Dynamics of correlated genetic systems III. Behaviour of chromosomal segments under lethal selection

The effect of lethal selection on linked marker loci was investigated in experimental populations of Drosophila melanogaster. Replicate experimental populations were initiated using flies heterozygous for the lethal gene Stubble and with the enzyme loci esterase-C and phosphoglucomutase in linkage disequilibrium with Stubble. The dynamical behavior of the lethal and marker genes was followed through generation 41 when the experimental was terminated. The major findings of the experiment are: (1) the lethal gene was eliminated from all replicate populations; (2) the marker gene frequency behavior could not be accounted for by lethal selection and recombination alone; and (3) linkage disequilibrium among the marker genes stabilized at high levels. The results of this experiment are contrasted with those of a previous experiment, of similar design, involving the lethal gene Glued. New data from generations 40 and 41 of the Glued experiment are also presented. The qualitative agreement among experiments are also presented. The both experiments indicate the existence of other strongly selected factors in the region spanned by the marker genes.This research was supported in part by National Science Foundation grants GB41116 and DEB76-82479.     

Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines (Open Access publication)

We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL) regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed F_st values greater than 0.15. However, the non-significant difference (P > 0.05) between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone.     

Dynamics of Correlated Genetic Systems. V. Rates of Decay of Linkage Disequilibria in Experimental Populations of DROSOPHILA MELANOGASTER

The dynamic behavior of four-locus gametic frequency distributions was studied in five replicate cage populations of Drosophila melanogaster for up to 50 generations. The joint frequency distributions were resolved into gene frequencies and various disequilibrium measures. In addition, F statistics for marginal single-locus genotypic frequency distributions were followed through time. The gene frequency, disequilibrium and F statistics were obtained for four chromosome 3 enzyme marker loci [isocitrate dehydrogenase (3–27.1), esterase-6 (3–36.8), phosphoglucomutase (3–43.4) and esterase-C (3–49.0)]. The initial structure of the experimental populations featured random mating proportions, and two complementary gametic types with respect to the marker loci, thus assuring complete pairwise linkage disequilibrium among the markers.——The experimental results indicate: (1) the between-replicate variance in gene frequency varied substantially among loci, with isocitrate dehydrogenase showing the greatest between-replicate variance, and esterase-C the least. (2) The F statistics initially were strongly negative but decayed to the neighborhood of zero for all marker loci except esterase-C. The rate at which the F statistics approached zero varied among the marker loci, indicating substantial differences in the distribution of selective effects along the chromosome. The centromeric region, marked by esterase-C, shows the strongest selective effects. (3) The rate of decay of linkage disequilibrium was much faster than expected for pairs of neutral loci, averaging 1.82 times the neutral rate over all replicates and pairs of loci. This acceleration, which was observed for all six pairwise combinations of loci, was interpreted as resulting from the interaction between selection and recombination. Our experimental results are consistent with many investigations of linkage disequilibrium in natural populations of Drosophila melanogaster that show little or no disequilibrium among enzyme loci. (4) A fortuitous contamination of two cages revealed an apparent regulatory interaction between the migrant and nonmigrant chromosomes at the esterase-C locus. The migrant chromosomes were very rapidly absorbed into the recipient populations, despite this interaction. This result suggests that the dynamics of migration in populations may be phenomenologically richer than anticipated by simple theory.     

Selection for complex traits leaves little or no classic signatures of selection

Background

Selection signatures aim to identify genomic regions underlying recent adaptations in populations. However, the effects of selection in the genome are difficult to distinguish from random processes, such as genetic drift. Often associations between selection signatures and selected variants for complex traits is assumed even though this is rarely (if ever) tested. In this paper, we use 8 breeds of domestic cattle under strong artificial selection to investigate if selection signatures are co-located in genomic regions which are likely to be under selection.

Results

Our approaches to identify selection signatures (haplotype heterozygosity, integrated haplotype score and F_ST) identified strong and recent selection near many loci with mutations affecting simple traits under strong selection, such as coat colour. However, there was little evidence for a genome-wide association between strong selection signatures and regions affecting complex traits under selection, such as milk yield in dairy cattle. Even identifying selection signatures near some major loci was hindered by factors including allelic heterogeneity, selection for ancestral alleles and interactions with nearby selected loci.

