notion becomes more pronounced with the finding of a distinct haplotype in the Dades river system, whose origin appears to coalesce with the nascent stage of the basal mtDNA evolutionary lineages of brown trout. According to our results, Salmo akairos, Salmo pellegrini and "green trout" from Lake Isli do not exhibited any character states that distinctively separate them from the other brown trout populations studied. Therefore, their status as distinct species was not confirmed.     

Spatial and temporal population structure of sea trout at the Island of Gotland, Sweden, delineated from mitochondrial DNA

In a study of the genetic relationships among 879 anadromous brown trout Salmo trutta from 13 streams at the Island of Gotland, Sweden, using RFLP analysis of a mitochondrial DNA segment (NADH dehydrogenase-1 gene), six haplotypes were detected. Significant genetic divergence was observed among streams as well as between cohorts within streams. Approximately 8–9% of the total variation was due to differences between populations, and 4–5% was explained by differences between cohorts within populations. The female effective population size ( N _ef) was assessed from temporal haplotype frequency differences between consecutive cohorts; the estimated average N _ef over all populations was just below 30, suggesting that these populations were effectively quite small. With such small effective sizes the populations are expected to loose genetic variability quickly, but the observed levels do not appear particularly low. This indicates that female migration between streams occurs. The observed level of differentiation does not support the presumption that a particular pre-smolt migratory behaviour observed in Gotland streams, with large portions of fry leaving for the sea soon after hatching, results in a reduced homing ability. From a conservation management perspective the Gotland brown trout streams should be regarded as a population system where the vitality and survival of brown trout in one stream is dependent on the opportunity of contact and exchange of individuals from other streams.     

Efficiency of Portable Antennas for Detecting Passive Integrated Transponder Tags in Stream-Dwelling Salmonids

Portable antennas have become an increasingly common technique for tracking fish marked with passive integrated transponder (PIT) tags. We used logistic regression to evaluate how species, fish length, and physical habitat characteristics influence portable antenna detection efficiency in stream-dwelling brown trout (Salmo trutta), bull trout (Salvelinus confluentus), and redband trout (Oncorhynchus mykiss newberrii) marked with 12-mm PIT tags. We redetected 56% (20/36) of brown trout, 34% (68/202) of bull trout, and 33% (20/61) of redband trout after a recovery period of 21 to 46 hours. Models indicate support for length and species and minor support for percent boulder, large woody debris, and percent cobble as parameters important for describing variation in detection efficiency, although 95% confidence intervals for estimates were large. The odds of detecting brown trout (1.5 ± 2.2 [mean ± SE]) are approximately four times as high as bull trout (0.4 ± 1.6) or redband trout (0.3 ± 1.8) and species-specific differences may be related to length. Our reported detection efficiency for brown trout falls within the range of other studies, but is the first reported for bull trout and redband trout. Portable antennas may be a relatively unbiased way of redetecting varying sizes of all three salmonid species.     

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.     

Trout Salmo spp. complex in Serbia and adjacent regions of the western Balkans: reconstruction of evolutionary history from external morphology

The multivariate phenetic approach to the classification of Salmo spp. samples from Serbia and adjacent regions of western Balkans for 22 continuous external morphological characters suggests the occurrence of the following distinct stocks: West Danubian (Crno Osoje Stream and upper Zeta River) Salmo taleri , marble trout Salmo marmoratus (Trebuščica River), hatchery-reared Atlantic Salmo trutta , Mlava River drainage (Mlava and Krupaja rivers and Buk Stream) trout Salmo cf. trutta , Velika Morava River system (Godljevača, Bela and Resava rivers) trout S. cf. trutta , Ohrid Lake belvica Salmo ohridana and Aegean coastal drainage Salmo macedonicus (Božica River). In contrast to the phenetic similarity, the phylogenetic reconstruction places the Lake Ohrid belvica as part of an unresolved polytomy with other trout groups. Salmo cf. trutta in the Mlava River appears to form the basal group for the trout species in the region. The position of marble trout implies its independent and more recent origin from the West Danubian trout stock.     

