Microsatellite DNA variation in wild populations and farmed strains of turbot from Ireland and Norway: a preliminary study

Turbot Scophthalmus maximus is the focus of a rapidly expanding aquaculture industry, while at the same time wild catches appear to be in decline. As a preliminary investigation into the effects of hatchery rearing, genetic variation at three polymorphic microsatellite loci was assessed in two wild populations and two farmed strains of turbot, from Ireland and Norway. Although a considerable loss of rare alleles was observed in the Irish farmed strain, no statistically significant reductions were found in mean heterozygosity or allelic diversity in farmed strains compared to wild populations. Significant genetic heterogeneity was found between wild and farmed samples from each country but not between the two wild populations. Genetic differentiation between the farmed strains was presumed to be caused by drift in the hatcheries. The utility of these particular microsatellite loci in comparing these samples and the importance of molecular genetic testing of farmed strains is stressed.     

Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species

Caenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.     

Identifying footprints of selection in stocked brown trout populations: a spatio‐temporal approach

Studies of interactions between farmed and wild salmonid fishes have suggested reduced fitness of farmed strains in the wild, but evidence for selection at the genic level is lacking. We studied three brown trout populations in Denmark which have been significantly admixed with stocked hatchery trout (19–64%), along with two hatchery strains used for stocking. The wild populations were represented by contemporary samples (2000–2006) and two of them by historical samples (1943–1956). We analysed 61 microsatellite loci, nine of which showed putative functional relationships [expressed sequence tag (EST)‐linked or quantitative trait loci]. F_ST‐based outlier tests provided support for diversifying selection at chromosome regions marked by three loci, two anonymous and one EST‐linked. Patterns of differentiation suggested that the loci were candidates for being under diversifying hitch‐hiking selection in hatchery vs. wild environments. Analysis of hatchery strain admixture proportions showed that in one wild population, two of the loci showed significantly lower admixture proportions than the putatively neutral loci, implying contemporary selection against alleles introduced by hatchery strain trout. In the most strongly admixed population, however, there was no evidence for selection, possibly because of immigration by stocked trout overcoming selection against hatchery‐derived alleles or supportive breeding practices allowing hatchery strain trout to escape natural selection. To our knowledge, this is the first study demonstrating footprints of selection in wild salmonid populations subject to spawning intrusion by farmed fish.     

Population Genetic Structure and Conservation of the Galápagos Petrel (Pterodroma phaeopygia)

The Galápagos petrel (Pterodroma phaeopygia) is endemic to the Galápagos archipelago, where it is known to breed only on five islands. The species has been listed as critically endangered due to habitat deterioration and predation by introduced mammals. Significant morphological and behavioural differences among petrels nesting on different islands suggest that island populations may differ genetically. Furthermore, nesting phenology suggests that genetically differentiated seasonal populations may exist within at least one island. We analysed variation in six microsatellite loci and part of the mitochondrial ATPase 6/8 gene in 206 Galápagos petrels sampled from all five islands. No evidence of genetic structuring within islands was found, although statistical power was low. In contrast, significant differences occurred among island populations. For the microsatellite loci, private alleles occurred at all islands, sometimes at high frequency; global and pairwise estimates of genetic differentiation were all statistically significant; Bayesian analysis of genotypes frequencies provided strong support for three genetic populations; and most estimates of migration between populations did not differ significantly from zero. Only two ATPase haplotypes were found, but the geographic distribution of haplotypes indicated significant differentiation among populations. For conservation purposes, populations from Floreana, Santa Cruz, San Cristóbal and Santiago should be regarded as separate genetic management units. Birds from Isabela appear to be derived recently from the Santiago population, and the population on San Cristóbal appears to be a mixture of birds from other populations. However, considering ecological and behavioural differences among birds from different islands, we recommend that all five populations be protected.     

