The probability of genetic parallelism and convergence in natural populations

Genomic and genetic methods allow investigation of how frequently the same genes are used by different populations during adaptive evolution, yielding insights into the predictability of evolution at the genetic level. We estimated the probability of gene reuse in parallel and convergent phenotypic evolution in nature using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies. The probability declines with increasing age of the common ancestor of compared taxa, from about 0.8 for young nodes to 0.1–0.4 for the oldest nodes in our study. Probability of gene reuse is higher when populations begin from the same ancestor (genetic parallelism) than when they begin from divergent ancestors (genetic convergence). Our estimates are broadly consistent with genomic estimates of gene reuse during repeated adaptation to similar environments, but most genomic studies lack data on phenotypic traits affected. Frequent reuse of the same genes during repeated phenotypic evolution suggests that strong biases and constraints affect adaptive evolution, resulting in changes at a relatively small subset of available genes. Declines in the probability of gene reuse with increasing age suggest that these biases diverge with time.     

QTL mapping and the genetic basis of adaptation: recent developments

Quantitative trait loci (QTL) mapping has been used in a number of evolutionary studies to study the genetic basis of adaptation by mapping individual QTL that explain the differences between differentiated populations and also estimating their effects and interaction in the mapping population. This analysis can provide clues about the evolutionary history of populations and causes of the population differentiation. QTL mapping analysis methods and associated computer programs provide us tools for such an inference on the genetic basis and architecture of quantitative trait variation in a mapping population. Current methods have the capability to separate and localize multiple QTL and estimate their effects and interaction on a quantitative trait. More recent methods have been targeted to provide a comprehensive inference on the overall genetic architecture of multiple traits in a number of environments. This development is important for evolutionary studies on the genetic basis of multiple trait variation, genotype by environment interaction, host–parasite interaction, and also microarray gene expression QTL analysis.     

Mapping multiple QTL of different effects: comparison of a simple sequential testing strategy and multiple QTL mapping

The aim of this study was to explore, by computer simulation, the mapping of QTLs in a realistic but complex situation of many (linked) QTLs with different effects, and to compare two QTL mapping methods. A novel method to dissect genetic variation on multiple chromosomes using molecular markers in backcross and F₂ populations derived from inbred lines was suggested, and its properties tested using simulations. The rationale for this sequential testing method was to explicitly test for alternative genetic models. The method consists of a series of four basic statistical tests to decide whether variance was due to a single QTL, two QTLs, multiple QTLs, or polygenes, starting with a test to detect genetic variance associated with a particular chromosome. The method was able to distinguish between different QTL configurations, in that the probability to `detect' the correct model was high, varying from 0.75 to 1. For example, for a backcross population of 200 and an overall heritability of 50%, in 78% of replicates a polygenic model was detected when that was the underlying true model. To test the method for multiple chromosomes, QTLs were simulated on 10 chromosomes, following a geometric series of allele effects, assuming positive alleles were in coupling in the founder lines For these simulations, the sequential testing method was compared to the established Multiple QTL Mapping (MQM) method. For a backcross population of 400 individuals, power to detect genetic variance was low with both methods when the heritability was 0.40. For example, the power to detect genetic variation on a chromosome on which 6 QTLs explained 12.6% of the genetic variance, was less than 60% for both methods. For a large heritability (0.90), the power of MQM to detect genetic variance and to dissect QTL configurations was generally better, due to the simultaneous fitting of markers on all chromosomes. It is concluded that when testing different QTL configurations on a single chromosome using the sequential testing procedure, regions of other chromosomes which explain a significant amount of variation should be fitted in the model of analysis. This study reinforces the need for large experiments in plants and other species if the aim of a genome scan is to dissect quantitative genetic variation.     

The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli

Pleiotropy plays a central role in theories of adaptation, but little is known about the distribution of pleiotropic effects associated with different adaptive mutations. Previously, we described the phenotypic effects of a collection of independently arising beneficial mutations in Escherichia coli. We quantified their fitness effects in the glucose environment in which they evolved and their pleiotropic effects in five novel resource environments. Here we use a candidate gene approach to associate the phenotypic effects of the mutations with the underlying genetic changes. Among our collection of 27 adaptive mutants, we identified a total of 21 mutations (18 of which were unique) encompassing five different loci or gene regions. There was limited resolution to distinguish among loci based on their fitness effects in the glucose environment, demonstrating widespread parallelism in the direct response to selection. However, substantial heterogeneity in mutant effects was revealed when we examined their pleiotropic effects on fitness in the five novel environments. Substitutions in the same locus clustered together phenotypically, indicating concordance between molecular and phenotypic measures of divergence.     

