Search

In early 1992, the European bumblebee, Bombus terrestris, was first seen in Tasmania and currently has spread to most of the island. Here, we report on the genetic structure, using micro-satellites, of the invading population from samples collected in the years 1998-2000, a few years after the first sighting of the species in its new area. The data show that the Tasmanian population has a very low genetic diversity, with less than half of the allelic richness (Richness=2.89 alleles; H(exp)=0.591) and lower levels of heterozygosity as compared to populations in New Zealand (4.24 alleles; H(exp)=0.729) and Europe (5.08 alleles; H(exp)=0.826). In addition, the genetic data suggest that the invasion must have happened once, probably around late 1991, and was the result of very few, perhaps only two, individuals arriving in Tasmania. Furthermore, these founders came from the New Zealand population. Today, the population in the south of Tasmania seems to act as a source population from which individuals migrate into other parts of the state. A similar source-sink structure seems also the case for New Zealand. The data show that B. terrestris is a highly invasive species capable of establishing itself even after a dramatic genetic bottleneck. B. terrestris may be an invasive species due to the haplo-diploid sex determination system, which exposes recessive, deleterious mutations to selection. Offspring of such purged lines may then be able to tolerate high levels of inbreeding.

The genetic architectures of four morphometric traits in the housefly, Musca domestica L., were analysed using a paternal half-sib design on a large outbred base population and on two populations each established with two pairs of flies from the base population. By including parents with the offspring in the analysis, phenotypic variance was subdivided into components for additive, dominance, additive-by-additive epistasis and environmental variation. In relation to the nonbottlenecked base population, narrow sense hertitability was lower in the bottle-necked populations, largely because of an increase in the level of the environmental component of variance. Averaged over the four traits in the nonbottlenecked base population, nonadditive components contributed nearly 60 per cent of the phenotypic variance, with more than half of this being attributable to epistasis. Two of the four traits showed reduced additive genetic variance in the bottlenecked lines, whereas two of the traits showed increased additive genetic variance. A major difference in the genetic architecture between traits showing these two disparate bottleneck effects was the presence of epistasis in the nonbottlenecked base population for the traits which showed an increase in the additive component. Overall, there was a significant positive relationship between the initial percentage contribution of epistasis in the base population and the gain in the additive component in the bottleneck lines, as predicted by models incorporating additive-by-additive epistasis.

Bottleneck effects in local populations of fossorial Ctenomys (Rodentia, Ctenomyidae) affected by vulcanism

The genetic consequences of a bottleneck, and the spatial genetic structure within and between populations, were studied in the rare and geographically restricted species Stylidium coroniforme. Thirteen out of 15 aflozyme loci analysed were polymorphic. The level of polymorphism was relatively high for an insect-pollinated outcrossing species. In one population, which was subjected to a prolonged decline in numbers resulting in a bottleneck, probably of three plants, there was no measurable reduction in either allelic diversity of average heterozygosity. Maintenance of heterozygosity in this population could be attributed to rapid recovery after the bottleneck, the progressive elimination of selfed or otherwise inbred products during seed development and selection favouring heterozygotes as plants mature. Evidence for the latter was a significant decrease in the fixation index from younger (F = 0.28) to older plants (F = 0.14). Bottleneck-flush cycles are considered to be a major factor contributing to the relatively high level of differentiation observed between the three Wongan Hills populations, which suggests that the bottleneck observed was not atypical for these populations. The allozyme divergence between the two population systems within this taxon (D = 0.29) may be indicative of two different but morphologically cryptic species. Spatial autocorrelation techniques revealed no spatial genetic structure in one population sampled at its maximum density. It was concluded that high levels of genetic diversity in small populations are typical of S. coroniforme, which is relatively short lived, disturbance-adapted and has population systems which probably undergo frequent bottleneck-flush cycles.

Purifying selection tends to reduce nucleotide and haplotype diversity leading to increased linkage disequilibrium. However, detection of evidence for selection is difficult as the signature is confounded by wide variation in the recombination rate which has a complex relationship with selection. The effective bottleneck time (the ratio of the linkage disequilibrium map to the genetic map in Morgans) controls for variability in the recombination rate. Reduced effective bottleneck times indicate stronger residual linkage disequilibrium, consistent with increased selection. Using whole genome sequence data from one European and three Sub-Saharan African human populations we find, in the African samples, strong correlations between high gene densities and reduced effective bottleneck time for autosomal chromosomes. This suggests that gene-dense autosomes have been subject to increased purifying selection reducing effective bottleneck times compared to gene-poor autosomes. Although previous studies have shown unusually strong linkage disequilibrium for the sex chromosomes variation within the autosomes has not been recognised. The strongest relationship is between effective bottleneck time and the density of essential genes, which are likely targets of greater selective pressure (p = 0.006, for the 22 autosomes). The magnitude of the reduction in chromosome-specific effective bottleneck times from the least to the most gene-dense autosomes is ~17-21% for Sub-Saharan African populations. The effect size is greater in Sub-Saharan African populations, compared to a European sample, consistent with increased efficiency of selection in populations with larger effective population sizes which have not been subject to intense population bottlenecks as experienced by populations of European ancestry. The findings highlight the value of deeper analyses of selection within Sub-Saharan African populations.

Whether wind pollination in trees can offset the negative genetic consequences of anthropogenic forest fragmentation is not clearly established. To answer this question, we examined the demographic genetics of Quercus bambusifolia over a 70-year recovery period in highly fragmented forests in Hong Kong. We sampled 1138 individuals from 37 locations, and genetically analysed the chronosequence through the classification of tree diameters from the same populations using 13 microsatellite markers. Our study reveals that severe fragmentation caused a significant genetic bottleneck with very few remaining but genetically diverse individuals. We observed an enhanced genetic diversity during demographic recovery. We found full-sibs within populations and half-sibs across the study range. This reflects a limited seed dispersal and extensive pollen flow. Despite reduced genetic structure both among and within populations, overall a strong persisting genetic differentiation (F′(ST) = 0.240, P

Understanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of Ircinia campana, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (

Recent advances in genomics have enabled researchers to shed light on the evolutionary processes driving human adaptation, by revealing the genetic architectures underlying traits ranging from lactase persistence, to skin pigmentation, to hypoxic response, to arsenic tolerance. Complicating the identification of targets of positive selection in modern human populations is their complex demographic history, characterized by population bottlenecks and expansions, population structure, migration, and admixture. In particular, founder effects and recent strong population size reductions, such as those experienced by the indigenous peoples of the Americas, have severe impacts on genetic variation that can lead to the accumulation of large allele frequency differences between populations due to genetic drift rather than natural selection. While distinguishing the effects of demographic history from selection remains challenging, neglecting neutral processes can lead to the incorrect identification of candidate loci. We here review the recent population genomic insights into the genetic basis of arsenic tolerance in Andean populations, and utilize this example to highlight both the difficulties pertaining to the identification of local adaptations in strongly bottlenecked populations, as well as the importance of controlling for demographic history in selection scans.

