Loss of genetic integrity correlates with stocking intensity in brook charr (Salvelinus fontinalis)

Supportive breeding and stocking performed with non‐native or domesticated fish to support sport fishery industry is a common practice throughout the world. Such practices are likely to modify the genetic integrity of natural populations depending on the extent of genetic differences between domesticated and wild fish and on the intensity of stocking. The purpose of this study is to assess the effects of variable stocking intensities on patterns of genetic diversity and population differentiation among nearly 2000 brook charr (Salvelinus fontinalis) from 24 lakes located in two wildlife reserves in Québec, Canada. Our results indicated that the level of genetic diversity was increased in more intensively stocked lakes, mainly due to the introduction of new alleles of domestic origin. As a consequence, the population genetic structure was strongly homogenized by intense stocking. Heavily stocked lakes presented higher admixture levels and lower levels of among lakes genetic differentiation than moderately and un‐stocked lakes. Moreover, the number of stocking events explained the observed pattern of population genetic structure as much as hydrographical connections among lakes in each reserve. We discuss the implications for the conservation of exploited fish populations and the management of stocking practices.     

Heritability of life-history tactics and genetic correlation with body size in a natural population of brook charr (Salvelinus fontinalis)

A common dimorphism in life-history tactic in salmonids is the presence of an anadromous pathway involving a migration to sea followed by a freshwater reproduction, along with an entirely freshwater resident tactic. Although common, the genetic and environmental influence on the adoption of a particular life-history tactic has rarely been studied under natural conditions. Here, we used sibship-reconstruction based on microsatellite data and an 'animal model' approach to estimate the additive genetic basis of the life-history tactic adopted (anadromy vs. residency) in a natural population of brook charr, Salvelinus fontinalis. We also assess its genetic correlation with phenotypic correlated traits, body size and body shape. Significant heritability was observed for life-history tactic (varying from 0.52 to 0.56 depending on the pedigree scenario adopted) as well as for body size (from 0.44 to 0.50). There was also a significant genetic correlation between these two traits, whereby anadromous fish were genetically associated with bigger size at age 1 (r(G) = -0.52 and -0.61). Our findings thus indicate that life-history tactics in this population have the potential to evolve in response to selection acting on the tactic itself or indirectly via selection on body size. This study is one of the very few to have successfully used sibship-reconstruction to estimate quantitative genetic parameters under wild conditions.     

Seawater acclimation of diploid and triploid brook charr (Salvelinus fontinalis), diploid Arctic charr (Salvelinus alpinus), and their diploid and triploid hybrids

Seawater acclimation of diploid (FF) and triploid (F2F) brook charr Salvelinus fontinalis , diploid (AA) Arctic charr Salvelinus alpinus , and diploid (FA) and triploid (F2A) hybrids between female brook charr and male Arctic charr was investigated. Triploidization of brook charr and the hybrid did not have any effect on the acclimation. Seawater acclimation of the hybrid was achieved during the experimental period and was comparable to that observed in brook charr. Acclimation could not be ascertained in Arctic charr since the level of cortisol, a stress indicator, was still high at the end of the experiment. No relationship between either length or condition factors and plasma osmolality was observed. Elevated plasma cortisol concentrations in Arctic charr and in diploid or triploid hybrids, both in fresh water and sea water, indicate more favourable rearing conditions for brook charr.     

Genetic discrimination of wild and hatchery populations of brook charr, Salvelinus fontinalis (Mitchill), in Ontario using mitochondrial DNA analysis

Two brood stocks of brook charr, Sulvelinus fontinalis , are currently maintained by the Ontario Ministry of Natural Resources. The Nipigon brood stock originated from Lake Nipigon, in north-central Ontario, while the Hills Lake stock is believed to have been produced by hybridizing several strains (including charr from a Pennsylvania hatchery as well as charr from Ontario) in the past. The mitochondrial DNA (mtDNA) variability of these brood stocks was characterized using 51 hexanucleotide restriction enzymes. Eleven restriction enzymes, Acc I, Am I, Bun I, Bun II, Hind III, Nco I, Nde I, Nhe I, Nsi I, Pst I and Sph I, were polymorphic between the two brood stocks. Eight hatchery mtDNA haplotypes were detected showing a maximum of 0.41 % sequence divergence. Seven haplotypes are present in the Hills Lake strain, and two in the Nipigon strain. These mtDNA haplotypes are useful markers to determine the degree of reproductive success between planted and native fish. In one comparison in southern Ontario, less than 20% of the wild fish sampled from the head water regions of a small drainage entering Lake Erie could have resulted from random introgression with hatchery fish planted further downstream, because most of these fish possessed a unique Acc 1 cut site. This is one of the few examples in stock analysis studies where such a high degree of genetic discrimination is evident between hatchery and native fish.     