Conclusions

Selection signatures detect loci with large effects under strong selection. However, the methodology is often assumed to also detect loci affecting complex traits where the selection pressure at an individual locus is weak. We present empirical evidence to suggests little discernible ‘selection signature’ for complex traits in the genome of dairy cattle despite very strong and recent artificial selection.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-246) contains supplementary material, which is available to authorized users.     

The Effects of Lethal Selection on the EST-6 to PGM Region of Chromosome 3 in DROSOPHILA MELANOGASTER

A powerful means of studying the effects of selection on chromosome segments in Drosophila melanogaster has been described by Clegg et. al. (1976, 1978). This method utilizes a recessive lethal, dominant visible allele whose selection dynamics can be accurately modelled to predict the fates of nonlethal alleles at linked loci. Results of these experiments indicate that strong epistatic interactions among loci occur that effect fitnesses associated with gametic types in the basal region of chromosome 3. We have used similar methods in studying a different segment of chromosome 3, that spanned by Est-6 (3-36.8) and Pgm (3-43.4), with the aim of determining whether the results of Clegg and his colleagues could be reproduced when a different region was studied. Our experiment showed that selection did operate on a region of the chromosome marked by Pgm, but that no evidence of selection at loci marked by Est-6 was apparent. Weak evidence for epistatic interactions among loci within the marked region was also found. Three possible explanations for the discrepancies between our experiments and those of Clegg et al. are suggested. First, the geographically homogeneous origin of our populations may preclude selectively significant changes as a result of recombination. Second, the results seen by Clegg et al. may have been unique to the regions they studied, which included the basal heterochromatin of the chromosomes. Finally, the three loci employed may not adequately mark the unit of selection, so that actual departures from predictions of selective neutrality may not have been apparent.     

Genetic differentiation of neutral markers and quantitative traits in predominantly selfing metapopulations: confronting theory and experiments with Arabidopsis thaliana

The comparison of the genetic differentiation of quantitative traits (QST) and molecular markers (FST) can inform on the strength and spatial heterogeneity of selection in natural populations, provided that markers behave neutrally. However, selection may influence the behaviour of markers in selfing species with strong linkage disequilibria among loci, therefore invalidating this test of detection of selection. We address this issue by monitoring the genetic differentiation of five microsatellite loci (FST) and nine quantitative traits (QST) in experimental metapopulations of the predominantly selfing species Arabidopsis thaliana, that evolved during eight generations. Metapopulations differed with respect to population size and selection heterogeneity. In large populations, the genetic differentiation of neutral microsatellites was much larger under heterogeneous selection than under uniform selection. Using simulations, we show that this influence of selection heterogeneity on FST can be attributable to initial linkage disequilibria among loci, creating stronger genetic differentiation of QTL than expected under a simple additive model with no initial linkage. We found no significant differences between FST and QST regardless of selection heterogeneity, despite a demonstrated effect of selection on QST values. Additional data are required to validate the role of mating system and linkage disequilibria in the joint evolution of neutral and selected genetic differentiation, but our results suggest that FST/QST comparisons can be conservative tests to detect selection in selfing species.     

A high-resolution map of the vicinity of the R1 locus on chromosome V of potato based on RFLP and AFLP markers

The R1 allele confers on potato a race-specific resistance to Phytophthora infestans. The corresponding genetic locus maps on chromosome V in a region in which several other resistance genes are also located. As part of a strategy for cloning R1, a high-resolution genetic map was constructed for the segment of chromosome V that is bordered by the RFLP loci GP21 and GP179 and includes the R1 locus. Bulked segregant analysis and markers based on amplified fragment length polymorphisms (AFLP markers) were used to select molecular markers closely linked to R1. Twenty-nine of approximately 3200 informative AFLP loci displayed linkage to the R1 locus. Based on the genotypic analysis of 461 gametes, eight loci mapped within the GP21–GP179 interval. Two of those could not be seperated from R1 by recombination. For genotyping large numbers of plants with respect to the flanking markers GP21 and GP179 PCR based assays were also developed which allowed marker-assisted selection of plants with genotypes Rr and rr and of recombinant plants.     

AFLPs and Mitochondrial Haplotypes Reveal Local Adaptation to Extreme Thermal Environments in a Freshwater Gastropod

The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher F_ST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence.     

