Postglacial genetic differentiation of reproductive ecotypes of kokanee Oncorhynchus nerka in Okanagan Lake, British Columbia

Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales

The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan® SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.

An assessment of terminology for intraspecific diversity in fishes, with a focus on "ecotypes" and "life histories"

Understanding and preserving intraspecific diversity (ISD) is important for species conservation. However, ISD units do not have taxonomic standards and are not universally recognized. The terminology used to describe ISD is varied and often used ambiguously. We compared definitions of terms used to describe ISD with use in recent studies of three fish taxa: sticklebacks (Gasterosteidae), Pacific salmon and trout (Oncorhynchus spp., "PST"), and lampreys (Petromyzontiformes). Life history describes the phenotypic responses of organisms to environments and includes biological parameters that affect population growth or decline. Life-history pathway(s) are the result of different organismal routes of development that can result in different life histories. These terms can be used to describe recognizable life-history traits. Life history is generally used in organismal- and ecology-based journals. The terms paired species/species pairs have been used to describe two different phenotypes, whereas in some species and situations a continuum of phenotypes may be expressed. Our review revealed overlapping definitions for race and subspecies, and subspecies and ecotypes. Ecotypes are genotypic adaptations to particular environments, and this term is often used in genetic- and evolution-based journals. "Satellite species" is used for situations in which a parasitic lamprey yields two or more derived, nonparasitic lamprey species. Designatable Units, Evolutionary Significant Units (ESUs), and Distinct Population Segments (DPS) are used by some governments to classify ISD of vertebrate species within distinct and evolutionary significant criteria. In situations where the genetic or life-history components of ISD are not well understood, a conservative approach would be to call them phenotypes.

Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka)

Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.

Hawksbill turtle terra incognita: conservation genetics of eastern Pacific rookeries

Prior to 2008 and the discovery of several important hawksbill turtle (Eretmochelys imbricata) nesting colonies in the EP (Eastern Pacific), the species was considered virtually absent from the region. Research since that time has yielded new insights into EP hawksbills, salient among them being the use of mangrove estuaries for nesting. These recent revelations have raised interest in the genetic characterization of hawksbills in the EP, studies of which have remained lacking to date. Between 2008 and 2014, we collected tissue samples from 269 nesting hawksbills at nine rookeries across the EP and used mitochondrial DNA sequences (766 bp) to generate the first genetic characterization of rookeries in the region. Our results inform genetic diversity, population differentiation, and phylogeography of the species. Hawksbills in the EP demonstrate low genetic diversity: We identified a total of only seven haplotypes across the region, including five new and two previously identified nesting haplotypes (pooled frequencies of 58.4% and 41.6%, respectively), the former only evident in Central American rookeries. Despite low genetic diversity, we found strong stock structure between the four principal rookeries, suggesting the existence of multiple populations and warranting their recognition as distinct management units. Furthermore, haplotypes EiIP106 and EiIP108 are unique to hawksbills that nest in mangrove estuaries, a behavior found only in hawksbills along Pacific Central America. The detected genetic differentiation supports the existence of a novel mangrove estuary "reproductive ecotype" that may warrant additional conservation attention. From a phylogeographic perspective, our research indicates hawksbills colonized the EP via the Indo-Pacific, and do not represent relict populations isolated from the Atlantic by the rising of the Panama Isthmus. Low overall genetic diversity in the EP is likely the combined result of few rookeries, extremely small reproductive populations and evolutionarily recent colonization events. Additional research with larger sample sizes and variable markers will help further genetic understanding of hawksbill turtles in the EP.

Genetic evidence for ecological divergence in kokanee salmon

The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has provided tools for investigating the genetic basis of this process in natural populations of nonmodel organisms. Kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), occurs as two reproductive ecotypes, which differ in spawning habitat (tributaries vs. shorelines); however, outside of the spawning season the two ecotypes co-occur in many lakes and lack diagnostic morphological characteristics. We used restriction site-associated DNA (RAD) sequencing to identify 6145 SNPs and genotype kokanee from multiple spawning sites in Okanagan Lake (British Columbia, Canada). Outlier tests revealed 18 loci putatively under divergent selection between ecotypes, all of which exhibited temporally stable allele frequencies within ecotypes. Six outliers were annotated to sequences in the NCBI database, two of which matched genes associated with early development. There was no evidence for neutral genetic differentiation; however, outlier loci demonstrated significant structure with respect to ecotype and had high assignment accuracy in mixed composition simulations. The absence of neutral structure combined with a small number of highly divergent outlier loci is consistent with theoretical predictions for the early stages of ecological divergence. These outlier loci were then applied to a realistic fisheries scenario in which additional RAD sequencing was used to genotype kokanee collected by trawl in Okanagan Lake, providing preliminary evidence that this approach may be an effective tool for conservation and management.