Microsatellite and mitochondrial DNA assessment of population structure and stocking effects in Arctic charr Salvelinus alpinus (Teleostei: Salmonidae) from central Alpine lakes

Despite geographical isolation and widespread phenotypic polymorphism, previous population genetic studies of Arctic charr, Salvelinus alpinus , have detected low levels of intra- and interpopulation variation. In this study, two approaches were used to test the generality of low genetic diversity among 15 Arctic charr populations from three major drainages of the central Alpine region of Europe. First, a representative subsample of each drainage was screened by PCR–RFLP analysis of mtDNA using 31 restriction enzymes. All individuals but one shared an identical haplotype. In contrast, microsatellite DNA variation revealed high levels of genetic diversity within and among populations. The number of alleles per locus ranged from six to 49, resulting in an overall expected heterozygosity from 0.72 ± 0.09 to 0.87 ± 0.04 depending on the locus. Despite evidence for fish transfers among Alpine charr populations over centuries, genetic diversity was substantially structured, as revealed by hierarchical Φ statistics. Eighteen per cent of total genetic variance was apportioned to substructuring among Rhône, Rhine, and Danube river systems, whereas 19% was due to partitioning among populations within each drainage. Cluster analyses corroborated these results by drainage-specific grouping of nonstocked populations, but also revealed damaging effects of stocking practices in others. However, these results suggest that long-term stocking practices did not generally alter natural genetic partitioning, and stress the importance of considering genetic diversity of Arctic charr in the Alpine region for sound management. The results also refute the general view of Arctic charr being a genetically depauperate species and show the potential usefulness of microsatellite DNAs in addressing evolutionary and conservation issues in this species.     

Microsatellite variation and genetic structure of brook trout (Salvelinus fontinalis) populations in Labrador and neighboring Atlantic Canada: evidence for ongoing gene flow and dual routes of post-Wisconsinan colonization

In conservation genetics and management, it is important to understand the contribution of historical and contemporary processes to geographic patterns of genetic structure in order to characterize and preserve diversity. As part of a 10-year monitoring program by the Government of Newfoundland and Labrador, Canada, we measured the population genetic structure of the world's most northern native populations of brook trout (Salvelinus fontinalis) in Labrador to gather baseline data to facilitate monitoring of future impacts of the recently opened Trans-Labrador Highway. Six-locus microsatellite profiles were obtained from 1130 fish representing 32 populations from six local regions. Genetic diversity in brook trout populations in Labrador (average H(E)= 0.620) is within the spectrum of variability found in other brook trout across their northeastern range, with limited ongoing gene flow occurring between populations (average pairwise F(ST)= 0.139). Evidence for some contribution of historical processes shaping genetic structure was inferred from an isolation-by-distance analysis, while dual routes of post-Wisconsinan recolonization were indicated by STRUCTURE analysis: K= 2 was the most likely number of genetic groups, revealing a separation between northern and west-central Labrador from all remaining populations. Our results represent the first data from the nuclear genome of brook trout in Labrador and emphasize the usefulness of microsatellite data for revealing the extent to which genetic structure is shaped by both historical and contemporary processes.     

Influences of logging history and riparian forest characteristics on macroinvertebrates and brook trout (Salvelinus fontinalis) in headwater streams (New Hampshire, U.S.A.)

1. Logging can strongly affect stream macroinvertebrate communities, but the direction and magnitude of these effects and their implications for trout abundance are frequently region‐specific and difficult to predict. 2. In first‐order streams in northern New England (U.S.A.) representing a chronosequence of logging history (<2 to >80 years since logging), we measured riparian forest conditions, stream macroinvertebrate community characteristics and brook trout (Salvelinus fontinalis) abundance. Principal component analysis was used to collapse forest data into two independent variables representing variation in logging history, riparian forest structure and canopy cover. We used these data to test whether logging history and associated forest conditions were significant predictors of macroinvertebrate abundance and functional feeding group composition, and whether brook trout abundance was related to logging‐associated variation in invertebrate communities. 3. Catchments with high PC1 scores (recently logged, high‐density stands with low mean tree diameter) and low PC2 scores (low canopy cover) had significantly higher total macroinvertebrate abundance, particularly with respect to chironomid larvae (low PC2 scores) and invertebrates in the grazer functional feeding group (high PC1 scores). In contrast, proportional representation of macroinvertebrates in the shredder functional feeding group increased with time since logging and canopy cover (high PC2 scores). Brook trout density and biomass was significantly greater in young, recently logged stands (high PC1 scores) and was positively related to overall macroinvertebrate abundance. In addition, three variables – trout density, invertebrate abundance and shredder abundance – successfully discriminated between streams that were less‐impacted versus more‐impacted by forestry. 4. These results indicate that timber harvest in northern New England headwater streams may shift shredder‐dominated macroinvertebrate communities supporting low trout abundance to a grazer/chironomid‐dominated macroinvertebrate community supporting higher trout abundance. However, while local effects on brook trout abundance may be positive, these benefits may be outweighed by negative effects of brook trout on co‐occurring species, as well as impairment of habitat quality downstream. Research testing the generality of these patterns will improve understanding of how aquatic ecosystems respond to anthropogenic and natural trajectories of forest change.     