The genetic breakdown of self-incompatibility (SI) and subsequent mating system shifts to inbreeding has intrigued evolutionary geneticists for decades. Most of our knowledge is derived from interspecific comparisons between inbreeding species and their outcrossing relatives, where inferences may be confounded by secondary mutations that arose after the initial loss of SI. Here, we study an intraspecific breakdown of SI and its consequences in North American Arabidopsis lyrata to test whether: (1) particular S-locus haplotypes are associated with the loss of SI and/or the shift to inbreeding; (2) a population bottleneck may have played a role in driving the transition to inbreeding; and (3) the mutation(s) underlying the loss of SI are likely to have occurred at the S-locus. Combining multiple approaches for genotyping, we found that outcrossing populations on average harbour 5 to 9 S-locus receptor kinase (SRK) alleles, but only two, S1 and S19, are shared by most inbreeding populations. Self-compatibility (SC) behaved genetically as a recessive trait, as expected from a loss-of-function mutation. Bulked segregant analysis in SC × SI F2 individuals using deep sequencing confirmed that all SC plants were S1 homozygotes but not all S1 homozygotes were SC. This was also revealed in population surveys, where only a few S1 homozygotes were SC. Together with crossing data, this suggests that there is a recessive factor that causes SC that is physically unlinked to the S-locus. Overall, our results emphasise the value of combining classical genetics with advanced sequencing approaches to resolve long outstanding questions in evolutionary biology.

Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection or demographic factors could explain the absence of mtDNA variation in F. albicilla. Eighteen nuclear genes were sequenced to estimate the two species' phylogeographic histories, and for comparison to the mtDNA data. Multilocus coalescence analyses suggested that F. albicilla experienced a population expansion perhaps following a population bottleneck. Simulations based on this demographic history, however, did not replicate the extremely low level of mtDNA variation. Historical range changes based on ecological niche models also failed to explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA) suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a transmembrane-skewed distribution of nonsynonymous substitutions between the two species, three of which caused functional change; the results implied that positive selection could have targeted mtDNA. Several lines of evidence support selection rather than demographic history as the main force influencing the patterns of mtDNA variation. Despite the influence of natural selection, many of the phylogeographic inferences derived from mtDNA were robust, including species limits and a high level of gene flow among populations within species.

Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

The European bison (Bison bonasus) has recovered successfully after a severe bottleneck about 90 years ago. Pedigree analysis indicates that over 80% of the genes in the contemporary population descend from just 2 founder individuals and the pedigree-based inbreeding coefficient averages almost 0.5, while microsatellite heterozygosity is around 0.3. This paper presents a comparison of the effectiveness of 17 microsatellite and 960 SNP markers in paternity and identity analysis in the Lowland line of European bison ('pure' European bison). Identity analysis revealed that 16% of the microsatellite-based genotypes were common to more than one individual while a smaller set of SNP-based genotypes were all unique, even. Microsatellite-based paternity analysis did not succeed due to low marker heterozygosity. Using SNP markers, simulations suggest that 80-90 randomly selected loci would be sufficient to ensure successful paternity analysis, or just 50-60 of the most heterozygous loci. For the purpose of standardizing future parentage and identity analysis, a panel of 50-60 SNPs characterized by high heterozygosity and an even distribution in the genome could be selected. This panel of selected markers could be typed using e.g. Veracode (Illumina) or SNPlex (ABI) technologies to provide an efficient and reliable method for parentage and identity analysis in European bison. Customizing off-the-shelf SNP marker panels created for domestic species can provide powerful, low-cost tools for genetic analysis in related species Udgivelsesdato: October The European bison (Bison bonasus) has recovered successfully after a severe bottleneck about 90 years ago. Pedigree analysis indicates that over 80% of the genes in the contemporary population descend from just 2 founder individuals and the pedigree-based inbreeding coefficient averages almost 0.5, while microsatellite heterozygosity is around 0.3. This paper presents a comparison of the effectiveness of 17 microsatellite and 960 SNP markers in paternity and identity analysis in the Lowland line of European bison ('pure' European bison). Identity analysis revealed that 16% of the microsatellite-based genotypes were common to more than one individual while a smaller set of SNP-based genotypes were all unique, even. Microsatellite-based paternity analysis did not succeed due to low marker heterozygosity. Using SNP markers, simulations suggest that 80-90 randomly selected loci would be sufficient to ensure successful paternity analysis, or just 50-60 of the most heterozygous loci. For the purpose of standardizing future parentage and identity analysis, a panel of 50-60 SNPs characterized by high heterozygosity and an even distribution in the genome could be selected. This panel of selected markers could be typed using e.g. Veracode (Illumina) or SNPlex (ABI) technologies to provide an efficient and reliable method for parentage and identity analysis in European bison. Customizing off-the-shelf SNP marker panels created for domestic species can provide powerful, low-cost tools for genetic analysis in related species

Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations.

Populations may, during their evolutionary history, go through drastic changes in population size due to bottlenecks or founder events upon colonization of new areas. This involves a subsample of haplotypes, causing the allele frequencies to be different from the original population. In addition, the period of recovery after a bottleneck can be of considerable length. If reproduction is unequal among individuals but random with regard to haplotype, large deviations from the patterns expected in a stable population may result. By means of computer simulation, I have analysed the patterns arising when populations undergo bottlenecks and then slowly recover, and used two new statistical tests for the detection of the bottleneck. A test based on the variance of the relative frequency of haplotypes had generally high power even at low sample size (n=25). This statistic was most powerful after very strong bottlenecks and lost power with increasing propagule size. A test based on the variance of the pairwise differences shows slightly less power. As expected, power was reduced when migration into the founder population was allowed from the source population. This suggests that the test is particularly suited for detecting relatively recent and strong bottlenecks, and thus may be a valuable tool for identifying population events on a fine temporal scale, such as colonisations after the last glaciation.