Genetic analysis of differentiation among breeding ponds reveals a candidate gene for local adaptation in Rana arvalis

One of the main questions in evolutionary and conservation biology is how geographical and environmental features of the landscape shape neutral and adaptive genetic variation in natural populations. The identification of genomic polymorphisms that account for adaptive variation can aid in finding candidate loci for local adaptation. Consequently, a comparison of spatial patterns in neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection at the landscape scale. Many amphibians breed in wetlands, which differ in environmental conditions and in the degree of isolation, enhancing the potential for local adaptation. We used microsatellite markers to measure genetic differentiation among 17 local populations of Rana arvalis breeding in a network of wetlands. We found that locus RC08604 deviated from neutral expectations, suggesting that it is a good candidate for directional selection. We used a genetic network analysis to show that the allele distribution in this locus is correlated with habitat characteristics, whereas this was not the case at neutral markers that displayed a different allele distribution and population network in the study area. The graph approach illustrated the genomic heterogeneity (neutral loci vs. the candidate locus for directional selection) of gene exchange and genetic divergence among populations under directional selection. Limited gene flow between wetlands was only observed at the candidate genomic region under directional selection. RC08604 is partially located inside an up‐regulated thyroid‐hormone receptor (TRβ) gene coordinating the expression of other genes during metamorphosis and appears to be linked with variation in larval life‐history traits found among R. arvalis populations. We suggest that directional selection on genes coding larval life‐history traits is strong enough to maintain the divergence in these genomic regions, reducing the effective recombination of locally adapted alleles but not in other regions of the genome. Integrating this knowledge into conservation plans at the landscape scale will improve the design of management strategies to preserve adaptive genetic diversity in wetland networks.     

Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea

Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca × P. engelmannii hybrid zone across a broad latitudinal (40–60 degrees) and elevational (350–3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.     

Assessing genetic structure with multiple classes of molecular markers: a case study involving the introduced fire ant Solenopsis invicta.

We used 30 genetic markers of 6 different classes to describe hierarchical genetic structure in introduced populations of the fire ant Solenopsis invicta. These included four classes of presumably neutral nuclear loci (allozymes, codominant random amplified polymorphic DNAs (RAPDs), microsatellites, and dominant RAPDs), a class comprising two linked protein-coding nuclear loci under selection, and a marker of the mitochondrial DNA (mtDNA). Patterns of structure revealed by F statistics and exact tests of differentiation were highly concordant among the four classes of neutral nuclear markers, although the microsatellites were the most effective markers for detecting structure. The results from the mtDNA complemented those from the neutral nuclear markers by revealing that strong limitations to female-mediated gene flow were the cause of the local structure registered by the nuclear markers. The pattern of structure inferred from the selected nuclear loci was markedly different from the patterns derived from the other sets of markers but was predictable on the basis of the presumed mode of selection acting on these loci. In general, the results for all six classes of markers can be explained by known features of the social and reproductive biology of fire ants. Thus, the results from these diverse sets of markers, combined with detailed natural history data, provide an unusually complete picture of how the fundamental evolutionary forces of gene flow, drift, and selection govern the distribution of genetic variation within and between fire ant populations.     

Mutations Affecting Functions of the Drosophila Gene Glued

Glued mutations in Drosophila comprise an essential complementation group with complex developmental effects. The original Glued mutation (Gl) has dominant nonlethal effects in heterozygous flies, principally on the morphogenesis of the visual system. Gl also has a recessive lethal effect early in development. Mutations that reverse the dominant visual effects of Gl (GlR mutations) were induced by gamma-radiation or by insertions of the transposable P element. The GlR(G) mutations induced by gamma-radiation do not reverse the lethal effect of Gl; these appear to be null mutations, some of which (and possibly all) delete segments of the Glued region. The GlR(P) mutations induced by insertion of the P element also reverse concomitantly a recessive lethal effect of Gl, suggesting that both the recessive and dominant effects are controlled by the same gene. The reversal of a lethal effect of Gl by the P element is remarkable, since it indicates that an essential gene function can be restored by insertion of unrelated DNA. Another class of lethal Glued mutations was induced in the normal Gl+ strain by ethyl methanesulfonate (EMS). The EMS mutations belong to the same essential complementation group as Gl, but do not have the strong dominant effects of Gl on the visual system. The GlR(P) mutations provide a molecular marker for the Glued gene, which was used to map the gene to the 70C2 band of chromosome 3L by in situ hybridization of a P element probe to polytene chromosomes from the GlR(P) strains and also to isolate clones of Glued genomic DNA for molecular studies of the normal gene and the various Glued mutations.     