Population genetic structure and dispersal across a fragmented landscape in cerulean warblers (<Emphasis Type="Italic">Dendroica cerulea</Emphasis>)

Cerulean warblers (Dendroica cerulea) have experienced significant declines across their breeding range and presently exist in disjunct populations, largely because of extensive loss and fragmentation of their breeding and wintering habitat. Despite this overall decline, a recent north-eastern expansion of the breeding range has been proposed, and some researchers have suggested that the eastern Ontario population may be acting as a source population maintaining sink populations elsewhere. However, little is known about either the geographic distribution of genetic variation or dispersal in these birds. We assayed variation in five microsatellite loci and a 366 base-pair fragment of the mitochondrial control region among 154 cerulean warblers from five populations throughout the breeding range. No evidence of population genetic structure was found. Assignment tests suggested that six individuals were either inter-population migrants or descendants of recent migrants. The lack of population genetic structure is probably due to a combination of historical association and contemporary dispersal. Population decline does not appear to have reduced genetic variation yet. Overall results suggest that cerulean warblers from Ontario, Illinois, Arkansas and Tennessee should be considered a single genetic management unit for conservation.     

Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees

In some wild Atlantic salmon populations, rapid declines in numbers of wild returning adults has been associated with an increase in the prevalence of farmed salmon. Studies of phenotypic variation have shown that interbreeding between farmed and wild salmon may lead to loss of local adaptation. Yet, few studies have attempted to assess the impact of interbreeding at the genome level, especially among North American populations. Here, we document temporal changes in the genetic makeup of the severely threatened Magaguadavic River salmon population (Bay of Fundy, Canada), a population that might have been impacted by interbreeding with farmed salmon for nearly 20 years. Wild and farmed individuals caught entering the river from 1980 to 2005 were genotyped at 112 single-nucleotide polymorphisms (SNPs), and/or eight microsatellite loci, to scan for potential shifts in adaptive genetic variation. No significant temporal change in microsatellite-based estimates of allele richness or gene diversity was detected in the wild population, despite its precipitous decline in numbers over the last two decades. This might reflect the effect of introgression from farmed salmon, which was corroborated by temporal change in linkage-disequilibrium. Moreover, SNP genome scans identified a temporal decrease in candidate loci potentially under directional selection. Of particular interest was a SNP previously shown to be strongly associated with an important quantitative trait locus for parr mark number, which retained its genetic distinctiveness between farmed and wild fish longer than other outliers. Overall, these results indicate that farmed escapees have introgressed with wild Magaguadavic salmon resulting in significant alteration of the genetic integrity of the native population, including possible loss of adaptation to wild conditions.     

Molecular evidence for a founder effect in invasive house finch (Carpodacus mexicanus) populations experiencing an emergent disease epidemic

The impact of founder events on levels of genetic variation in natural populations remains a topic of significant interest. Well-documented introductions provide a valuable opportunity to examine how founder events influence genetic diversity in invasive species. House finches (Carpodacus mexicanus) are passerine birds native to western North America, with the large eastern North American population derived from a small number of captive individuals released in the 1940s. Previous comparisons using amplified fragment length polymorphism (AFLP) markers found equivalent levels of diversity in eastern and western populations, suggesting that any genetic effects of the founder event were ameliorated by the rapid growth of the newly established population. We used an alternative marker system, 10 highly polymorphic microsatellites, to compare levels of genetic diversity between four native and five introduced house finch populations. In contrast to the AFLP comparisons, we found significantly lower allelic richness and heterozygosity in introduced populations across all loci. Three out of five introduced populations showed significant reductions in the ratio of the number of alleles to the allele size range, a within-population characteristic of recent bottlenecks. Finally, native and introduced populations showed significant pairwise differences in allele frequencies in every case, with stronger isolation by distance within the introduced than native range. Overall, our results provide compelling molecular evidence for a founder effect during the introduction of eastern house finches that reduced diversity levels at polymorphic microsatellite loci and may have contributed to the emergence of the Mycoplasma epidemic which recently swept the eastern range of this species.     