A growing body of experimental work has shown that the additive genetic variance of fitness components can increase following a founder event or a bottleneck of population size. This is usually explained theoretically by the conversion of dominance variance and/or epistatic variance to additive variance following bottlenecks. The present analysis considers the effects of deviation from Hardy–Weinberg proportions (DHW) and linkage disequilibrium (LD) caused by bottlenecks. It is shown that DHW may also cause an increase in the additive variance for rare recessive genes, the largest increase arising with completely recessive genes of low initial frequency in intermediate-sized populations. LD among nonadditive loci results in a large increase in genotypic variance and also a small increase in additive variance. Even for the case of no linkage among the loci and linkage equilibrium in the ancestral population, severe bottlenecks result in a significant increase in genotypic variance as a result of LD among dominant loci. More restrictive conditions (many linked loci with large dominance coefficients and rare recessive genes), however, are required for LD to cause an evident increase in the additive variance. The effects of LD on genetic variances enhance with an increase in number of loci and dominance coefficients and with a decrease in recombination fractions, bottleneck sizes and initial recessive gene frequencies. Although the effects of LD on genetic variance decline gradually in the flush population, they may persist for some generations, especially when there is high linkage among the relevant loci.

Genetic variation in European starlings in North America was examined using enzyme electrophoresis and compared to that in their home range. The effect of the founding bottleneck matched theoretical predictions. Heterozygosity was unaffected, whereas allelic diversity may have decreased. Results from this study and others suggest that theoretical predictions of bottlenecks are robust for allozyme data, and applicable under a wide variety of conditions.

Spiranthes romanzoffiana Cham. is restricted in Europe to the British Isles, where it is recognised as a conservation priority species due to frequent extirpation of populations along with no evidence of seed set; vegetative reproduction has been invoked as the sole means of perpetuation and dispersal. To investigate the reproductive ecology of this species, 17 populations have been sampled for chloroplast microsatellites and amplified fragment length polymorphisms (AFLPs). These markers revealed a previously unsuspected genetic-geographic split in the species, which correlates with differences in patterns of within-population variation. Northern populations were fixed for one chloroplast haplotype but showed high levels of AFLP genotypic diversity consistent with sexual reproduction (proportion of genotypes distinguishable, PD = 0.98). More southerly populations showed fixed differences from the northern populations in their chloroplast haplotype and for 10 AFLP markers. They harboured only 12 unique multilocus genotypes among 113 individuals from six populations (PD = 0.11). These genotypes differed mostly by single bands, and none by more than 4/138 loci, with identical multilocus genotypes occurring in widely separated populations. This uniformity in southern populations is consistent with agamospermous or autogamous reproduction, and/or an extreme population bottleneck. Finally, the observed patterns of population differentiation in S. romanzoffiana are compared with other studies of orchids, revealing a wide range of values that belie recent contrasting published generalisations that claim that orchids show either higher, or lower, levels of population differentiation than other plant families.

Fragmentation is generally considered to have negative impacts on widespread outbreeders but impacts on gene flow and diversity in patchy, naturally rare, self-compatible plant species remain unclear. We investigated diversity, gene flow and contemporary pollen-mediated gene immigration in the rare, narrowly distributed endemic shrub Calothamnus quadrifidus ssp. teretifolius. This taxon occurs in an internationally recognized biodiversity hotspot subjected to recent human-induced fragmentation and the condition of the remnants ranges from intact to highly degraded. Using microsatellites, we found that inbreeding, historically low gene flow and significant population differentiation have characterized the genetic system of C. quadrifidus ssp. teretifolius. Inbreeding arises from self-pollination, a small amount of biparental inbreeding and significant correlation of outcross paternity but fecundity was high suggesting populations might have purged their lethals. Paternity analyses show that pollinators can move pollen over degraded and intact habitat but populations in both intact and degraded remnants had few pollen parents per seed parent and low pollen immigration. Genetic diversity did not differ significantly between intact and degraded remnants but there were signs of genetic bottlenecks and reduced diversity in some degraded remnants. Overall, our study suggests human-induced fragmentation has not significantly changed the mating system, or pollen immigration to, remnant populations and therefore genetic connectivity need not be the highest conservation priority. Rather, for rare species adapted to higher levels of inbreeding, conservation efforts may be best directed to managing intact habitats and ecosystem processes.

The association between mtDNA haplotypes and chromosomal arrangements in a natural population of Drosophila subobscura from Calvia (Balearic Islands, Spain) was studied in order to search for linkage disequilibria, in an attempt to explain the populational dynamics of the mtDNA haplotypes of this species in nature. The presence of Wolbachia was not detected. Two main haplotypes (I and II) were found, as well as a series of less common ones. The Tajima D-test seemed to indicate some kind of seasonal population bottleneck. An analysis of linkage disequilibrium and factorial analysis of correspondences detected an association between haplotype I and the J(ST) inversion and haplotype II and the J(1) inversion.

Wild boar (Sus scrofa), one of the most widespread wildlife species, has entered a stage of continuous growth in Europe, and could even be considered a pest species. We analysed microsatellite variability in 723 wild boars from across Europe, including the northern Dinaric Balkans. Our aims were: (1) to define the population structure of wild boars in the Balkans and its relation with other European populations; (2) to estimate effective populations sizes, levels of intra- and inter-population diversity, inbreeding migration and gene flow patterns; (3) to test subpopulations for bottlenecks; (4) to interpret these results in light of current knowledge about the demographic history of wild boars in Europe; and (5) to discuss the relevance of these findings for management and conservation. Strong population structuring was observed and 14 subpopulations were revealed. High genetic diversity was found, and besides the well-known identity of the Italian populations of Sardinia and Castelporziano, we bring new insights into other potential relevant, refugial populations such as Littoral Slovenia, South Portugal, North-western Iberia and an entire cluster in the Balkans. There was evidence of gene flow going from these refugial subpopulations towards less peripheral and more admixed subpopulations. Recent population bottlenecks and expansions were detected, mostly in the peninsular refuge subpopulations. The results are consistent with the fluctuations of wild boar numbers in Europe since the beginning of the twentieth century. These results should be taken into account in future conservation and management plans for wild boar populations in Europe.

The reconstruction of recent historical population sizes allowed us to investigate the influence of random evolutionary processes on present-day genetic diversity in populations of Dryopteris cristata. This long-lived, allotetraploid fern is rare and endangered in the study area at the southwestern border of its European distribution. Random amplified polymorphic DNA (RAPD) diversity of 280 individuals from 14 populations of D. cristata was extraordinarily low, suggesting an ancient bottleneck in the species' history. Analysis of molecular variance (AMOVA) of 25 different RAPD multiband phenotypes revealed significant genetic variation among three geographical regions (15%) and among populations within regions (34%); 51% of total variance was attributed to variation within populations. High population differentiation indicated limited gene flow among populations, and genetic divergence was not correlated with geographical distance. There was no relationship between genetic variation within population, estimated as molecular variance, and present-day population size. Populations with recent historical bottlenecks of fewer than 25 individuals showed a substantial and significant reduction in genetic variation, compared with populations without bottlenecks. Comparatively high levels of genetic variation were still maintained in small remnants (60-110 individuals) of formerly large populations. Average deviations of frequencies of widespread polymorphic markers within populations from their frequencies in the whole dataset were significantly higher in small or recently bottlenecked populations than in constantly large populations, thus providing evidence for random sampling effects during genetic bottlenecks and drift in small populations. The present investigation demonstrates the importance of population history for understanding present-day genetic diversity within natural populations, as well as for conservation biology.