Speciation in Freshwater Fishes

The extraordinary species richness of freshwater fishes has attracted much research on mechanisms and modes of speciation. We here review research on speciation in freshwater fishes in light of speciation theory, and place this in a context of broad-scale diversity patterns in freshwater fishes. We discuss several major repeated themes in freshwater fish speciation and the speciation mechanisms they are frequently associated with. These include transitions between marine and freshwater habitats, transitions between discrete freshwater habitats, and ecological transitions within habitats, as well as speciation without distinct niche shifts. Major research directions in the years to come include understanding the transition from extrinsic environment-dependent to intrinsic reproductive isolation and its influences on species persistence and understanding the extrinsic and intrinsic constraints to speciation and how these relate to broad-scale diversification patterns through time.

Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon

Background

Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit (AtpA) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat.

Results

We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats.

Conclusions

We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with environmental sampling to better understand the ecology of pathogen infection in this species.

Electronic supplementary material

The online version of this article (doi:10.1186/1756-0500-7-778) contains supplementary material, which is available to authorized users.

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.

Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon

Background

High throughput next-generation sequencing technology has enabled the collection of genome-wide sequence data and revolutionized single nucleotide polymorphism (SNP) discovery in a broad range of species. When analyzed within a population genomics framework, SNP-based genotypic data may be used to investigate questions of evolutionary, ecological, and conservation significance in natural populations of non-model organisms. Kokanee salmon are recently diverged freshwater populations of sockeye salmon (Oncorhynchus nerka) that exhibit reproductive ecotypes (stream-spawning and shore-spawning) in lakes throughout western North America and northeast Asia. Current conservation and management strategies may treat these ecotypes as discrete stocks, however their recent divergence and low levels of gene flow make in-season genetic stock identification a challenge. The development of genome-wide SNP markers is an essential step towards fine-scale stock identification, and may enable a direct investigation of the genetic basis of ecotype divergence.

Results

We used pooled cDNA samples from both ecotypes of kokanee to generate 750 million base pairs of transcriptome sequence data. These raw data were assembled into 11,074 high coverage contigs from which we identified 32,699 novel single nucleotide polymorphisms. A subset of these putative SNPs was validated using high-resolution melt analysis and Sanger resequencing to genotype independent samples of kokanee and anadromous sockeye salmon. We also identified a number of contigs that were composed entirely of reads from a single ecotype, which may indicate regions of differential gene expression between the two reproductive ecotypes. In addition, we found some evidence for greater pathogen load among the kokanee sampled in stream-spawning habitats, suggesting a possible evolutionary advantage to shore-spawning that warrants further study.

Conclusions

This study provides novel genomic resources to support population genetic and genomic studies of both kokanee and anadromous sockeye salmon, and has the potential to produce markers capable of fine-scale stock assessment. While this RNAseq approach was successful at identifying a large number of new SNP loci, we found that the frequency of alleles present in the pooled transcriptome data was not an accurate predictor of population allele frequencies.

High male incidence and evolutionary implications of triploid form in northeast Asia Carassius auratus complex

Carassius auratus complex is believed to originate from East Eurasia and consist of diploid and triploid forms. Diploid form reproduces sexually, whereas triploid form possesses mixture modes of unisexual gynogenesis and sexual reproduction, which makes it a unique case to study evolutionary issues among vertebrates. In this study, we identified 337 triploid individuals from 386 specimens of Carassius auratus complex sampled from 4 different sites of Xingkai Lake and Suifen River on the northeast Asia transboundary areas of Russia and China, and found that triploids were ubiquitous, whereas diploids existed only in SII site of Suifen River. Triploid males were detected in all surveyed sites, and an unusually high triploid male incidence (23%) was found in the Chinese reach of Suifen River. Then, nuclear and cytoplasmic markers were used to analyze their genetic diversity and phylogenetic relationship. A total of 61 distinct tf alleles and 35 mtDNA CR haplotypes were revealed. Higher genetic diversity and divergence were confirmed in triploids than in diploids, and identical genetic background between triploid males and females was demonstrated. Moreover, evolutionary implications and roles of triploid males were suggested in population proliferation and diversity creation of the triploid form.