Mitochondrial DNA diversity among four sympatric morphs of Arctic charr, Salvelinus alpinus L., from Thingvallavatn, Iceland

Restriction fragment length polymorphisms in mitochondrial DNA (mtDNA) were examined in progeny of four sympatric morphs of Arctic charr ( Salvelinus alpinus L.) from Thingvallavatn, Iceland. The mtDNA analysis with 46 hexanucleotide restriction enzymes indicates that the Thingvallavatn morphs are very closely related. Sequence divergence was less than 0.2% between any of the five clones detected. Although not significant, the topology of the mtDNA UPGMA dendogram was similar to that from a previous allozyme survey. Icelandic Arctic charr show greater affinity to charr from the British Isles than those from North America supporting their current taxonomic distinction.     

Geographical extent of Arctic char (Salvelinus alpinus) mtDNA introgression in brook char populations (S. fontinalis) from eastern Québec, Canada

The geographical extent of Arctic char ( Salvelinus alpinus ) mitochondrial DNA introgression into brook char ( Salvelinus fontinalis ) populations found in eastern Québec was determined by analysing a total of 598 fish from 29 lakes. The nuclear genome was analysed by protein electrophoresis, whereas the ND-5,6 portion of the mitochondrial genome was analysed by restriction fragment length polymorphism. This survey revealed that introgressed S. fontinalis populations are restricted to only one river subdrainage of the Portneuf basin, where Arctic char is completely absent. Elsewhere, nonintrogressed pure S. fontinalis populations populate the lakes. These findings suggest that the initial hybridization event between the species is ancient and probably occurred shortly after recolonization of the area. At that time, the species would have been in contact and the chances of reproductive isolation mechanisms breaking down would have been high. We discuss the possibility that a combination of biogeographical conditions coupled with positive selection for mtDNA introgression led to the present-day distribution of introgressed S. fontinalis in northeastern North America.     

Genetic relationships among populations of wild resident, and wild and hatchery anadromous brook charr

To determine the genetic relationship of anadromous and resident life-history types within and among drainages, and compare several hatchery strains to their progenitor populations, brook charr Salvelinus fontinalis were examined for allozyme and mitochondrial DNA variation. Greater genetic similarity of sympatric anadromous and resident charr was found compared to similar life-history forms allopatrically, suggesting the two life-history types are not reproductively isolated. Low divergence among the mtDNA haplotypes suggests that the two life-history types are members of the same evolutionary lineage. Population differentiation from mtDNA data exceeded that from estimates based on allozymes. Genetic deviations from expectations suggest that the hatchery strains were derived from few individuals.     

Genetic variation,inheritance, and quaternary structure of malic enzyme in brook trout (Salvelinus fontinalis)

Electrophoretic variation is described for malic enzyme (ME) for the first time in brook trout (Salvelinus fontinalis). Since the quaternary structure of ME was not clear from examination of banding patterns in brook trout alone, ME phenotypes in rainbow trout (Salmo gairdneri) × brook trout hybrids as well as in esocid species demonstrated that ME is tetrameric. A model of two duplicated loci is proposed to account for the observed variation. One locus (ME-2) is fixed and one locus (ME-1) is variable with three electrophoretically distinct alleles; the protein products of ME-1 are reduced in activity relative to the protein products of ME-2. Joint segregation was examined between ME-1 and ten other biochemical loci in brook trout, and between ME-1, ME-2, and nine other biochemical loci in a splake—lake trout (Salvelinus namaycush) × brook trout hybrid—backcross. All pairwise examinations showed random assortment except ME-2 with an isocitrate dehydrogenase locus (IDH-3), which showed complete linkage in the splake backcross. This may be due to a chromosomal aberration.Authorized for publication as Paper No. 5599 in the Journal Series of The Pennsylvania Agricultural Experiment Station, University Park, Pennsylvania, in cooperation with the Benner Spring Fish Research Station, The Pennsylvania Fish Commission, Bellefonte, Pennsylvania. M.S. was supported by an NSF Graduate Fellowship.     