T he days of the neutral theory are seemingly over. In time for the Darwin year celebrations, recent research has allowed a remarkable comeback for selection as the dominant force in shaping the diversity of genotypes and phenotypes. This change in perception results mainly from the emerging field of evolutionary genomics. On the basis of newly available genome-wide polymorphism and divergence data, and driven by Big Genomics endeavours like the human HapMap Project, selection is detected without a phenotype, directly from DNA sequence data. Two main results emerge: (1) selection affects non-coding regions throughout the genome as well as coding regions, leading almost to a shortage of sequence material that can be considered reliably neutral in some species (Wright and Andolfatto, 2008). (2) There is evidence for frequent positive selection in the recent history of several species, including fruitflies, mice and particularly humans. Thousands of candidate regions for recent positive selection have been identified in 420 genome-wide scans in humans (Akey, 2009). Using a haplotype test, Hawks et al. (2007) found traces of adaptations in 7% of all human genes in as few as 40 000 years (3000 generations). Even higher estimates have been reported by Foll and Gaggiotti (2008). They used an FST based test and data from 53 human populations to find evidence for positive or balancing selection in 131 out of 560 (423%) randomly distributed STR marker loci. This is a staggering number, but how reliable are these estimates? It has long been known that demographic effects can confound the results, but how severe are these problems in real world applications? A new study by Excoffier et al. (2009) suggests that they can be very severe indeed. In particular, the findings demonstrate the importance of an accurate characterization of population structure for methods based on FST. Genomic tests for selection can be distinguished with respect to the summary statistics they use. Several of these statistics are used to detect hitchhiking events, also known as selective sweeps (Schlotterer, 2003; Pavlidis et al., 2008). These methods build on the characteristic footprint of recent positive selection on linked neutral DNA. The main effect is a local reduction in polymorphism, but the signal can also be picked up in the frequency spectrum and the local linkage disequilibrium or haplotype pattern. The strengths and weaknesses of the hitchhiking approach are quite well understood (Teshima et al., 2006; Thornton et al., 2007). The problem that is considered most severe is that certain events in the demographic history of a population can mimic the polymorphism patterns produced by selection. Population bottlenecks of a critical strength are the most dreaded alternative scenario. The reason is easy to understand: bottlenecks readily lead to large variances in the genealogical (coalescent) history of samples from different loci along a chromosome. These histories can either be short if the entire sample coalesces to a common ancestor during the bottleneck, or very much longer if several lines of descent extend through the bottleneck into a large ancestral population. As a result, almost all summary statistics show large variances, turning a population bottleneck into a neutral null-model that is hard to reject. Similarly, if a simpler demography is (wrongly) assumed, tests will produce an excess of false positives. An alternative method to detect selection from genomic data goes back to Lewontin and Krakauer (1973). It is based on genetic diversity between subpopulations (demes) as measured by FST and follows a simple intuition: regions under diversifying selection should exhibit larger divergence among demes than neutral loci (high FST). Similarly, regions under uniform balancing selection in all demes should be less differentiated (low FST). More recently, these ideas have been developed into sophisticated statistical frameworks to detect selection from genome scans (for example, Beaumont and Nichols, 1996; Beaumont and Balding, 2004; Foll and Gaggiotti, 2008). Compared with the hitchhiking approach, the FST method focuses on a different selection scenario: diversifying local selection instead of populationwide positive selection. Consequently, one expects to detect partly complementary sets of candidate loci. The method was criticised early on by Robertson (1975) concerning robustness with respect to demography; however, recent theoretical considerations and a limited number of simulations have led to speculations that the method might be less vulnerable (Beaumont, 2005). With the new work by Excoffier et al. (2009), this issue can be considered as settled. The authors convincingly establish a neutral model with hierarchical population structure as the ‘bottleneck scenario’ of the FST based approach. The reason is analogous to the case of sweeps and bottlenecks: due to hierarchical structure (and similarly due to range expansion or sequential population splits and mergers) different demes draw from different migrant pools, leading to higher levels of variance in FST than expected under an island model. To avoid excessive false positives, knowledge about the population structure needs to be built into the null distribution of FST that is used. For a hierarchical model, Excoffier et al. (2009) show how this can be done. The results are drastic—and sobering. In their reanalysis of human STR data, introduction of hierarchical structure based on five previously established geographic regions reduces the frequency of selection candidates from 23% (Foll and Gaggiotti, 2008) to no more than expected by chance (that is, comparable with the 1% significance level applied). What do these results imply? Certainly that many numbers in published studies are up for revision. But not necessarily that selection is rare. The problem is that our knowledge about false negatives is even more rudimentary than about false positives. For panmictic populations, the power of many tests to detect selection is known to be rather low. For a structured population, this information is basically missing. Realistic models of selection should further account for local adaptation, adaptation from standing genetic variation or interference among selected loci. It will be important to characterize the expected genomic footprints under realistic scenarios in much more detail and to construct adequate (combinations of) summary statistics to detect the Heredity (2009) 103, 283–284 & 2009 Macmillan Publishers Limited All rights reserved 0018-067X/09 $32.00

The long-term viability of a metapopulation depends partly on the gene flow among sub-populations. Management approaches such as translocations and supportive breeding between closely related populations may affect gene flow and overall structure, and therefore viability. Here, we examined temporal changes in the fine-scale population structure of coho salmon (Oncorhynchus kisutch) by comparing archived (1938) and modern (2001-2005) populations in six rivers within a single conservation unit (Puget Sound, Washington) sampled before and after an extended period of between-river transfers and releases of millions of cultured salmon. Genotype frequencies at eight microsatellite loci showed that current populations descended from historical Puget Sound populations, but populations in different rivers that exchanged fish for hatchery propagation share more of their ancestry recently than they did historically. Historically, populations in different rivers were isolated by geographic distance, but that relationship is no longer significant. Allelic richness among all populations declined significantly, suggesting that genetic drift has increased because of a population bottleneck. Populations in different rivers and within the same river have become more diverged, providing further evidence for a widespread bottleneck. Previously, we observed that genetic distance significantly decreased with the number of fish exchanged; however, some populations apparently resisted introgression. Altered gene flow and lost diversity may affect the complexity, and therefore resiliency of sub-populations within a conservation unit. Plans for artificial culture need to maintain existing genetic diversity and avoid disrupting the fine-scale structure by using local populations for parents whenever possible.