Detection of outlier loci and their utility for fisheries management

Genetics-based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where gene flow persists. In such cases, genetic markers exhibiting locus-specific (‘outlier’) effects associated with divergent selection may provide promising alternatives to loci that reflect genome-wide (‘neutral’) effects for guiding fisheries management. Okanagan Lake kokanee (Oncorhynchus nerka), a fishery of conservation concern, exhibits two sympatric ecotypes adapted to different reproductive environments; however, previous research demonstrated the limited utility of neutral microsatellites for assigning individuals. Here, we investigated the efficacy of an outlier-based approach to fisheries management by screening >11 000 expressed sequence tags for linked microsatellites and conducting genomic scans for kokanee sampled across seven spawning sites. We identified eight outliers among 52 polymorphic loci that detected ecotype-level divergence, whereas there was no evidence of divergence at neutral loci. Outlier loci exhibited the highest self-assignment accuracy to ecotype (92.1%), substantially outperforming 44 neutral loci (71.8%). Results were robust among-sampling years, with assignment and mixed composition estimates for individuals sampled in 2010 mirroring baseline results. Overall, outlier loci constitute promising alternatives for informing fisheries management involving recently diverged stocks, with potential applications for designating management units across a broad range of taxa.

Predictability of phenotypic differentiation across flow regimes in fishes

Fish inhabit environments greatly varying in intensity of water velocity, and these flow regimes are generally believed to be of major evolutionary significance. To what extent does water flow drive repeatable and predictable phenotypic differentiation? Although many investigators have examined phenotypic variation across flow gradients in fishes, no clear consensus regarding the nature of water velocity's effects on phenotypic diversity has yet emerged. Here, I describe a generalized model that produces testable hypotheses of morphological and locomotor differentiation between flow regimes in fishes. The model combines biomechanical information (describing how fish morphology determines locomotor abilities) with ecological information (describing how locomotor performance influences fitness) to yield predictions of divergent natural selection and phenotypic differentiation between low-flow and high-flow environments. To test the model's predictions of phenotypic differentiation, I synthesized the existing literature and conducted a meta-analysis. Based on results gathered from 80 studies, providing 115 tests of predictions, the model produced some accurate results across both intraspecific and interspecific scales, as differences in body shape, caudal fin shape, and steady-swimming performance strongly matched predictions. These results suggest that water flow drives predictable phenotypic variation in disparate groups of fish based on a common, generalized model, and that microevolutionary processes might often scale up to generate broader, interspecific patterns. However, too few studies have examined differentiation in body stiffness, muscle architecture, or unsteady-swimming performance to draw clear conclusions for those traits. The analysis revealed that, at the intraspecific scale, both genetic divergence and phenotypic plasticity play important roles in phenotypic differentiation across flow regimes, but we do not yet know the relative importance of these two sources of phenotypic variation. Moreover, while major patterns within and between species were predictable, we have little direct evidence regarding the role of water flow in driving speciation or generating broad, macroevolutionary patterns, as too few studies have addressed these topics or conducted analyses within a phylogenetic framework. Thus, flow regime does indeed drive some predictable phenotypic outcomes, but many questions remain unanswered. This study establishes a general model for predicting phenotypic differentiation across flow regimes in fishes, and should help guide future studies in fruitful directions, thereby enhancing our understanding of the predictability of phenotypic variation in nature.