The effect of salty diets and gradual transfer to sea water on osmotic adaptation, gill Na+, K+-ATPase activation, and survival of brook charr, Salvelinus fontinalis, Mitchill

The intensity and duration of the period of osmotic disturbance during introduction of brook charr into sea water were decreased by introducing the fish according to a gradient of salinity over a period of 6 days. Survival in summer increased from 25 to 90% with the use of a salinity gradient. However, kinetics and levels of activation of the gill Na⁺, K⁺-ATPase were not affected by the mode used for introducing brook charr into sea water. Neither was its level of activity modified by the use of a salted diet when the fish were in fresh water. The addition of 8 and 12% of salt to the diet prevented the plasma electrolyte surge of concentrations during the first days in sea water. In very cold water, survival rate was also drastically improved by giving an 8% salted diet during the 6 weeks preceding the introduction into sea water. These results show that both salty diets and exposure to brackish water during 6 days help brook charr face osmotic stress and improve their survival rate when introduced into full-strength sea water. The combined use of these preconditioning strategies might facilitate rearing this species in sea cages or silos.     

Distribution of mitochondrial DNA variation in lake sturgeon (Adpenser fulvescens) from the Moose River basin, Ontario, Canada

We analysed mitochondrial DNA (mtDNA) variation of lake sturgeon ( Adpenser fulvescens ) from the Moose River basin. Our objective was to address various proximate and ultimate factors which may influence the distribution of lake sturgeon mtDNA haplotype lineages in this watershed. The lake sturgeon sampled were characterized by only two mtDNA hapiotypes based on a restriction fragment length polymorphism analysis with 40 restriction endonucleases and direct sequencing of 275 nucleotides in the mtDNA control region. We detected no heterogeneity in the mtDNA haplotype frequencies of lake sturgeon captured from different sites within rivers including those separated by major hydroelectric installations. However, lake sturgeon from one tributary had significantly different haplotype frequencies than those from other tributaries suggesting that they composed a discrete genetic stock. These results suggest that gene flow among most sites is significant and is an important factor affecting the distribution of mtDNA variation in this species. The genetic structuring and diversity are discussed in relation to lake sturgeon management and conservation.     

Phylogeography and population history of the endangered golden sun moth (Synemon plana) revealed by allozymes and mitochondrial DNA analysis

A combination of allozyme and mitochondrial DNA markers were used to determine the contribution of recent and ancient causes of patterns of genetic variation within and among 46 populations of the endangered golden sun moth, Synemon plana. Allozyme analysis grouped the 46 populations into 5 major genetic clusters that corresponded closely with geographic location following a classic isolation-by-distance model. Phylogenetic analysis of 14 mtDNA haplotypes revealed two reciprocally monophyletic groups. One of these groups (containing 4 geographically distant populations) was clearly identified by allozyme analysis and represents a distinct evolutionary unit. The remaining 4 allozyme groups were not distinguishable by mtDNA analysis. The evidence suggests that the populations within these groups derived from a small founding population that underwent rapid demographic expansion in ancient times. This was followed by more recent population bottlenecks resulting from habitat fragmentation associated with the widespread introduction of agriculture into the region. The generally low levels of allozyme and nucleotide diversity within these populations support this hypothesis. This revised version was published online in July 2006 with corrections to the Cover Date.     

Mitochondrial DNA variation and population genetic structure of the white-clawed crayfish, Austropotamobius pallipes pallipes

Here we report a high level of mtDNA variationfrom RFLP analysis within A. p. pallipes from 21 French and 4British populations. Seventeen haplotypes were recorded among 269individuals. Nucleotide sequence divergence (p) among mtDNAhaplotypes ranged from 0.0019 to 0.0425. Nucleotide diversity ()ranged from 0.01 to 0.006 (mean = 0.0031) and from 0 to 0.001(mean = 0.00037) for populations located in southern and northernFrance, respectively. Graphical representation from principalcoordinate analysis based on Nei's genetic distance values amongpopulations showed two groups, cluster A, including the 16populations sampled in the north-western and north-easternFrance, England and Wales and cluster B containing 9 populationssampled in the central and southern of France. No geneticdifferences were noted among the most northern French and Englishpopulations whereas marked interpopulation genetic diversity wasobserved in southern populations. Such genetic heterogeneityamong populations of A. p. pallipes appears to be related tohabitat fragmentation and subsequent recolonizations fromrefugial areas during the Pleistocene. Implications for theconservation of A. p. pallipes are discussed.     