We investigated the relative importance of resource use and geography on genetic differentiation in the sister-species pair of generalist and specialist bark beetles: Dendroctonus ponderosae and D. jeffreyi (Coleoptera: Scolytidae). In two regions, where the distributions of these species overlap, we collected specimens of the generalist from multiple host species and specimens of the specialist from its single host species. Using allozyme techniques, we uncovered genetic differentiation between generalist populations on different host species in the same region (one locus in each region). However, a much stronger pattern of differentiation was found between specialist populations in the two distantly separated regions (three loci). With mtDNA, we found no significant differentiation between regions in the specialist, or among host species in the generalist, although there was some differentiation between regions in the generalist (AMOVA, P < 0.05). Overall, the generalist populations maintained approximately 10 times the genetic variation in mtDNA as the specialist populations, which suggests that the specialist either has generally smaller population sizes than the generalist, or has experienced a historical population bottleneck.

Experimental bottleneck lines were generated from a single outbred population of the housefly using one, four, or 16 pairs of flies. These lines were followed through one, three, or five successive founder-flush cycles. After each flush 30 individuals from each line were assayed for electrophoretic variation at four initially polymorphic loci. Electrophoretic variation largely followed neutral expectation, the major exception being that the differentiation among 16-pair lines was greater than expected. All bottleneck sizes showed significant losses in genetic variation compared to the control, particularly for losses in numbers of alleles. These findings contrast theoretical predictions in that few lines and loci would be required to detect historical bottlenecks.

Patterns of genetic differentiation among six populations of Tachigali versicolor (Fabaceae: Papilionoideae) on Barro Colorado Island, Panama were investigated. Average gene diversity within any one population (He) was 0.073 (SD 0.010), and He over all populations was 0.080. Populations showed relatively little genetic differentiation (mean GST=0.069), suggesting high levels of gene flow. A direct estimate of pollen flow indicated that 21% of the pollen received by a cluster of five trees had travelled at least 500 m. Genetic analyses of the mating system showed complete outcrossing (tm=0.998, SE±0.054; mean ts=1.001, SE±0.063). Estimates of F at different life stages showed a slight deficiency of heterozygotes in the six population samples, a slight excess among the 25 flowering adult trees, and no significant deviation in heterozygosity in progeny arrays. These differences may reflect the monocarpic life history of T. versicolor, in which adults flowering in a given year represent a temporal genetic bottleneck, producing a Wahlund effect in genotype frequencies in the overall population. This interpretation of genetic structure in T. versicolor suggests the overriding importance of ecological factors and life history on genetic processes in natural populations.

Population fragmentation is a widespread phenomenon usually associated with human activity. As a result of habitat transformation, the philopatric and steppe-specialist Lesser Kestrel Falco naumanni underwent a severe population decline during the last century that increased population fragmentation throughout its breeding range. In contrast, the ubiquitous Eurasian Kestrel Falco tinnunculus did not suffer such adverse effects, its breeding range still remaining rather continuous. Using microsatellites, we tested the effects of population fragmentation on large-scale spatial patterns of genetic differentiation and diversity by comparing these two sympatric and phylogenetically related species. Our results suggest that habitat fragmentation has increased genetic differentiation between Lesser Kestrel populations, following an isolation-by-distance pattern, while the population of Eurasian Kestrels is panmictic. Contrary to expectations, we did not detect significant evidence of reduced genetic variation or increased inbreeding in Lesser Kestrels. Although this study reports genetic differentiation in a species that has potential for long-distance dispersal but philopatry-limited gene flow, large enough effective population sizes and migration may have been sufficient to mitigate genetic depauperation. A serious reduction of genetic diversity in Lesser Kestrels would, therefore, only be expected after severe population bottlenecks following extreme geographic isolation.

Recent years have seen an explosion of interest in evidence for positive Darwinian selection at the molecular level. This quest has been hampered by the use of statistical methods that fail adequately to rule out alternative hypotheses, particularly the relaxation of purifying selection and the effects of population bottlenecks, during which the effectiveness of purifying selection is reduced. A further problem has been the assumption that positive selection will generally involve repeated amino-acid changes to a single protein. This model was derived from the case of the vertebrate major histocompatibility complex (MHC), but the MHC proteins are unusual in being involved in protein-protein recognition and in a co-evolutionary process of pathogens. There is no reason to suppose that repeated amino-acid changes to a single protein are involved in selectively advantageous phenotypes in general. Rather adaptive phenotypes are much more likely to result from other causes, including single amino-acid changes; deletion or silencing of genes or changes in the pattern of gene expression.

Hybridization is increasingly seen as a trigger for rapid evolution and speciation. To quantify and qualify divergence associated with recent homoploid hybrid speciation, we compared quantitative trait (QT) and molecular genetic variation between the homoploid hybrid species Senecio squalidus and its parental species, S. aethnensis and S. chrysanthemifolius, and also their naturally occurring Sicilian hybrids. S. squalidus originated and became invasive in the United Kingdom following the introduction of hybrid plants from Mount Etna, Sicily, about 300 years ago. We recorded considerable molecular genetic differentiation between S. squalidus and its parents and their Sicilian hybrids in terms of both reduced genetic diversity and altered allele frequencies, potentially due to the genetic bottleneck associated with introduction to the United Kingdom. S. squalidus is also distinct from its parents and Sicilian hybrids for QTs, but less so than for molecular genetic markers. We suggest that this is due to resilience of polygenic QTs to changes in allele frequency or lack of selection for hybrid niche divergence in geographic isolation. While S. squalidus is intermediate or parental-like for most QTs, some trangressively distinct traits were observed, which might indicate emerging local adaptation in its invasive range. This study emphasizes the important contribution of founder events and geographic isolation to successful homoploid hybrid speciation. © 2012 Macmillan Publishers Limited All rights reserved 0018-067X/12.