Interplay between ecological, behavioural and historical factors in shaping the genetic structure of sympatric walleye populations (Sander vitreus)

Disentangling ecological, behavioural and evolutionary factors responsible for the presence of stable population structure within wild populations has long been challenging to population geneticists. This study primarily aimed at decoding population structure of wild walleye (Sander vitreus) populations of Mistassini Lake (Québec, Canada) in order to define source populations to be used for the study of spatial partitioning using individual-based multilocus assignment methods, and decipher the dynamics of individual dispersal and resulting patterns of spatial resource partitioning and connectivity among populations. A second objective was to elucidate the relationships between biological characteristics (sex, size, age and population of origin) and an individual's probability to migrate and/or disperse. To do so, a total of 780 spawning individuals caught on five distinct spawning sites, and 1165 postspawning individuals, captured over two sampling seasons (2002-2003) were analysed by means of eight microsatellite loci. Four temporally stable walleye populations associated with distinct reproductive grounds were detected. These populations were differentially distributed among lake sectors during their feeding migration and their spatial distribution was stable over the two sampling seasons. Dispersing individuals were identified (n=61); these revealed asymmetrical patterns of dispersal between populations, which was also confirmed by divergent admixture proportions. Regression models underlined population of origin as the only factor explaining differential dispersal of individuals among populations. An analysis of covariance (ancova) indicated that larger individuals tended to migrate from their river of origin further away in the lake relative to smaller fish. In summary, this study underlined the relevance of using individual-based assignment methods for deciphering dynamics of connectivity among wild populations, especially regarding behavioural mechanisms such as differential spatial partitioning and dispersal responsible for the maintenance of genetic population structure.

Mitochondrial DNA differentiation between two forms of trout Salmo letnica, endemic to the Balkan Lake Ohrid, reflects their reproductive isolation

Mitochondrial haplotype diversity in sympatric populations of Ohrid trout, Salmo letnica was investigated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mtDNA control region and ND1, ND3/4, ND5/6 segments. A 310 bp fragment at the 5' end, and a 340-572 bp fragment at the 3' end of the control region were sequenced from representatives of the populations studied. Based on pairwise comparison of the sequences, five new haplotypes were identified plus one identical with the brown trout Andalusian haplotype from the southern Iberian Peninsula. The combination of both RFLP and sequence data sets yielded a total of 10 composite haplotypes. A high degree of genetic subdivision between S. letnica typicus and S. letnica aestivalis populations was observed. The notion of a sympatric origin for the two morphs is discussed. Length variation of the mtDNA control region due to the presence of an 82 bp unit, tandemly repeated one to four times, in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA is reported. Further, we demonstrate that a single duplication of the approximately 82 bp repeat unit is a common element of the salmonid mitochondrial control region. The unique genetic structure of Ohrid trout represents a highly valuable genetic resource that deserves appropriate management and conservation.

Consequences of unequal population size, asymmetric gene flow and sex-biased dispersal on population structure in brook charr (Salvelinus fontinalis)

Unravelling relationships between dispersal and population structure requires considering the impacts of assumption violations of indirect gene flow models in a given system. We combined temporal, individual and coalescent-based analyses of microsatellite DNA variation to explore the general hypothesis that unequal effective population size (Ne), asymmetric gene flow (m) and nonrandom (sex-biased) individual dispersal had an important effect on spatiotemporal population structuring in lake-dwelling brook charr (Salvelinus fontinalis). This integrative examination shed light on the dichotomous structuring observed between an outlet and three tributary-spawning populations and their potential for adaptive divergence. It revealed further that finer tributary population structuring incongruent with drainage structure has been shaped by asymmetric m from one population with a large Ne towards two populations of smaller Ne. Gene flow among the tributaries was also mediated mainly by male-biased dispersal. However, longer distance dispersal from tributaries to the outflow was female-biased. Spatially dependent sex-biased dispersal may have contributed therefore to gene flow at different levels of population structuring. Our results demonstrate how dispersal and population structure may interrelate to produce spatial variation in intraspecific diversity, and are therefore relevant for conservation programmes seeking to define conservation units or predict recolonization rates of extirpated populations.