Use of RAPD and ITE molecular markers in studying the genetic structure of the Crimean population of T. boeoticum Boiss

The influence of ecological factors on variation of random PCR markers (RAPD and inter-MITE polymorphism (IMP) primers) was evaluated in two wild Triticum boeoticum populations with contrasting climatic conditions in Crimea. The proportion of variation that undergoes natural selection was compared for these two types of molecular markers. The Sapun Mountain and Baidar Valley populations differed significantly in 24.7% of the analyzed loci, with a low Nei distance between these populations (0.0324). The number of significantly different RAPD and IMP markers in the two populations was nearly equal. Testing for evolutionary neutrality showed that 13 loci (17.8%) were influenced by natural selection. The Sapun Mountain population was more dependent on natural selection (ten loci, 13.7%) than the Baidar Valley population (four loci, 5.5%). Eleven out of the 13 loci undergoing selection were amplified with IMP primers.     

Continental-Scale Footprint of Balancing and Positive Selection in a Small Rodent (Microtus arvalis)

Genetic adaptation to different environmental conditions is expected to lead to large differences between populations at selected loci, thus providing a signature of positive selection. Whereas balancing selection can maintain polymorphisms over long evolutionary periods and even geographic scale, thus leads to low levels of divergence between populations at selected loci. However, little is known about the relative importance of these two selective forces in shaping genomic diversity, partly due to difficulties in recognizing balancing selection in species showing low levels of differentiation. Here we address this problem by studying genomic diversity in the European common vole (Microtus arvalis) presenting high levels of differentiation between populations (average F _ST = 0.31). We studied 3,839 Amplified Fragment Length Polymorphism (AFLP) markers genotyped in 444 individuals from 21 populations distributed across the European continent and hence over different environmental conditions. Our statistical approach to detect markers under selection is based on a Bayesian method specifically developed for AFLP markers, which treats AFLPs as a nearly codominant marker system, and therefore has increased power to detect selection. The high number of screened populations allowed us to detect the signature of balancing selection across a large geographic area. We detected 33 markers potentially under balancing selection, hence strong evidence of stabilizing selection in 21 populations across Europe. However, our analyses identified four-times more markers (138) being under positive selection, and geographical patterns suggest that some of these markers are probably associated with alpine regions, which seem to have environmental conditions that favour adaptation. We conclude that despite favourable conditions in this study for the detection of balancing selection, this evolutionary force seems to play a relatively minor role in shaping the genomic diversity of the common vole, which is more influenced by positive selection and neutral processes like drift and demographic history.     

A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus) populations

Background

Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci.

Methods

We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1) and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection.

Results

No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D'' values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively) were significantly (P < 0.05) higher than for non-syntenic markers (0.15). The Ewens-Watterson test, the Beaumont and Nichol''s modified frequentist test and the Bayesian F_ST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P < 0.05) from neutral expectations. Furthermore, lnRV, lnRH and lnRθ'' statistics were used for the pairwise population comparison tests and were significantly less variable in one population relative to the other, providing additional evidence of selection signatures for two of the 51 loci. Moreover, the three Finnish native populations showed evidence of subpopulation divergence at SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium.

Conclusion

Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations.     

QTL Location and Epistatic Effect Analysis of 100-Seed Weight Using Wild Soybean (Glycine soja Sieb. & Zucc.) Chromosome Segment Substitution Lines

Increasing the yield of soybean (Glycine max L. Merrill) is a main aim of soybean breeding. The 100-seed weight is a critical factor for soybean yield. To facilitate genetic analysis of quantitative traits and to improve the accuracy of marker-assisted breeding in soybean, a valuable mapping population consisting of 194 chromosome segment substitution lines (CSSLs) was developed. In these lines, different chromosomal segments of the Chinese cultivar Suinong 14 were substituted into the genetic background of wild soybean (Glycine soja Sieb. & Zucc.) ZYD00006. Based on these CSSLs, a genetic map covering the full genome was generated using 121 simple sequence repeat (SSR) markers. In the quantitative trait loci (QTL) analysis, twelve main effect QTLs (qSW-B1-1/2/3, qSW-D1b-1/2, qSW-D2-1/2, qSW-G-1/2/3, qSW-M-2 and qSW-N-2) underlying 100-seed weight were identified in 2011 and 2012. The epistatic effects of pairwise interactions between markers were analyzed in 2011 and 2012. The results clearly demonstrated that these CSSLs could be used to identify QTLs, and that an epistatic analysis was able to detect several sites with important epistatic effects on 100-seed weight. Thus, we identified loci that will be valuable for improving soybean 100-seed weight. These results provide a valuable foundation for identifying the precise location of genes of interest, and for designing cloning and marker-assisted selection breeding strategies targeting the 100-seed weight of soybean.     