Large numbers of crop plant accessions from all over the world have been amassed in gene banks to secure a gene pool for future breeding programmes. Maintenance of accessions held as seed samples in cold stores involves frequent rejuvenation cycles to ensure the viability of seeds. The practice of rejuvenation by multiplication of a sample of each accession in small field plots has the potential to create population bottlenecks, leading to loss of genetic diversity and changes in gene frequencies every rejuvenation cycle. In order to determine whether these undesirable effects occur, genetic diversity levels were assessed for morphological and isozyme markers within gene bank accessions of two barley landraces from Syria that had been stored for 10, 40 and 72 years. These were compared with genetic diversity levels for the same markers in barley landraces collected recently at locations in Syria where they are still under cultivation. Average gene diversity (H), alleles per locus (A) and percentage polymorphic loci (P (0.01)) all showed very significant declines with length of time in storage, and genetic differentiation FST among accessions increased over time. If the observed differences in genetic diversity are caused by genetic drift in gene bank accessions rejuvenated every 5.3 years, it was estimated that the effective population size Ne of rejuvenation populations over their period in storage was only 4.7. Implications for gene bank management are discussed.

Major genetic breaks between the Indian and Pacific oceans have been reported for marine fishes and invertebrates. The genetic structure and history of the Indian scad mackerel, Decapterus russelli, in the Indo-Malay archipelago were investigated using the cytochrome b gene sequence as mitochondrial marker and two length-polymorphic introns as nuclear markers. The existence of two major mitochondrial lineages separated by 2.2% average nucleotide divergence, and their heterogeneous geographical distributions, were confirmed. This indicated past geographic isolation, possibly caused by a Pleistocene drop in sea level. The presence, in sympatry, of the two mitochondrial lineages was thought to result from secondary contact. A recent population bottleneck and subsequent rapid population expansion were indicated by low genetic diversities and strongly negative Tajima's D-values. This evidence supports the hypothesis that the habitat available to D. russelli in the Pleistocene was restricted. Taking into account both mitochondrial and nuclear-DNA data, three geographically distinct populations were identified: one sampled in the Makassar Strait and Sulawesi Sea, one in the Arafura Sea and the third from the entire western region of the Indo-Malay archipelago. Considering the high hydrological connectivity of this region of the Indo-Pacific and the species pelagic life-history, the population structure may be maintained by homing behaviour and, perhaps, the association of spawning with retention zones.

Strong and persistent associations between sex and genotype frequencies at the Mpi allozyme locus (mannose-6-phosphate isomerase) were found in three lacustrine populations of Mysis relicta sp. I in eastern Finland. Almost all females were homozygotes 100/100, whereas most males were heterozygotes 107/100. This disequilibrium suggests a complete linkage between Mpi and a sex-determining factor in a male heterogametic system and provides the first evidence for a genetic sex-determining mechanism in the crustacean order Mysida. However, no disequilibria were found in other parts of the species range. Potential mechanisms involved in generating the disequilibria are considered (sex-specific selection, recombination modifiers, hitchhiking, population bottlenecks). The restricted geographical distribution of the sex–Mpi association can be related to the early postglacial geological evolution of the lakes studied. A detailed scenario for the colonization history and genetic changes in the populations is presented. This involves initial immigration using temporary connections among ice-marginal lakes in eastern Finland approximately 10000 BP, associated population bottlenecks, and the origin and local selective spread of a nonrecombining Y-Mpi107 chromosome in the Sotkamo area c. 9300 BP. Soon after the isolation of the three headwater lakes (c. 9100 BP), a new recombination modifier caused a breakdown of the association in populations downstream.

Anaecypris hispanica is a cyprinid fish which is endemic to the Guadiana River basin in the Iberian Peninsula, and whose abundance and geographical range have contracted considerably during the last 20 years. We investigated mitochondrial DNA cytochrome b and control region variation among specimens representative of nine tributaries, using direct sequencing and diagnostic restriction fragment length polymorphism. The samples from the Caia, Degebe, Ardila, and Odeleite rivers exhibited haplotypes that differed by a large number of site differences, which may be indicative of population bottlenecks that have caused stochastic extinction of haplotypes. In contrast, the populations from the Xevora, Chanca, Carreiras, Vascao and Foupana rivers exhibited low levels of nucleotide diversity, which together with high haplotype diversity may also be indicative of genetic bottleneck events, with subsequent population expansion. Phylogenetic analyses, a minimum spanning network, and an analysis of molecular variance revealed geographical structuring, suggesting limited or no gene flow between populations. The populations from extreme southern rivers (Foupana and Odeleite) are monophyletic entities, suggesting that they have been isolated, probably as a consequence of brackish water upstream of their confluence with the Guadiana. The results suggest that the Foupana and the Odeleite populations, and the remaining northern populations altogether should be managed as three distinct Evolutionary Significant Units (ESUs). Within the northern ESU, four Management Units (MUs) should be considered.

Strong frequency-dependent selection as found in the self-incompatibility loci of flowering plants maintains allelic lineages for extremely long time scales, such that allelic genealogies can shed insight into long-term demographic patterns of species. Effective mutation rate, as well as demographic change such as population bottlenecks, can influence genealogical structure. In addition, loss of functionality at the self-incompatibility locus is likely to affect radiation rates. Partial sequences for 21 S-RNase alleles of the mid-elevation tropical species Witheringia solanacea were obtained in order to compare their substitution rates and genealogy with those of Witheringia maculata and two species in the closely related genus Physalis. Sequences for W. solanacea fell into the three clades within the Solanaceae already identified for the genus. Terminal branch lengths for W. solanacea, scaled to the total depth of its phylogeny, were intermediate between the unusually short terminal branches of W. maculata and those of the two Physalis species. In contrast to the Physalis species, where interspecific dN/dS for closely related alleles exceeded 1.0 to the same degree as did intraspecific dN/dS, in Witheringia only intraspecific comparisons showed an excess of nonsynonymous substitutions, suggesting postspeciation radiation of alleles. Alleles associated with lowered S-RNase production and self-compatibility showed extremely short terminal branches. In summary, it appears that rapid recent diversification of alleles characterizes the Witheringia lineages. In some cases, this rapid diversification can be attributed to relaxed constraints due to breakdown of self-incompatibility.

Southern India, one of the last strongholds of the endangered Asian elephant (Elephas maximus), harbours about one-fifth of the global population. We present here the first population genetic study of free-ranging Asian elephants, examining within- and among-population differentiation by analysing mitochondrial DNA (mtDNA) and nuclear microsatellite DNA differentiation across the Nilgiris-Eastern Ghats, Anamalai, and Periyar elephant reserves of southern India. Low mtDNA diversity and 'normal' microsatellite diversity were observed. Surprisingly, the Nilgiri population, which is the world's single largest Asian elephant population, had only one mtDNA haplotype and lower microsatellite diversity than the two other smaller populations examined. There was almost no mtDNA or microsatellite differentiation among localities within the Nilgiris, an area of about 15,000 km2. This suggests extensive gene flow in the past, which is compatible with the home ranges of several hundred square kilometres of elephants in southern India. Conversely, the Nilgiri population is genetically distinct at both mitochondrial and microsatellite markers from the two more southerly populations, Anamalai and Periyar, which in turn are not genetically differentiated from each other. The more southerly populations are separated from the Nilgiris by only a 40-km-wide stretch across a gap in the Western Ghats mountain range. These results variably indicate the importance of population bottlenecks, social organization, and biogeographic barriers in shaping the distribution of genetic variation among Asian elephant populations in southern India.