Bimodal run distribution in a northern population of sockeye salmon (Oncorhynchus nerka): life history and genetic analysis on a temporal scale

Life history variation and genetic differentiation were analysed in sockeye salmon in Klukshu River, Yukon Canada over 7 years (1994-2000). Sockeye salmon return to the Klukshu River in two distinct runs, with a small 'early run' in June-August, and a larger 'late run' in August-September. A maximum likelihood test for clusters indicated that the return frequency distribution was bimodal in all the years analysed. Life history differences (fork length, sex ratio, age at maturity, fresh- and saltwater residency times) were found between the early and late runs; however, inconsistent patterns suggest that environmental effects outweigh, or strongly interact with, genetic effects for the life history characters evaluated. Analysis of variation at eight microsatellite loci showed that the early and late runs are genetically differentiated in all years examined (exact test). FST estimates between runs within years were significantly greater than zero (range: 0.018-0.041) for all years except one (0.004). The genetic variance explained by early vs. late runs (2.27%) was twice the variance among years (1.16%) based on analysis of molecular variance. Our neighbour-joining tree showed early and late runs generally clustering separately, indicating higher gene flow among the early or late run fish across years relative to between-run gene flow. Two years did not fit the general clustering pattern; although the early and late runs in 1995 and 2000 were genetically differentiated, they clustered separately from the rest of the groups. We cannot offer a definitive explanation for these anomalies; however, an analysis of possible cryptic population structure in early and late runs indicated that at least a few fish strayed between the runs in each year, and the highest rate of mixing was in 1995 and 2000. Our data indicate that the runs are at least partially reproductively isolated as a result of temporal and/or spatial isolating mechanisms. Such reproductive isolation has important implications for conservation and management of the Klukshu sockeye salmon, and make them an evolutionarily interesting group because of parallels with incipient speciation.

Divergent selection maintains adaptive differentiation despite high gene flow between sympatric rainbow smelt ecotypes (Osmerus mordax Mitchill)

In this study, we investigate the relative role of historical factors and evolutionary forces in promoting population differentiation in a new case of sympatric dwarf and normal ecotypes of the rainbow smelt (Osmerus mordax Mitchill) in Lac Saint-Jean (Québec, Canada). Our first objective was to test the hypothesis that the evolution of sympatric smelt ecotypes in Lac Saint-Jean has been contingent upon the secondary contact between two evolutionary lineages in postglacial times. Secondly, the QST method was applied to test the null hypothesis that the extent of phenotypic differences relative to that of neutral marker variation would be similar in comparisons involving populations within and among ecotypes. Thirdly, we applied a quantitative-genetic method as an exploratory assessment as to whether the amount of gene flow observed between populations could affect divergence in adaptive traits under specific conditions. This study revealed a unique situation of dwarf and normal smelt ecotypes that are, respectively, characterized by selmiparous and iteroparous life histories and the occurrence in each of two genetically distinct populations that synchronously use the same spawning habitat in two tributaries. Historical contingency has apparently played little role in the origin of these populations. In contrast, an important role of divergent natural selection in driving their phenotypic divergence was suggested. While divergent selection has apparently been strong enough to maintain phenotypic differentiation in the face of migration, this study suggests that gene flow has been sufficiently important to modulate the extent of adaptive differentiation being achieved between ecotypes, unless the extent of stabilizing selection acting on smelt ecotypes is much more pronounced than usually reported in natural populations.

Mitochondrial DNA diversity in Atherina boyeri populations as determined by RFLP analysis of three mtDNA segments

The genetic differentiation and the phylogenetic relationships of eight Atherina boyeri Greek populations have been investigated at the mtDNA level. The populations studied are from two different lakes, a lagoon, the interface zone between the lagoon and the sea, and four marine sites. RFLP analysis of three mtDNA segments (12s rRNA, 16s rRNA and D-loop) amplified by PCR was used. Six, seven and eight restriction enzymes were found to have at least one recognition site at 12s rRNA, 16s rRNA and D-loop respectively. Twenty-one different haplotypes were detected among the populations studied. Several restriction patterns were revealed. These patterns can be used for the discrimination of the populations living in the sea ('marine' type populations) from the others inhabiting the lagoon and the lakes ('lagoon' type populations). The estimated net nucleotide sequence divergence between the populations examined ranged from 0 to 10.385%, while the Nst value of 0.92 indicates the existence of high interpopulation genetic differentiation. This high degree of differentiation detected between the 'lagoon' and 'marine' type populations makes the classification of these two types of populations as a single taxon questionable.