Evaluating outlier loci and their effect on the identification of pedigree errors

Homozygosity outlier loci, which show patterns of variation that are extremely divergent from the rest of the genome, can be evaluated by comparison of the homozygosity under Hardy-Weinberg proportions (the sum of the squares of allele frequencies) with the expected homozygosity under neutrality. Such outlier loci are potentially under selection (balancing selection or directional selection) when genome-wide effects (such as bottleneck and rapid population growth) are excluded. Outlier loci show skewed allele frequencies with respect to neutrality and may therefore affect the identification of pedigree errors. However, choosing neutral markers (excluding outlier loci) for the identification of pedigree errors has been neglected thus far. Our results showed that 4.1%, 5.5%, and 1.5% of the microsatellite markers, Illumina single-nucleotide polymorphisms (SNPs), and Affymetrix SNPs, respectively, on the autosomes appear to be under balancing selection (p or=40%) appear to be under balancing selection. Pedigree structure errors in 15 of 143 pedigrees were detected using microsatellite markers from the autosomes and/or selected SNPs from chromosomes 1 to 18 of the Illumina and/or selected SNPs from chromosomes 1 to 16 of the Affymetrix. Outlier loci did not make a major difference to the identification of pedigree errors. The Collaborative Study on the Genetics of Alcoholism data has pedigree errors and some of them may be due to sample mix up.     

Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs

Genetic analysis across a whole plant genome based on pedigree information offers considerable potential for enhancing genetic gain from plant breeding programs through quantitative trait loci (QTL) mapping and marker-assisted selection. Here, we report its application for graphically genotyping varieties used in Chinese japonica rice (Oryza sativa L.) pedigree breeding programs. We identified 34 important chromosomal regions from the founder parent that are under selection in the breeding programs, and by comparing donor genomic regions that are under selection with QTL locations of agronomic traits, we found that QTL clustered in important genomic regions, in accordance with association analyses of natural populations and other previous studies. The convergence of genomic regions under selection with QTL locations suggests that donor genomic regions harboring key genes/QTL for important agronomic traits have been selected by plant breeders since the 1950s from the founder rice plants. The results provide better understanding of the effects of selection in breeding programs on the traits of rice cultivars. They also provide potentially valuable information for enhancing rice breeding programs through screening candidate parents for targeted molecular markers, improving crop yield potential and identifying suitable genetic material for use in future breeding programs.     

Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)

Given predicted rapid climate change, an understanding of how environmental factors affect genetic diversity in natural populations is important. Future selection pressures are inherently unpredictable, so forest management policies should maintain both overall diversity and identify genetic markers associated with the environmental factors expected to change most rapidly, like temperature and rainfall. In this study, we genotyped 648 individuals in 28 populations of Castanopsis fargesii (Fagaceae) using 32 expressed sequence tag (EST)-derived microsatellite markers. After removing six loci that departed from Hardy–Weinberg equilibrium, we measured genetic variation, population structure and identified candidate loci putatively under selection by temperature and precipitation. We found that C. fargesii populations possessed high genetic diversity and moderate differentiation among them, indicating predominant outcrossing and few restrictions to gene flow. These patterns reduce the possible impact of stochastic effects or the influence of genetic isolation. Clear footprints of divergent selection at four loci were discovered. Frequencies of five alleles at these loci were strongly correlated with environmental factors, particularly extremes in precipitation. These alleles varied from being near fixation at one end of the gradient to being completely absent at the other. Our study species is an important forest tree in the subtropical regions of China and could have a major role in future management and reforestation plans. Our results demonstrate that the gene flow is widespread and abundant in natural populations, maintaining high diversity, while diversifying selection is acting on specific genomic regions.