The rise and fall of isolation by distance in the anadromous brook charr (Salvelinus fontinalis Mitchill)

Geographic patterns of genetic diversity depend on a species' demographic properties in a given habitat, which may change over time. The rates at which patterns of diversity respond to changes in demographic properties and approach equilibrium are therefore pivotal in our understanding of spatial patterns of diversity. The brook charr Salvelinus fontinalis is a coastal fish exhibiting limited marine movements, such that a stable one-dimensional isolation-by-distance (IBD) pattern should be observed over the whole range. Its range, however, recently shifted northward such that northern populations may still be in the process of reaching equilibrium. We investigated variation in IBD patterns, genetic divergence, and allelic richness at six microsatellite markers in 2087 anadromous brook charr from 59 rivers along the most likely postglacial colonization route. We observed a decrease in allelic richness, together with an increase in differentiation and a decrease in IBD in the most recently colonized northern populations, as expected following recent colonization. Contrary to expectation, however, similar patterns were also observed at the southernmost part of the range, despite the fact that these populations are not considered to be newly colonized. We propose that the loss of dispersal capabilities associated with anadromy may have caused the southernmost populations to evolve relatively independently of one another. This study thus demonstrated that changes in a species' geographic range and dispersal capabilities may contribute to shaping geographic patterns of genetic diversity.     

Environmental factors associated with genetic and phenotypic divergence among sympatric populations of Arctic charr (Salvelinus alpinus)

The mechanisms by which phenotypic and genetic divergence may occur among sympatric, conspecific populations have been widely discussed but are still not well understood. Possible mechanisms include assortative mating based on morphology or variation in the reproductive behaviour of phenotypes, and both have been suggested to be relevant to the differentiation of salmonid populations in post-glacial lakes. Here, we studied Arctic charr (Salvelinus alpinus) in Windermere, where putative populations are defined by spatial and temporal variation in spawning. Genetic differentiation was assessed based on nine microsatellite loci, and phenotypic variation was assessed from morphometric characters. We test hypotheses about the relative role of morphology, spawning season and spawning habitat in the evolution of genetic divergence among these populations. Distinct from other lake systems, we find that both morphological and genetic differentiation are restricted primarily to one of two interconnecting basins, that genetic and morphological differentiation are decoupled in this lake and that both phenotype and environment have changed over the last 20 years. The implication is that breeding habitat plays a primary role in isolating populations that differentiate by drift and that phenotypically plastic changes, potentially related to foraging specializations, have either become secondarily decoupled from the genetically defined populations or were never fundamental in driving the evolution of genetic diversity in the Windermere system.     

Distinguishing between juvenile anadromous and resident brook trout (Salvelinus fontinalis) using morphology

Phenotypic variation linked to habitat use has been observed in fish, both between and within species. In many river systems, migratory and resident forms of salmonids coexist, including anadromous (migrant) and resident brook trout, Salvelinus fontinalis. In such populations, juvenile anadromous (migrant) brook trout, prior to migration, inhabit regions of higher current velocity than residents. Because it is more costly to occupy fast currents than slow currents, differences in morphology minimizing the effects of drag were expected between the two forms. As predicted, migrant brook trout were found to be more streamlined (narrower and shallower bodies) than resident brook trout, and these differences persisted into the marine life of the fish. Migrants also exhibited shorter pectoral fins, which facilitate pelagic swimming, indicating that migrants, prior to their migration to the sea, possess the appropriate morphology for swimming in open water habitats. The reported differences between migrants and residents were powerful enough to derive discriminant functions, using only five of the seven measured traits, allowing for accurate classification of brook trout as either migrants or residents with an overall correct classification rate of 87%. Importantly, this study contributes to the notion that a link exists between morphology, habitat use, metabolic costs and life-history strategies. Contribution to the program of CIRSA (Centre Interuniversitaire de Recherche sur le Saumon Atlantique).     

A comparative mitogenomic analysis of the potential adaptive value of Arctic charr mtDNA introgression in brook charr populations (Salvelinus fontinalis Mitchill)