Adaptive divergence and the balance between selection and gene flow: lake and stream stickleback in the Misty system

We investigated the interplay between natural selection and gene flow in the adaptive divergence of threespine stickleback (Gasterosteus aculeatus) that reside parapatrically in lakes and streams. Within the Misty Lake system (Vancouver Island, British Columbia), stickleback from the inlet stream (flowing into the lake) have fewer gill rakers and deeper bodies than stickleback from the lake--differences thought to facilitate foraging (benthic macroinvertebrates in the stream vs. zooplankton in the open water of the lake). Common-garden experiments demonstrated that these differences have a genetic basis. Reciprocal transplant enclosure experiments showed that lake and inlet stickleback grow best in their home environments (although differences were subtle and often not significant). Release-recapture experiments in the inlet showed that lake fish are less well-suited than inlet fish for life in the stream (higher mortality or emigration in lake fish). Morphological divergence in the wild and under common rearing was greater between the lake and the inlet than between the lake and the outlet. Genetic divergence (mitochondrial DNA and microsatellites) was greatest between the lake and the upper inlet (1.8 km upstream from the lake), intermediate between the lake and the lower inlet (0.9 km upstream), and least between the lake and the outlet stream (1.2 km downstream). Relative levels of gene flow estimated from genetic data showed the inverse pattern. The negative association between morphological divergence and gene flow is consistent with the expectation that gene flow can constrain adaptation. Estimated absolute levels of gene flow also implied a constraint on adaptation in the outlet but not the inlet. Our results suggest that natural selection promotes the adaptive divergence of lake and stream stickleback. but that the magnitude of divergence can be constrained by gene flow.

Inferring sex-biased dispersal from population genetic tools: a review

Sex-biased dispersal, where individuals of one sex stay or return to their natal site (or group) to breed while individuals of the other sex are prone to disperse, is a wide-spread pattern in vertebrate organisms. In general, mammals exhibit male-biased dispersal whereas birds exhibit female-bias. Dispersal estimates are often difficult to obtain from direct field observations. Here we describe different methods for inferring sex-specific dispersal using population genetic tools and discuss the problems they can raise. We distinguish two types of methods: those based on bi-parental markers (eg comparison of male/female relatedness, F(st) and assignment probabilities) and those relying on the comparison between markers with different modes of inheritance (eg mtDNA markers and microsatellites). Finally, we discuss statistical problems that are encountered with these different methods (eg pseudoreplication, problems due to the comparison of distinct markers). While the genetic methods to detect sex-biased dispersal are now relatively well developed, their interpretation can prove problematic due to the confounding effects of factors such as the mating system of the species. Moreover, the relative power of these methods is not well known and requires further investigation.

A rapid fish radiation associated with the last sea-level changes in southern Brazil: the silverside Odontesthes perugiae complex

Coastal freshwater fishes provide valuable models for studying the role of the last glaciations in promoting speciation. To date, the great majority of studies are of Northern Hemisphere taxa, and reflect the influence of vicariant events during, or prior to, the Pleistocene. Microsatellite markers and mitochondrial DNA sequences were used to investigate patterns of population divergence and evolutionary relationships in a freshwater group of silverside fishes (Odontesthes perugiae complex), endemic to the recently formed coastal plain of southern Brazil. Lacustrine morphotypes showed concordant patterns of genetic and morphological divergence consistent with the geographical history of the coastal plain. The results support the proposal of a silverside radiation chronologically shaped by the sea-level changes of the Pleistocene and Holocene. The radiating lineage comprises a minimum of three allopatric and two sympatric lacustrine species. Four species displayed extremely high levels of genetic variation and some of the most rapid speciation rates reported in fishes. These features were related to a marine-estuarine origin of the radiation. To the best of our knowledge, this study represents the first molecular phylogeographic survey of a coastal radiation in South America.

Fine-scale genetic structure, estuarine colonization and incipient speciation in the marine silverside fish Odontesthes argentinensis

The identification of incipient ecological species represents an opportunity to investigate current evolutionary process where adaptive divergence and reproductive isolation are associated. In this study we analysed the genetic structure of marine and estuarine populations of the silverside fish Odontesthes argentinensis using nine microsatellite loci and 396 bp of the mitochondrial DNA (mtDNA) control region. Our main objective was to investigate the relationship among estuarine colonization, divergent selection and speciation in silversides. Significant genetic structure was detected among all marine and estuarine populations. Despite the low phylogeographic structure in mtDNA haplotypes, there was clear signal of local radiations of haplotypes in more ancient populations. Divergence among marine populations was interpreted as a combined result of homing behaviour, isolation by distance and drift. On the other hand, ecological shifts due to the colonization of estuarine habitats seem to have promoted rapid adaptive divergence and reproductive isolation in estuarine populations, which were considered as incipient ecological species. This conclusion is supported by the existence of a set of environmental factors required for successful reproduction of estuarine ecotypes. The pattern of genetic structure indicates that phenotypic and reproductive divergence evolved in the face of potential gene flow between populations. We suggest that the 'divergence-with-gene-flow' model of speciation may account for the diversification of estuarine populations. The approach used can potentially identify 'incipient estuarine species', being relevant to the investigation of the evolutionary relationships of silversides in several coastal regions of the world.