During the last two centuries, the Spanish ibex (Capra pyrenaica) has shown a significant demographic decline as a result of the progressive destruction of its natural habitat, disease epidemics, and uncontrolled hunting. Partial sequencing of the class II MHC DRB1 gene revealed that the Spanish ibex has remarkably low levels of genetic variation at this locus, with only six different DRB1 alleles and an observed heterozygosity of 0.429-0.579. The rates of nonsynonymous vs synonymous substitutions were significantly different in the peptide-binding region (dN/dS=5.347, P=0.002), a feature that indicates that the DRB1 gene is under positive selection. A phylogenetic analysis of the Spanish ibex and a set of domestic goat DRB1 alleles revealed that the reported sequences represent four major allelic lineages. The limited allelic repertoire of the DRB1 gene in the Spanish ibex is likely the direct result of the recent history of population bottlenecks and marked demographic decline of this species. A genetic survey of 13 microsatellite loci was consistent with this idea. The Spanish ibex subspecies C. p. hispanica and C. p. victoriae consistently showed considerably lower levels of microsatellite heterozygosity (Ho=0.184-0.231) and allelic diversity (mean number of alleles per locus=2-2.4) than those reported in other wild ruminants. This study demonstrates the significance of both natural selection and the demographic history of populations in determining patterns of genetic variation at MHC loci. In addition, our results emphasize the importance of locally adapted populations for the preservation of genetic diversity.

Variation at 15 microsatellite loci was characterized for a population of the solitary Patagonian tuco-tuco (Ctenomys haigi) and a population of group-living colonial tuco-tuco (C. sociabilis), both of which were located in the Limay River Valley of south western Argentina. All loci examined were characterized by uninterrupted di- or trinucleotide repeats in both species; seven of these loci had been isolated from C. haigi and eight had been isolated from C. sociabilis. Across all loci, there was a significant tendency for both number of alleles and heterozygosity to be greater in C. haigi than in C. sociabilis. Cloning and sequencing of multiple PCR products per locus per population revealed no significant biases in allele length, suggesting that this difference in variability was not due to ascertainment bias or to population-wide differences in rates of microsatellite evolution. Instead, differences in microsatellite variation between C. haigi and C. sociabilis were more consistent with current demographic and suspected historical differences between these populations. In particular, interpopulation differences in the distribution of microsatellite allele sizes and allele frequencies suggested that C. sociabilis has been more subject to historical reductions in population size (e.g. population bottlenecks) than has C. haigi. These findings indicate that analyses of microsatellite structure can yield important insights into the population-level phenomena that contribute to diversity at these markers, including differences in population history that continue to influence levels of genetic variability.

The European wild rabbit (Oryctolagus cuniculus) is an introduced species in Britain, and populations have been profoundly influenced by both man and disease. In stable environmental conditions, distinct social behaviour is observed, and this social structure leads to significant genetic structuring at the intrapopulation level. In this study, European wild rabbits were sampled from 17 sites across the East Anglian region of Britain and genotyped with nine microsatellite loci. Genotypical proportions deviated significantly from Hardy–Weinberg equilibrium, reflecting a degree of population subdivision and non-random mating. Several estimates of measures of population genetic structure revealed that populations are genetically distinct and have small effective population sizes. These distinctive properties are seen to be the combined effects of the social structure and random drift acting on bottlenecked populations after myxomatosis. It is concluded that the genetic structure seen in rabbit populations today is unlikely to reflect historical structuring present before myxomatosis, but that it results from recent events.

Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60 K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.

The effective size of a natural Drosophila subobscura population has been computed by drawing together various pieces of ecological information. The value, for both variance and inbreeding effective numbers, is approximately 400. This is largely due to reductions caused by a winter bottleneck and non-random distributions of family sizes. Areas where such estimates might be refined further are pointed out, and the implications of the results are discussed.

The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris. We further sequenced 8 nuclear genes to provide a neutral reference, and investigated the evolution of S-alleles via genealogical and population genetic analyses. Both shared ancestral polymorphism and an excess of non-synonymous substitution were detected in the S-RNases of the tribe Maleae in Rosaceae, indicating the action of long-term balancing selection. Approximate Bayesian Computations based on the reference neutral loci revealed a severe bottleneck in four of the six studied M. sieversii populations, suggesting that the low number of S-alleles found in this species is mainly the result of diversity loss due to a drastic population contraction. Such a bottleneck may lead to ambiguous footprints of ongoing balancing selection detected at the S-locus. This study not only elucidates the constituents and number of S-alleles in M. sieversii but also illustrates the potential utility of S-allele number shifts in demographic inference for self-incompatible plant species.

Conservation genetic theory suggests that small and isolated populations should be subject to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproductive adult population size of only 65 adult adders (range 12-171), the population maintains high levels of heterozygosity and allelic diversity similar to that observed in two mainland populations. Even a 14-year major "bottleneck " i.e., a reduction in adult adder numbers, encompassing at least four adder generations, did not result in any reduction in the island adders' heterozygosity and allelic diversity. Female adders are polyandrous, and fertilisation is non-random, which our empirical data and modelling suggest are underpinning the maintenance of the population's high level of heterozygosity. Our empirical results and subsequent modelling suggest that the positive genetic effects of polyandry in combination with non-random fertilisation, often overlooked in conservation genetic analyses, deserve greater consideration when predicting long-term survival of small and isolated populations.

Species colonizing new areas disjunct from their original habitat may be subject to novel selection pressures, and exhibit adaptive genetic changes. However, if colonization occurs through a small number of founders, the genetic composition of the colonized population may differ from that of the original population simply due to genetic drift. Disentangling the effects of founder drift and selection after colonization is crucial to understanding the adaptive process. Drosophila buzzatii colonized Australia some 600-700 generations ago, and spread rapidly over a wide geographical range. Genetic variation for 15 microsatellite loci in each of nine populations in eastern Australia was used to estimate the size of the bottleneck, and to determine if any of these microsatellites marked genomic regions subject to recent selection. We estimate that on its introduction to Australia, D. buzzatii went through a moderate bottleneck (approximately 30-40 founders). Linkage disequilibrium was common, both intrachromosomal and between loci on different chromosomes. Of the 15 loci, 2 showed evidence of selection, one exhibiting local adaptation in different populations and the other balancing selection. We conclude that linkage disequilibria may be far more common in natural populations than is generally assumed, and the loci apparently affected by selection may well be marking selection in large genome regions including many loci that are not necessarily closely linked.