Polymorphism in a Cyclic Parthenogenetic Species: SIMOCEPHALUS SERRULATUS

A survey of sixteen isozyme loci using electrophoretic techniques was conducted for three isolated natural populations and one laboratory population of the cyclic parthenogenetic species, Simocephalus serrulatus. The proportion of polymorphic loci (33%-60%) and the average number of heterozygous loci per individual (6%-23%) in the three natural populations were found to be comparable to those found in most sexually reproducing organisms. Detailed analyses were made for one of these populations using five polymorphic loci. The results indicated that (1) seasonal changes in genotypic frequencies took place, (2) apomicitic parthenogenesis does not lead to genetic homogeneity, and (3) marked gametic disequilibrium at these five loci was present in the population, indicating that selection acted on coadapted groups of genes.     

Age-dependent genetic variance in a life-history trait in the mute swan

Genetic variance in characters under natural selection in natural populations determines the way those populations respond to that selection. Whether populations show temporal and/or spatial constancy in patterns of genetic variance and covariance is regularly considered, as this will determine whether selection responses are constant over space and time. Much less often considered is whether characters show differing amounts of genetic variance over the life-history of individuals. Such age-specific variation, if present, has important potential consequences for the force of natural selection and for understanding the causes of variation in quantitative characters. Using data from a long-term study of the mute swan Cygnus olor, we report the partitioning of phenotypic variance in timing of breeding (subject to strong natural selection) into component parts over 12 different age classes. We show that the additive genetic variance and heritability of this trait are strongly age-dependent, with higher additive genetic variance present in young and, particularly, old birds, but little evidence of any genetic variance for birds of intermediate ages. These results demonstrate that age can have a very important influence on the components of variation of characters in natural populations, and consequently that separate age classes cannot be assumed to be equivalent, either with respect to their evolutionary potential or response.     

Genetic Variation in Natural Populations of Five Drosophila Species and the Hypothesis of the Selective Neutrality of Protein Polymorphisms

We have studied genetic variation at 30-32 loci coding for enzymes in natural populations of five species of Drosophila. The average proportion of heterozygous loci per individual is 17.7 +/- 0.4%. The average proportion of polymorphic loci per population is 69.2 +/- 2.6% or 49.8 +/- 2.2%, depending on what criterion of polymorphism is used. The following generalizations are advanced: (1) The amount of genetic polymorphism varies considerably from locus to locus. (2) At a given locus, populations of the same species are very similar in the amount and pattern of genetic variation. (3) However, at some loci large differences sometimes occur between local populations of the same species. (4) The amount of variation at a given locus is approximately the same in all five species. (5) When different species are compared, the pattern of the variation is either essentially identical or totally different at a majority of loci. We have tested the hypothesis that protein polymorphisms are selectively neutral by examining four predictions derived from the hypothesis. Our results are at variance with every one of the predictions. We have measured the amount of genetic differentiation, D, between taxa of various degrees of evolutionary divergence. The average value of D is 0.033 for local populations, 0.228 for subspecies, 0.226 for semispecies, 0.538 for sibling species, and 1.214 for morphologically distinguishable species. Our results indicate that a substantial degree of genetic differentiation (22.8 allelic substitutions for every 100 loci) occurs between allopatric populations that have diverged to the point where they might become different species if they were to become sympatric. However, very little additional genetic change is required for the development of complete reproductive isolation. After the speciation process is completed, species continue to diverge genetically from each other.     

SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)

Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen‐induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre‐epizootic western US birds, introduced birds from Hawaii and the eastern United States, post‐epizootic eastern birds, and western birds sampled across a similar time span. We found 14% and 7% reductions in nucleotide diversity, respectively, in Hawaiian and pre‐epizootic eastern birds relative to pre‐epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre‐epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.     

Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip

Genetic interactions between farmed and wild conspecifics are of special concern in fisheries where large numbers of domesticated individuals are released into the wild. In the Atlantic salmon (Salmo salar), selective breeding since the 1970's has resulted in rapid genetic changes in commercially important traits, such as a doubling of the growth rate. Each year, farmed salmon escape from net pens, enter rivers, and interbreed with wild salmon. Field experiments demonstrate that genetic introgression may weaken the viability of recipient populations. However, due to the lack of diagnostic genetic markers, little is known about actual rates of gene flow from farmed to wild populations. Here we present a panel of 60 single nucleotide polymorphisms (SNPs) that collectively are diagnostic in identifying individual salmon as being farmed or wild, regardless of their populations of origin. These were sourced from a pool of 7000 SNPs comparing historical wild and farmed salmon populations, and were distributed on all but two of the 29 chromosomes. We suggest that the generic differences between farmed and wild salmon at these SNPs have arisen due to domestication. The identified panel of SNPs will permit quantification of gene flow from farmed to wild salmon populations, elucidating one of the most controversial potential impacts of aquaculture. With increasing global interest in aquaculture and increasing pressure on wild populations, results from our study have implications for a wide range of species.     

Origin, fate, and architecture of ecologically relevant genetic variation

Recent advances in molecular genetics combined with field manipulations are yielding new insight into the origin, evolutionary fate, and genetic architecture of phenotypic variation in natural plant populations, with two surprising implications for the evolution of plant genomes. First, genetic loci exhibiting antagonistic pleiotropy across natural environments appear rare relative to loci that are adaptive in one or more environments and neutral elsewhere. These 'conditionally neutral' alleles should sweep to fixation when they arise, yet genome comparisons find little evidence for such selective sweeps. Second, genes under biotic selection tend to be of larger effect than genes under abiotic selection. Recent theory suggests this may be a consequence of high gene flow among populations under selection for local adaptation.     

Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions

Twenty-five single nucleotide polymorphisms (SNPs) were analyzed in 20 distinct chicken breeds. The SNPs, each located in a different gene and mostly on different chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phylogenetic trees were constructed from these data. When bootstrap values were used as a criterion for the tree repeatability, doubling the number of SNPs from 12 to 25 improved tree repeatability more than doubling the number of individuals per population, from five to ten. Clustering results of these 20 populations, based on the software STRUCTURE, are in agreement with those previously obtained from the analysis of microsatellites. When the number of clusters was similar to the number of populations, affiliation of birds to their original populations was correct (>95%) only when at least the 22 most polymorphic SNP loci (out of 25) were included. When ten populations were clustered into five groups based on STRUCTURE, we used membership coefficient (Q) of the major cluster at each population as an indicator for clustering success level. This value was used to compare between three marker types; microsatellites, SNPs in or close to genes (g-SNPs) and SNPs in random fragments (r-SNPs). In this comparison, the same individuals were used (five to ten birds per population) and the same number of loci (14) used for each of the marker types. The average membership coefficients (Q) of the major cluster for microsatellites, g-SNPs and r-SNPs were 0.85, 0.7, and 0.64, respectively. Analysis based on microsatellites resulted in significantly higher clustering success due to their multi-allelic nature. Nevertheless, SNPs have obvious advantages, and are an efficient and cost-effective genetic tool, providing broader genome coverage and reliable estimates of genetic relatedness.     

GENETIC VARIATION IN CACTOPHILIC DROSOPHILA FOR OVIPOSITION ON NATURAL YEAST SUBSTRATES

Theory predicts that environmental heterogeneity in space or in time can maintain genetic polymorphism. Stable polymorphisms are expected to be more readily maintained if there are genotype specific habitat preferences. Genotype specific preferences for oviposition sites in Drosophila could be a major factor promoting habitat selection, and thus the maintenance of genetic variation. This hypothesis is being tested using the cactophilic species, D. buzzatii and D. aldrichi, where available evidence indicates a potential for such habitat selection, the habitats (oviposition sites) being yeast species found in the natural environment of these flies (cactus rots). Genetic variation for oviposition preferences was tested using isofemale lines—for D. buzzatii, a total of 60 lines from seven localities widely distributed through the species range in Australia, and for D. aldrichi, 21 lines from three of these localities. Females were given a choice of five yeast species as oviposition sites. Genetic variation for oviposition preferences on these natural substrates was demonstrated. There was significant variation among isofemale lines within populations in their patterns of preferences for oviposition on the five yeast species. However, analyses of preferences for each yeast species separately showed that the genetic variation for preferences relates to only three of the five species. Heritabilities of individual female preferences for these three species were low, ranging up to 9%. Little geographic differentiation was apparent among populations, most likely due to similar selection regimes within each population. Within populations, this kind of habitat selection could act to maintain polymorphisms, both at loci determining the habitat preferences and at other loci in linkage disequilibrium with them.     