Wild brook charr populations (Salvelinus fontinalis) completely introgressed with the mitochondrial genome (mtDNA) of arctic charr (Salvelinus alpinus) are found in several lakes of northeastern Québec, Canada. Mitochondrial respiratory enzymes of these populations are thus encoded by their own nuclear DNA and by arctic charr mtDNA. In the present study we performed a comparative sequence analysis of the whole mitochondrial genome of both brook and arctic charr to identify the distribution of mutational differences across these two genomes. This analysis revealed 47 amino acid replacements, 45 of which were confined to subunits of the NADH dehydrogenase complex (Complex I), one in the cox3 gene (Complex IV), and one in the atp8 gene (Complex V). A cladistic approach performed with brook charr, arctic charr, and two other salmonid fishes (rainbow trout [Oncorhynchus mykiss] and Atlantic salmon [Salmo salar]) revealed that only five amino acid replacements were specific to the charr comparison and not shared with the other two salmonids. In addition, five amino acid substitutions localized in the nad2 and nad5 genes denoted negative scores according to the functional properties of amino acids and, therefore, could possibly have an impact on the structure and functional properties of these mitochondrial peptides. The comparison of both brook and arctic charr mtDNA with that of rainbow trout also revealed a relatively constant mutation rate for each specific gene among species, whereas the rate was quite different among genes. This pattern held for both synonymous and nonsynonymous nucleotide positions. These results, therefore, support the hypothesis of selective constraints acting on synonymous codon usage.     

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.     

Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis)

Salmonid fishes rank among species being most severely affected by introgressive hybridization as a result of a long tradition of stocking with hatchery-reared conspecifics. The objectives of this study were (i) to evaluate the genetic consequences of stocking and resulting introgression rates on the genetic integrity of natural populations of brook charr, (ii) to identify genomic regions potentially associated with adaptation to natural and artificial rearing environments, and (iii) to test the null hypothesis that introgression from domesticated brook charr into wild populations is homogeneous among loci. A total of 336 individuals were sampled from nine lakes, which were stocked at different intensities with domestic fish. Individuals were genotyped at 280 SNPs located in transcribed regions and developed by means of next-generation sequencing. As previously reported with microsatellites, we observed a positive relationship between stocking intensity and genetic diversity among stocking groups, and a decrease in population differentiation. Individual admixture proportions also increased with stocking intensity. Moreover, genomic cline analysis revealed 27 SNPs, seven of which were also identified as outliers in a genome scan, which showed an introgression rate either more restricted or enhanced relative to neutral expectations. This indicated that selection, mainly for growth-related biological processes, has favored or hampered the introgression of genomic blocks into the introgressed wild populations. Overall, this study highlights the usefulness of investigating the impact of stocking on the dynamics of introgression of potentially adaptive genetic variation to better understand the consequences of such practice on the genomic integrity of wild populations.     

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.     

The influence of gene-environment interactions on GHR and IGF-1 expression and their association with growth in brook charr, Salvelinus fontinalis (Mitchill)

Background

Information transfer systems in Archaea, including many components of the DNA replication machinery, are similar to those found in eukaryotes. Functional assignments of archaeal DNA replication genes have been primarily based upon sequence homology and biochemical studies of replisome components, but few genetic studies have been conducted thus far. We have developed a tractable genetic system for knockout analysis of genes in the model halophilic archaeon, Halobacterium sp. NRC-1, and used it to determine which DNA replication genes are essential.

Results

Using a directed in-frame gene knockout method in Halobacterium sp. NRC-1, we examined nineteen genes predicted to be involved in DNA replication. Preliminary bioinformatic analysis of the large haloarchaeal Orc/Cdc6 family, related to eukaryotic Orc1 and Cdc6, showed five distinct clades of Orc/Cdc6 proteins conserved in all sequenced haloarchaea. Of ten orc/cdc6 genes in Halobacterium sp. NRC-1, only two were found to be essential, orc10, on the large chromosome, and orc2, on the minichromosome, pNRC200. Of the three replicative-type DNA polymerase genes, two were essential: the chromosomally encoded B family, polB1, and the chromosomally encoded euryarchaeal-specific D family, polD1/D2 (formerly called polA1/polA2 in the Halobacterium sp. NRC-1 genome sequence). The pNRC200-encoded B family polymerase, polB2, was non-essential. Accessory genes for DNA replication initiation and elongation factors, including the putative replicative helicase, mcm, the eukaryotic-type DNA primase, pri1/pri2, the DNA polymerase sliding clamp, pcn, and the flap endonuclease, rad2, were all essential. Targeted genes were classified as non-essential if knockouts were obtained and essential based on statistical analysis and/or by demonstrating the inability to isolate chromosomal knockouts except in the presence of a complementing plasmid copy of the gene.

Conclusion

The results showed that ten out of nineteen eukaryotic-type DNA replication genes are essential for Halobacterium sp. NRC-1, consistent with their requirement for DNA replication. The essential genes code for two of ten Orc/Cdc6 proteins, two out of three DNA polymerases, the MCM helicase, two DNA primase subunits, the DNA polymerase sliding clamp, and the flap endonuclease.     