Wild common bean (Phaseolus vulgaris L.) is distributed throughout the Americas from Mexico to northern Argentina. Within this range, the species is divided into two gene pools (Andean and Middle American) along a latitudinal gradient. The diversity of 24 wild common bean genotypes from throughout the geographic range of the species was described by using sequence data from 13 loci. An isolation-migration model was evaluated using a coalescent analysis to estimate multiple demographic parameters. Using a Bayesian approach, Andean and Middle American subpopulations with high percentage of parentages were observed. Over all loci, the Middle American gene pool was more diverse than the Andean gene pool (π(sil)=0.0089 vs 0.0068). The two subpopulations were strongly genetically differentiated over all loci (F(st)=0.29). It is estimated that the two current wild gene pools diverged from a common ancestor ∼111 000 years ago. Subsequently, each gene pool underwent a bottleneck immediately after divergence and lasted ∼40 000 years. The Middle American bottleneck population size was ∼46% of the ancestral population size, whereas the Andean was 26%. Continuous asymmetric gene flow was detected between the two gene pools with a larger number of migrants entering Middle American gene pool from the Andean gene pool. These results suggest that because of the complex population structure associated with the ancestral divergence, subsequent bottlenecks in each gene pool, gene pool-specific domestication and intense selection within each gene pool by breeders; association mapping would best be practised within each common bean gene pool.

The potential factors that may influence the genetic structure of the gynodioecious annual Phacelia dubia were assessed using electrophoretic and ecological information at a locality in which the population size changed by about three orders of magnitude. Fluctuations in population size appeared to have little influence on the allelic composition, heterozygosity and mixed mating system of the population. Despite wide fluctuations in total population size, the estimated effective population size during (Ne = 20) and after the bottleneck (Ne = 28) was little changed. Also, a significant spatial substructuring, evidenced by a cline in MDH and by the F-statistics, was observed before and after the bottleneck. The recovery of the population and the preservation of genetic diversity was attributable in part to the seed bank in the soil. Spatial gene flow via seeds was small compared with pollen flow and both were restricted. Nevertheless, substructuring contributes to a small portion of the total inbreeding. Also, the rate of apparent selfing of male steriles did not provide evidence of biparental inbreeding. Most of the inbreeding, however, was within subpopulations and autogamy appears to be the major contributor. It was concluded that the mating system is the leading factor determining the genetic structure and that the seed bank ensures genetic constancy in time in the face of large fluctuations in population size.

The globally invasive Round Goby (Neogobius melanostomus) was introduced to the Great Lakes around 1990, spreading widely and becoming the dominant benthic fish in many areas. The speed and scope of this invasion is remarkable and calls into question conventional secondary spread models and scenarios. We utilized nine microsatellites to identify large-scale genetic structure in Round Goby populations in the eastern Great Lakes, and assessed the role of colonization vs. secondary transport and dispersal in developing this structure. We identified three clusters, corresponding with Lake Huron, eastern Lake Erie, and western Lake Erie plus eastern Lake Ontario, along with three highly divergent populations. Bottleneck analysis identified founder effects in two divergent populations. Regression analyses of isolation by distance and allelic richness vs. distance from the initial invasion site were consistent with limited migration. However, some populations in eastern Lake Erie and Lake Ontario showed anomalously low genetic distance from the original site of colonization, consistent with secondary transport of large numbers of individuals via ballast water. We conclude that genetic structure of Round Goby in the Great Lakes principally resulted from long-distance secondary transport via ballast water with additional movement of individual via bait buckets and natural dispersal. The success of Round Gobies represents an interesting model for colonization characterization; however, those same attributes present significant challenges for conservation and fisheries management. Current management likely prevents many new species from arriving in the Great Lakes, but fails to address the transport of species within the lakes after they arrive; this is an issue of clear and pressing importance.

Invasive species exert a serious impact on native fauna and flora and have been the target of many eradication and management efforts worldwide. However, a lack of data on population structure and history, exacerbated by the recency of many species introductions, limits the efficiency with which such species can be kept at bay. In this study we generated a novel genome of high assembly quality and genotyped 4735 genome-wide single nucleotide polymorphic (SNP) markers from 78 individuals of an invasive population of the Javan Myna Acridotheres javanicus across the island of Singapore. We inferred limited population subdivision at a micro-geographic level, a genetic patch size (~13-14 km) indicative of a pronounced dispersal ability, and barely an increase in effective population size since introduction despite an increase of four to five orders of magnitude in actual population size, suggesting that low population-genetic diversity following a bottleneck has not impeded establishment success. Landscape genomic analyses identified urban features, such as low-rise neighborhoods, that constitute pronounced barriers to gene flow. Based on our data, we consider an approach targeting the complete eradication of Javan Mynas across Singapore to be unfeasible. Instead, a mixed approach of localized mitigation measures taking into account urban geographic features and planning policy may be the most promising avenue to reducing the adverse impacts of this urban pest. Our study demonstrates how genomic methods can directly inform the management and control of invasive species, even in geographically limited datasets with high gene flow rates.

Human-mediated changes in landscapes can facilitate niche expansion and accelerate the adaptation of insect species. The interaction between the evolutionary history of the sugarcane borer, Diatraea saccharalis Fabricius, and historical and modern agricultural activity in Brazil shaped its spatial genetic structure, facilitating ecological divergence and incipient host shifting. Based on microsatellite data, STRUCTURE analyses identified two (K = 2) and three (K = 3) significant genetic clusters that corresponded to: (a) a strong signal of spatial genetic structure and, (b) a cryptic signal of host differentiation. We inferred that K = 2 reflects the footprint of agricultural activity, such as expansion of crop production (sugarcane and maize), unintentional dispersion of pests, and management practices. In contrast, K = 3 indicated incipient host differentiation between larvae collected from sugarcane or maize. Our estimates of population size changes indicated that a historical bottleneck was associated with a reduction of sugarcane production ≈200 years ago. However, a more recent population expansion was detected (>1950s), associated with agricultural expansion of large crop production into previously unfarmed land. Partial Mantel tests supported our hypothesis of incipient host adaptation, and identified isolation-by-environment (e.g., host plant) in São Paulo and Minas Gerais states, where sugarcane has been traditionally produced in Brazil. The impact of agricultural production on D. saccharalis may continue, as the current population structure may hinder the efficacy of refuge plants in delaying insect resistance evolution to Bt toxin.