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

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

Genetic Variation of Microsatellite Loci in the Major Histocompatibility Complex (MHC) Region in the Southeast Asian House Mouse (<Emphasis Type="Italic">Mus musculus castaneus</Emphasis>)

Major histocompatibility complex (MHC) genes are the most polymorphic loci known for vertebrates. Here we employed five microsatellite loci closely linked to the MHC region in an attempt to study the amount of genetic variation in 19 populations of the southeast Asian house mouse (Mus musculus castaneus) in Taiwan. The overall polymorphism at the five loci was high (H_e = 0.713), and the level of polymorphism varied from locus to locus. Furthermore, in order to investigate if selection is operating on MHC genes in natural mouse populations, we compared the extent and pattern of genetic variation for the MHC-linked microsatellite loci (the MHC loci) with those for the microsatellite loci located outside the MHC region (the non-MHC loci). The number of alleles and the logarithm of variance in repeat number were significantly higher for the MHC loci than for the non-MHC loci, presumably reflecting linkage to a locus under balancing selection. Although three statistical tests used do not provide support for selection, their lack of support may be due to low statistical power of the tests, to weakness of selection, or to a profound effect of genetic drift reducing the signature of balancing selection. Our results also suggested that the populations in the central and the southwestern regions of Taiwan might be one part of a metapopulation structure.     

Population genetic structure of wild and farmed rusa deer (<Emphasis Type="Italic">Cervus timorensis russa</Emphasis>) in New-Caledonia inferred from polymorphic microsatellite loci

Historical records indicate that 12 rusa deer (Cervus timorensis russa) were introduced in New-Caledonia during the 1870s. We used eight polymorphic microsatellite DNA loci to assess the genetic differentiation and diversity of farmed and wild deer populations. Past genetic bottlenecks were detected in both sub-populations, although higher genetic diversity was maintained in farmed populations, probably due to the regular introduction of reproducers from wild populations and from other farms. The genetic structure of farmed and wild populations differed significantly. There was a significant isolation by distance for wild populations, whereas farmed populations were significantly differentiated between farms independently from their geographical proximity. Wild rusa deer consisted of small populations (with effective population sizes ranging between 7 and 19 individuals depending on the methods used), with a low parent–offspring dispersion range (0.20–2.02 km). Genetic tools and direct observations provided congruent estimates of dispersion and population sizes. We discuss the relevance of our results for management purposes.     

Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis)

Analysis of fine scale genetic structure in continuous populations of outcrossing plant species has traditionally been limited by the availability of sufficient markers. We used a set of 468 SNPs to characterize fine‐scale genetic structure within and between two dense stands of the wild ancestor of maize, teosinte (Zea mays ssp. parviglumis). Our analyses confirmed that teosinte is highly outcrossing and showed little population structure over short distances. We found that the two populations were clearly genetically differentiated, although the actual level of differentiation was low. Spatial autocorrelation of relatedness was observed within both sites but was somewhat stronger in one of the populations. Using principal component analysis, we found evidence for significant local differentiation in the population with stronger spatial autocorrelation. This differentiation was associated with pronounced shifts in the first two principal components along the field. These shifts corresponded to changes in allele frequencies, potentially due to local topographical features. There was little evidence for selection at individual loci as a contributing factor to differentiation. Our results demonstrate that significant local differentiation may, but need not, co‐occur with spatial autocorrelation of relatedness. The present study represents one of the most detailed analyses of local genetic structure to date and provides a benchmark for future studies dealing with fine scale patterns of genetic diversity in natural plant populations.