Lacustrine spatial distribution of landlocked Atlantic salmon populations assessed across generations by multilocus individual assignment and mixed-stock analyses

The objective of this study was to assess the spatiotemporal distribution of four landlocked Atlantic salmon (Salmo salar) populations during their sympatric feeding phase in lake St-Jean (Québec, Canada). A total of 1100 fish captured over a period of 25 years was genotyped at six microsatellite loci in order to assess the temporal stability of the relative proportion of each population in different lake sectors using both individual-based assignment and mixed-stock analysis. Estimates of relative proportions obtained from both methods were highly correlated. A nonrandom spatial distribution of populations was observed for each period and, despite the fact that the overall proportion of each population varied over time, the pattern of differential distribution remained generally stable over time. Furthermore, there were indications that the extent of horizontal spatial overlap among populations was negatively correlated with that of their genetic differentiation at both microsatellites and a major histocompatibility complex locus, and independent of the geographical distance between the rivers of origin. We discuss the hypothesis that the temporal stability of spatial distribution, the lack of an association between spatial partitioning and geographical distance between rivers of origin, and the apparent negative correlation between spatial overlap and genetic differentiation, reflect the outcome of selective pressures driving behavioural differences for spatial niche partitioning among populations.

Rapid evolution of reproductive isolation in the wild: evidence from introduced salmon

Colonization of new environments should promote rapid speciation as a by-product of adaptation to divergent selective regimes. Although this process of ecological speciation is known to have occurred over millennia or centuries, nothing is known about how quickly reproductive isolation actually evolves when new environments are first colonized. Using DNA microsatellites, population-specific natural tags, and phenotypic variation, we tested for reproductive isolation between two adjacent salmon populations of a common ancestry that colonized divergent reproductive environments (a river and a lake beach). We found evidence for the evolution of reproductive isolation after fewer than 13 generations.

Congruence between allozyme and cytochrome b gene sequence data in assessing genetic differentiation within the Iberian endemic Chondrostoma lemmingii (Pisces: cyprinidae)

To understand further the fragmentation of the hydrographical basins and the processes of divergence and speciation of freshwater fishes of the Iberian Peninsula, 10 populations of the Iberian endemic cyprinid Chondrostoma lemmingii were studied using 26 loci encoding 19 enzymes and the complete nucleotide sequence of the mitochondrial cytochrome b gene. Nuclear and mitochondrial DNA markers showed complete congruence in assessing the genetic differentiation among the samples analysed. This congruence was supported by a Mantel test in which a significant correlation (r=0.89) between Nei's genetic distances and sequence divergence (uncorrected p distances) was obtained. Diagnostic loci, Nei's genetic distances, and FST values, as well as the percentage of sequence divergence indicate that the Duero basin population accumulates the highest level of genetic differentiation. A moderate divergence was also observed among populations of the rest of the basins. Phenetic and phylogenetic relationships support the hypothesis that the differentiation process was not only due to hydrographical basin isolation but also due to an ancient endorrheism event, previous to hydrographical configuration, that could explain the marked differentiation of the Duero basin population.

Determination of the complete nucleotide sequence and haplotypes in the D-loop region of the mitochondrial genome in the oriental white stork, Ciconia boyciana

The complete nucleotide sequence of the mitochondrial genome of the Oriental white stork, Ciconia boyciana, has been determined from captive storks by a novel method incorporating Long PCR and shotgun sequencing. 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes were identified as in other vertebrate mitochondrial genomes. The position and direction of the NADH6 and tRNA-Glu genes were the same as previously reported for avian mitochondrial genomes. A 71 bp direct repeat and long CAAA repeat sequences were found at the 3' end of the D-loop region, together with SCB-1, SCB-2, SCB-3, and three TAS sequences. Direct sequencing of the PCR fragments in the D-loop region in 26 captive Oriental white storks originating from Japan, China, and Russia revealed nucleotide differences at 18 sites along 1,248 bp, and a total of nine haplotypes have been identified. It was found that one pair of individuals in the Japanese captive breeding program were of the same haplotype, suggesting that they were caught from the same nest. The pair has since been dissolved in consideration of the possibility of inbreeding depression.