Parasites of freshwater resident and anadromous Arctic charr (Salvelinus alpinus) in Greenland

Twenty-one metazoan parasite species were found in Arctic charr at three coastal sites in west Greenland, including Neascus sp. and the nematode Pseudoterranova decipiens , new records for Arctic charr. Twelve species are new records for Arctic charr in Greenland. The quantitative composition of the parasite communities varied, but the freshwater species ( Diphyllobothrium ditremwn, Eubothriutn salvelini, Proteocephalus longicollis, Crepidostotnutn farianis ) were usually numerically dominant, even in anadromous fish. The absence from Greenland of Mysidacea, Amphipoda, Ephemeroptera and Odonata excludes parasites requiring such organisms as intermediate hosts, including the cestode Cyathocephalus truncatus , nematodes of the genus Cystidicola , and freshwater acanthocephalans.     

Water temperature, light intensity and zooplankton density and the feeding activity of juvenile brook charr (Salvelinus fontinalis)

SUMMARY 1. The objective of this study was to evaluate the effects of zooplankton biomass (as a measure of density), fish biomass, light intensity and water temperature on the attack rate and swimming characteristics (i.e. swimming speed and angle of turn) of juvenile (1+) brook charr (Salvelinus fontinalis) in field enclosures. We used a portable underwater camera system in a series of pelagic enclosures to quantify the feeding behaviour of brook charr over a gradient of natural conditions. 2. In simple linear or non‐linear regression models we found (i) that attack rate and angle of turn were positively related to water temperature, (ii) that attack rate and swimming speed were positively related to zooplankton biomass and light intensity and (iii) that attack rate was positively related to swimming speed. In multiple regression models, fish biomass, light intensity and variance of the angle of turn accounted for 87% of the variation in attack rate. Light intensity and water temperature accounted for 86% of the variation in swimming speed. Fish gut fullness and attack rate accounted for 83% of the variation in the variance of the angle of turn executed by fish. 3. The increase in the number of attacks as zooplankton biomass increases conforms to the general positive functional response observed in other fish species. Our results also support the hypothesis that swimming speed increases with prey biomass. We did not observe a plateau in attack rate as zooplankton biomass increased. As our experiments were performed under natural biotic and abiotic conditions, factors other than zooplankton biomass might affect or limit this response, such as water temperature and light intensity. 4. Because zooplankton biomass was correlated with water temperature and light intensity, it was not possible to evaluate the independent contribution of these factors on the attack rate and swimming characteristics (swimming speeds and angle of turn) of brook charr. However, this study highlighted the impact of these factors on the feeding behaviour of juvenile brook charr when feeding in the pelagic habitat under natural conditions, and their importance in future models of optimal foraging and fish habitat quality.     

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.     

Breeding success of male brook trout (Salvelinus fontinalis) in the wild

Competition for females generally results in some males adopting alternative reproductive tactics to acquire matings. For fish, the ecological and evolutionary consequences of these tactics are not well understood because of an inability to link directly the interactions of individuals on the breeding grounds with genetic data. This study combines behavioural observations with genetic estimates of male reproductive success within an intensively studied wild population of lacustrine brook trout (Salvelinus fontinalis). Male brook trout exhibit a conditional reproductive strategy with small males adopting a peripheral position to that of larger dominant males in their proximity to spawning females. Parentage analysis of eggs collected from wild redds confirmed the reproductive success of individual males. Males relegated to peripheral positions during spawning participated frequently in spawning events, but in most cases the first male to spawn was the sole contributor, and no more than two males contributed successfully to a single brood. While behavioural observations of salmonines suggests that reproduction is partitioned among males in a manner dependent upon body size and proximity to spawning females, the genetic evidence from this study suggests a more limited distribution of reproductive success in the field. The genetic contributions of male brook trout are highly skewed towards larger males for this population. A review of the salmonine literature suggests little difference in individual reproductive success for males exhibiting size-related tactics within a conditional mating strategy vs. precocial maturation. Collectively, these genetic studies provide new insights on the evolution of alternative life histories among salmonines.     

Abundance and distribution of Salmincola edwardsii (Copepoda) on anadromous brook trout, Salvelinus fontinalis, (Mitchill) in the Moisie River system, Quebec

Riviere a la Truite, a tributary of the Moisie River, is probably a focus of Salmincola edwardsii transmission within the system. Differences in prevalence of the copepod on fish between Riviére à la Truite and the main river suggested that up to 41% of anadromous brook trout, Salvelinus fontinalis , in the Moisie River system overwinter in the tributary. Infected fish were generally less than 200 mm long and copepods were attached almost exclusively to the fins and their bases. The primary site of copepod attachment at low intensities of infection was the adipose fin but at high intensities the dorsal fin was most frequently infected. This displacement in attachment location with increased intensity may result in density-dependent mortality of copepods. Copepods were overdispersed on the host population at each major sampling time and data fit a negative binomial distribution (k ranged from 0.2 to 0.8).     