Morphological differentiation among local trout (Salmo trutta) populations

The trout (Salmo trutta) has been divided into three forms: sea-run trout, lake-run brown trout, and resident brown trout. They differ in their living environment, migratory behaviour, growth and appearance. As local trout populations are often isolated, and gene flow between them is minimal, differentiation between populations can be expected. The morphology of 1-year-old trout from ten populations representing all three forms was studied in a common-garden experiment. The fish were reared under similar environmental conditions, and 20 morphometric characters were measured from each individual fish. Marked morphological differentiation was found, and differences between populations were greater than differences between forms. The results suggest that the differences have a genetic basis, and they are likely to indicate adaptation to local environmental conditions in the native habitat of the trout.     

Evaluation of the contribution of supplemental plantings of brown trout Salmo trutta (L.) to a self-sustaining fishery in the Sydenham River, Ontario, Canada

An autumn planting of 4000 tagged yearling brown trout Salmo trutta (L.) in 1969 resulted in an over-winter survival of 26%, an angler recovery the following year of 8·1 % and made up 22 % of the March, 1970 standing population of the species. August standing populations of brown trout increased from 142 trout/ha (17·6 kg/ha) in 1969 to 360 trout/ha (39·3 kg/ha in 1970 while angler harvest of the species increased from 61 trout/ha (12·7 kg/ha) at a rate of 0·26 fish/h to 89 trout/ha (18·5 kg/ha) at a rate of 0·34/h. Using angler recovery and standing population as criteria the planting contributed substantially to the fishery. Actual contribution of stocked trout however, is questioned after detailed analysis of resident population structure and the potential of natural recruitment. It is suggested that the true benefit of stocked trout may be measured by the presence of those stocked fish in excess of the number of resident trout of that size predictable from a normal length distribution curve in waters with self-sustaining populations. Complexities in evaluating the merits of supplemental plantings of hatchery-reared brown trout to existing stream fisheries are examined.     

Is genetic variability so important? Non-native salmonids in South America

Three salmonid species introduced in Patagonian national parks in Argentine have experienced different degrees of expansion. Atlantic salmon Salmo salar is restricted to a few river-lake systems and its populations have been declining over recent years. Both rainbow Oncorhynchus mykiss and brown trout Salmo trutta populations have expanded from their introduction sites and now occupy a wide range of freshwater ecosystems. Genetic variation at the same neutral markers (microsatellite loci) was examined for different populations of the three species acclimatized to the same areas, and compared with that of native populations. Founder effects denoted as reduced variability and great differentiation with respect to the native populations were detected. Significant reduction in variability has not been an obstacle for successful adaptation of rainbow and brown trout, indicating that genetic variability per se cannot be claimed as the reason for their different outcomes in the new habitats.     

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.     

Phylogeography and taxonomic status of trout and salmon from the Ponto‐Caspian drainages,with inferences on European Brown Trout evolution and taxonomy

Current taxonomy of western Eurasian trout leaves a number of questions open; it is not clear to what extent some species are distinct genetically and morphologically. The purpose of this paper was to explore phylogeography and species boundaries in freshwater and anadromous trout from the drainages of the Black and the Caspian Seas (Ponto‐Caspian). We studied morphology and mitochondrial phylogeny, combining samples from the western Caucasus within the potential range of five nominal species of trout that are thought to inhabit this region, and using the sequences available from GenBank. Our results suggest that the genetic diversity of trout in the Ponto‐Caspian region is best explained with the fragmentation of catchments. (1) All trout species from Ponto‐Caspian belong to the same mitochondrial clade, separated from the other trout since the Pleistocene; (2) the southeastern Black Sea area is the most likely place of diversification of this clade, which is closely related to the clades from Anatolia; (3) The species from the Black Sea and the Caspian Sea drainages are monophyletic; (4) except for the basal lineage of the Ponto‐Caspian clade, Salmo rizeensis, all the lineages produce anadromous forms; (5) genetic diversification within the Ponto‐Caspian clade is related to Pleistocene glacial waves; (6) the described morphological differences between the species are not fully diagnostic, and some earlier described differences depend on body size; the differences between freshwater and marine forms exceed those between the different lineages. We suggest a conservative taxonomic approach, using the names S. rizeensis and Salmo labrax for trout from the Black Sea basin and Salmo caspius and Salmo ciscaucasicus for the fish from the Caspian basin.