Matrilineal genetic structure and female-mediated gene flow in red grouse (Lagopus lagopus scoticus): an analysis using mitochondrial DNA

DNA sequence variation at the hypervariable 5' end of the mitochondrial control region was examined in 247 individuals to detect genetic divergence among 14 populations of red grouse (Lagopus lagopus scoticus) in northeastern Scotland. Ten haplotypes were resolved, several of which were shared among populations. Analysis of molecular variance, Nei's gamma ST, and a cladistic estimate of the amount of gene flow indicated a lack of overall population differentiation. Patterns of overall panmixia are in stark contrast to previous reports of localized subdivision among the same set of populations detected using hypervariable microsatellite markers. Because grouse cocks are territorial and show extreme natal philopatry and females are the dispersing sex, such discordance could be explained by sex-biased dispersal, with extensive female-mediated gene flow preventing mitochondrial DNA divergence. However, it is difficult to reconcile how effective dispersal of females would not homogenize both mitochondrial and nuclear structure simultaneously. We use a model that examines the spatial and temporal dynamics of diparentally and uniparentally inherited genes to show that, under realistic ecological scenarios and with specific differences in the dispersal of males and females, the local effective size of the nuclear genome can be less than that of the mitochondrial and the patterns of structuring we observe are meaningful.

Genetic differentiation and phylogenetic relationships among greek silurus glanis and silurus aristotelis (Pisces, siluridae) populations, assessed by PCR-RFLP analysis of mitochondrial DNA segments

Mitochondrial DNA diversity of seven Silurus glanis populations (six from Greece and one from the Danube Delta) and three populations of the endemic Greek Silurus aristotelis was investigated. RFLP analysis of four regions of mitochondrial DNA (cytochrome b, D-loop, ND-5/6) amplified by PCR was used. Ten and nine haplotypes were found in S. glanis and S. aristotelis, respectively. No haplotype was shared between the two species. Significant geographical substructuring was observed in the distribution of haplotypes, with most populations possessing private haplotypes. These haplotypes can serve as genetic 'tags' and therefore warrant protection. Haplotype diversity was very low for all Greek S. glanis populations, possibly because the small size and large annual fluctuations of Greek inland waters do not support large fish populations. Nucleotide divergence was in the range of 0.00-0.52% among S. glanis populations, and 0. 00-0.11% among S. aristotelis populations. Historical factors such as glaciations could account for these low values. The value of 6. 75% sequence divergence of the two species refutes the classification of the two species in different genera, as proposed by some authors. This study constitutes the first attempt, based on mitochondrial molecular data, to address the complicated evolutionary history of the two species which belong to the widely distributed and economically important Siluridae family.

Rheotactic response of fry from beach-spawning populations of sockeye salmon: evolution after selection is relaxed

Rheotactic response was quantified for newly emerged sockeye salmon (Oncorhynchus nerka) fry from a beach population (Pleasure Point) and from an adjacent inlet population (Cedar River). The Pleasure Point population was small in number and had been established by straying from the much larger Cedar River population no more than 13 generations previously. When tested in laboratory raceways, fry from the Cedar River population were displaced downstream in the dark but not in the light. Such behavior is typical of inlet populations and presumably reflects selection for rapid movement to rearing lakes with minimal losses to predation. Fry from the Pleasure Point population showed greater downstream displacement than the Cedar River fry. Behavioral divergence of the Pleasure Point population could not be explained by selection, because water movement was absent from the beach environment. Genetic drift appeared to be a more plausible divergence mechanism. We suggest that the rheotactic response of beach populations should reflect the founding genotypes, gene flow from other populations, and random genetic drift. The results of previously published studies on the rheotactic response of beach fry in two other lake systems qualitatively support our hypothesis.