Gene flow and lack of population differentiation in Atlantic cod, Gadus morhua L., from Iceland, and comparison of cod from Norway and Newfoundland

Restriction analysis of mitochondrial DNA was used to study genetic variation and geographic population structure of Atlantic cod from localities around Iceland. Gene phylogenies were constructed and geographic locations superimposed on these. The variation was not localized. Estimated gene flow was large. Thus, Atlantic cod in Iceland belong to a single genetic population. Analyses of published sequence variation of cod from Norway and Newfoundland showed that the extensive continuity of intraspecific phylogeny of cod in Iceland, which is very similar to other marine organisms with a similar life history, extends from Norway to Newfoundland and possibly to larger areas of the Atlantic.     

Genetic diversity and structuring of the grey wolf population from the Central Balkans based on mitochondrial DNA variation

The Dinaric-Balkan grey wolf population used to be at a border between the large remaining Eastern European populations and the largely eradicated Western European populations. During the last few decades we have witnessed the Western European wolf population recovery. Substantial genetic variation has previously been reported in the Balkan wolf population, but rigorous genetic characterization has not been done for its central parts. The aims of this research were to determine genetic diversity based on mtDNA sequence variability, to infer possible population structuring, to find genetic signals of population expansions or bottlenecks and to evaluate phylogenetic position of the grey wolf population from the Central Balkans. Six haplotypes were detected, of which three have only been found in the Balkan region. These haplotypes belong to both haplogroups previously determined in Europe. Based on our mtDNA sequence analyses, the Dinaric-Balkan wolf population is vertically differentiated into “western” (Croatia/Bosnia and Herzegovina) and “eastern” (Serbia/Macedonia) subpopulations. None of the results support assumption of population expansion. Instead, significantly positive values for Tajima's D and Fu's Fs may suggest recent population bottleneck. Obtained data may be helpful in observation to which extent gene pool from the Balkans contribute to newly founded populations in Western Europe.     

Large discrepancies in differentiation of allozymes, nuclear and mitochondrial DNA loci in recently founded Pacific populations of the pearl oyster Pinctada margaritifera

This study presents a comparative analysis of population structure applied to the pearl oyster (Pinctada margaritifera) from the Central Pacific islands using three classes of molecular markers: two mitochondrial genes (mtDNA), five anonymous nuclear loci (anDNA), and eight polymorphic allozymes. Very low levels of haplotype diversity and nucleotidic divergence detected for mtDNA validate the hypothesis of a recent (re)colonization of Polynesian lagoons after their exondation during the last glaciations. Some nuclear loci, however, showed highly significant FST values, indicating a reduced amount of larval exchange between archipelagos at present. A large interlocus variance of FST was nevertheless observed. We discuss whether this pattern is inherent to the stochasticity of the drift process since recolonization, or if it could result from balancing selection acting on certain loci. This study illustrates once more the need to combine the analysis of several kinds of loci when unrelated phenomena are likely to leave their footprints on genetic structure.     

Population structure and gene flow of the Atlantic walrus (Odobenus rosmarus rosmarus) in the eastern Atlantic Arctic based on mitochondrial DNA and microsatellite variation

The population structure of the Atlantic walrus, Odobenus rosmarus rosmarus , was studied using 11 polymorphic microsatellites and restriction fragment length polymorphism detected in the NADH-dehydrogenase ND1, ND2 and ND3/4 segments in mtDNA. A total of 105 walrus samples were analysed from northwest (NW) Greenland, east (E) Greenland, Svalbard and Franz Joseph Land. Two of the 10 haplotypes detected in the four samples were diagnostic for the NW Greenland sample, which implied that the group of walruses in this area is evolutionary distinct from walruses in the other three areas. One individual sampled in E Greenland exhibited a Pacific haplotype, which proved a connection between the Pacific walrus and walruses in eastern Greenland. The Franz Joseph Land, Svalbard and E Greenland samples shared the most common haplotype, indicating very little differentiation at the mtDNA level. Gene flow ( Nm ) estimates among the four areas indicated a very restricted exchange of female genes between NW Greenland and the more eastern Atlantic Arctic samples, and a closer relationship between the three samples composing the eastern Atlantic Arctic. The genetic variation at 11 polymorphic microsatellite loci grouped individuals into three populations, NW Greenland, E Greenland and a common Franz Joseph Land–Svalbard population, which were connected by moderate gene flow.