Action spectrum and quantal thresholds of retinomotor responses in the brook trout,Salvelinus fontinalis (Mitchill)

Summary The radiant energy per unit area required to trigger retinomotor responses was determined for eight wavelengths. The curve's maximum at 520 nanometres corresponds to two microwatts per steradian per square metre. The threshold requires the absorption of 7000 quanta per second per square degree of the field by the scotopic pigment.

---

Zusammenfassung Die je Einheitsbereich erforderliche Strahlungsenergie für die Auslösung der retinomotorischen Reaktion wurde für acht Wellenlängen gemessen. Das Maximum der Kurve (520 Nanometer) entspricht zwei Mikrowatt pro Steradian pro Quadratmeter. Im Bereiche des Schwellenwertes ist eine Absorption des Feldes durch das skotopische Pigment von 7000 Quanten pro Sekunde, pro Quadratgrad benötigt.

---

---

Supported by a grant from the National Research Council of Canada.     

Pollination genetics of hybridization in sympatric populations of asclepias exaltata and a. syriaca (asclepiadaceae)

Enzyme electrophoresis of pollinia and seeds was used to identify pollinia on pollinators, interspecific pollinations, and hybrid seed production in sympatric populations of Asclepias exaltata and A. syriaca. The frequency of mixed pollinia loads on pollinators was low. Only 4.1% (N= 169 pollinia) and 8% (N= 244 pollinia) of the pollinia collected from pollinators of A. syriaca and A. exaltata, respectively, were identified as pollinia from the other species. Natural levels of interspecific pollination, 3.6% (N = 166 pollinia) on A. syriaca and 3.1% (N = 228 pollinia) on A. exaltata, were typically lower than the number of foreign pollinia carried by pollinators. Hybrid seeds were identified in only two of 208 A. syriaca fruits and one of 178 A. exaltata fruits. Hybrid seeds were largely underdeveloped in the single A. exaltata fruit. High fruit set (34.7%) and near normal seed set following hand-pollination of A. syriaca with A. exaltata pollinia suggest that hybridization is more likely between these taxa when A. syriaca is the maternal parent. Our findings indicate that the likelihood of hybridization between A. exaltata and A. syriaca is remote. Nevertheless, introgressive hybridization has been documented in these species, which suggests that hybridization remains a strong evolutionary force even for species that infrequently interbreed.     

Behavioural plasticity of lake charr (Salvelinus namaycush) x brook charr (S. fontinalis) F1 hybrids in response to varying social environment

Lake x brook F₁ hybrid charr were observed in heterogeneous groups with lake charr or brook charr to assess the effects of different species on hybrid social behaviour. Levels of behavioural plasticity were low in relation to the behavioural differences between the parental and hybrid types. Feeding behaviour showed the most dramatic change, with higher levels in the lake charr treatment and lower levels in the brook charr treatment than controls, suggesting social facilitation. Even though only two measures varied significantly between treatments, there was a tendency for the frequencies and durations of all agonistic measures to increase in the presence of lake charr and decrease with brook charr. A cost-benefit argument is presented to account for this trend.     

Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus Fontinalis Mitchill (Pisces,Salmonidae): a test of alternative hypotheses

Empirical studies of natural populations have commonly reported departures from Hardy-Weinberg expected proportions of heterozygote individuals. Recent advances in statistical population genetics now offer the potential to exploit individual multilocus genotypic information to test more rigorously for possible sources of heterozygote deficiencies. In a previous study in lacustrine brook charr (Salvelinus fontinalis), we reported stronger deficits in small than in large lakes. In the present paper, we propose a methodology for empirically testing alternative hypotheses to identify the cause of the deficits observed in three of the smallest lakes (85, 109 and 182 ha) analysed. First, as in several salmonid species, brook charr may exhibit a trophic polymorphism in north temperate lakes. If morphs are genetically divergent, indiscriminate sampling of both forms would result in less heterozygote individuals than expected in a randomly mating population (Wahlund effect). Using an individual-based method aiming at detecting cryptic population structure, we can reject this explanation as the sole source of deficits for all three lakes. Secondly, mating among relatives could also be frequent in small lakes and lead to heterozygote deficiencies. Significantly more fish than expected at random had low individual multilocus heterozygosity in two of the lakes, suggesting that inbred fish may have been present. Thirdly, sampling of genetically related fish would also lead to departures from Hardy-Weinberg proportions. In the same two lakes, the distribution of pairwise relatedness coefficients departed from its random expectation, suggesting that non-random sampling of kin may have occurred.