人类复杂遗传疾病QTL分析方法的理论探讨

利用连锁不平衡理论,人类遗传学家已能把影响人类疾病的质量基因定位在小至1cM区域内,有些基因已被克隆出来。罗泽伟等进一步发展统计分析方法检测及估算分子标记与QTL之间的连锁不平衡系数,从而提出了人类复杂遗传病高解析度基因定位的理论策略。以此为基础,进一步探讨了供试群体在双亲基因频率存在差异时检测QTL和检测QTL互作的方法,给出了有关的理论结果。     

Flowering time QTL in natural populations of Arabidopsis thaliana and implications for their adaptive value

The genetic basis of phenotypic traits is of great interest to evolutionary biologists, but their contribution to adaptation in nature is often unknown. To determine the genetic architecture of flowering time in ecologically relevant conditions, we used a recombinant inbred line population created from two locally adapted populations of Arabidopsis thaliana from Sweden and Italy. Using these RILs, we identified flowering time QTL in growth chambers that mimicked the natural temperature and photoperiod variation across the growing season in each native environment. We also compared the genomic locations of flowering time QTL to those of fitness (total fruit number) QTL from a previous three‐year field study. Ten total flowering time QTL were found, and in all cases, the Italy genotype caused early flowering regardless of the conditions. Two QTL were consistent across chamber environments, and these had the largest effects on flowering time. Five of the fitness QTL colocalized with flowering time QTL found in the Italy conditions, and in each case, the local genotype was favoured. In contrast, just two flowering time QTL found in the Sweden conditions colocalized with fitness QTL and in only one case was the local genotype favoured. This implies that flowering time may be more important for adaptation in Italy than Sweden. Two candidate genes (FLC and VIN3) underlying the major flowering time QTL found in the current study are implicated in local adaptation.     

QTL architecture of resistance and tolerance traits in Arabidopsis thaliana in natural environments

Quantitative-genetic approaches have offered significant insights into phenotypic evolution. However, quantitative-genetic analyses fail to provide information about the evolutionary relevance of specific loci. One complex and ecologically relevant trait for plants is their resistance to herbivory because natural enemies can impose significant damage. To illustrate the insights of combined molecular and ecological research, we present the results of a field study mapping quantitative trait loci (QTL) for resistance and tolerance to natural rabbit herbivory in the genetic model, Arabidopsis thaliana. Replicates of the Ler x Col recombinant inbred lines were planted into field sites simulating natural autumn and spring seasonal germination cohorts. Shortly after flowering, herbivores removed the main flowering inflorescence (apical meristem). We found several main-effect QTL for resistance within each seasonal cohort and significant QTL-season interactions, demonstrating that the loci underlying resistance to a single herbivore differ across seasonal environments. The presence of QTL x environment also shows that variation at specific loci is only available to selection in some environments. Despite significant among-line variance components, no QTL for tolerance were detected. The combined results of the quantitative-genetic and QTL analyses demonstrate that many loci of small effect underlie tolerance to damage by rabbits, and counter the hypothesis of locus-specific tradeoffs between resistance and tolerance. The results also provide insights as to the locus-specific nature of evolutionary constraints, i.e. some loci influence flowering time and resistance in both seasonal cohorts. Our results show how linking molecular-genetic tools with field studies in ecologically relevant settings can clarify the role of specific loci in the evolution of quantitative traits.     

Testing hypotheses regarding the genetics of adaptation

Many of the hypotheses regarding the genetics of adaptation require that one know specific details about the genetic basis of complex traits, such as the number and effects of the loci involved. Developments in molecular biology have made it possible to create relatively dense maps of markers that can potentially be used to map genes underlying specific traits. However, there are a number of reasons to doubt that such mapping will provide the level of resolution necessary to specifically address many evolutionary questions. Moreover, evolutionary change is built upon the substitution of individual mutations, many of which may now be cosegregating in the same allele. In order for this developing area not to become a mirage that traps the efforts of an entire field, the genetic dissection of adaptive traits should be conducted within a strict hypothesis-testing framework and within systems that promise a reasonable chance of identifying the specific genetic changes of interest. Continuing advances in molecular technology may lead the way here, but some form of genetic testing is likely to be forever required.     

QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch

The intra- and interspecific diversity of avian beak morphologies is one of the most compelling examples for the power of natural selection acting on a morphological trait. The development and diversification of the beak have also become a textbook example for evolutionary developmental biology, and variation in expression levels of several genes is known to causally affect beak shape. However, until now, no genomic polymorphisms have been identified, which are related to beak morphology in birds. QTL mapping does reveal the location of causal polymorphisms, albeit with poor spatial resolution. Here, we estimate heritability and genetic correlations for beak length, depth and width and perform a QTL linkage analysis for these traits based on 1404 informative single-nucleotide polymorphisms genotyped in a four-generation pedigree of 992 captive zebra finches (Taeniopygia guttata). Beak size, relative to body size, was sexually dimorphic (larger in males). Heritability estimates ranged from 0.47 for beak length to 0.74 for beak width. QTL mapping revealed four to five regions of significant or suggestive genome-wide linkage for each of the three beak dimensions (nine different regions in total). Eight out of 11 genes known to influence beak morphology are located in these nine peak regions. Five QTL do not cover known candidates demonstrating that yet unknown genes or regulatory elements may influence beak morphology in the zebra finch.     

Molecular mapping of Verticillium wilt resistance QTL clustered on chromosomes D7 and D9 in upland cotton

Verticillium wilt is a destructive disease with international consequences for cotton production. Breeding broad-spectrum resistant cultivars is considered to be one of the most effective means for reducing crop losses. A resistant cotton cultivar, 60182, was crossed with a susceptible cultivar, Jun-mian 1, to identify markers for Verticillium resistance genes and validate the mode of its inheritance. Genetic segregation analysis for Verticillium wilt resistance was evaluated based upon infected leaf percentage in the seedling stage using major gene-polygene mixed inheritance models and joint analysis of P₁, P₂, F₁, B₁, B₂ and F₂ populations obtained from the cultivar cross. We found that resis-tance of upland cotton cultivar 60182 to isolates BP2, VD8 and T9, and their isoconcentration mixture was controlled by two major genes with additive-dominance-epistatic effects, and the inheritance of the major gene was dominant. Furthermore, a genetic linkage map was constructed using F₂ segregating population and resistance phenotypic data were obtained using F_2︰3 families inoculated with different isolates and detected in different developmental stages. The genetic linkage map with 139 loci was comprised of 31 linkage groups covering 1165 cM, with an average distance of 8.38 cM between two markers, or 25.89% of the cotton genome length. From 60182, we found 4 QTL on chromosome D7 and 4 QTL on D9 for BP2, 5 QTL on D7 and 9 QTL on D9 for VD8, 4 QTL on D7 and 5 QTL on D9 for T9 and 3 QTL on D7 and 7 QTL on D7 for mixed pathogens. The QTL mapping results revealed that QTL clusters with high contribution rates were screened simultaneously on chromosomes D9 and D7 by multiple interval mapping (CIM), whether from resistance phenotypic data from different developmental stages or for different isolates. The result is consistent with the genetic model of two major genes in 60182 and suggests broad-spectrum resistance to both defoliating isolates of V. dahliae and nondefoliating iso-lates. The markers associated with resistance QTL may facilitate the use of Verticillium wilt resistance genes in improving breeding programs for cotton.     

PREDICTABILITY AND IRREVERSIBILITY OF GENETIC CHANGES ASSOCIATED WITH FLOWER COLOR EVOLUTION IN PENSTEMON BARBATUS

Two outstanding questions in evolutionary biology are whether, and how often, the genetic basis of phenotypic evolution is predictable; and whether genetic change constrains evolutionary reversibility. We address these questions by studying the genetic basis of red flower color in Penstemon barbatus. The production of red flowers often involves the inactivation of one or both of two anthocyanin pathway genes, Flavonoid 3′,5′‐hydroxylase (F3′5′h) and Flavonoid 3′‐hydroxylase (F3′h). We used gene expression and enzyme function assays to determine that redundant inactivating mutations to F3′5′h underlie the evolution of red flowers in P. barbatus. Comparison of our results to previously characterized shifts from blue to red flowers suggests that the genetic change associated with the evolution of red flowers is predictable: when it involves elimination of F3′5′H activity, functional inactivation or deletion of this gene tends to occur; however, when it involves elimination of F3′H activity, tissue‐specific regulatory substitutions occur and the gene is not functionally inactivated. This pattern is consistent with emerging data from physiological experiments indicating that F3′h may have pleiotropic effects and is thus subject to purifying selection. The multiple, redundant inactivating mutations to F3′5′h suggest that reversal to blue‐purple flowers in this group would be unlikely.     

Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower

The build‐up of the phenotypic differences that distinguish species has long intrigued biologists. These differences are often inherited as stable polymorphisms that allow the cosegregation of adaptive variation within species, and facilitate the differentiation of complex phenotypes between species. It has been suggested that the clustering of adaptive loci could facilitate this process, but evidence is still scarce. Here, we used QTL analysis to study the genetic basis of phenotypic differentiation between coastal populations of the Australian wildflower Senecio lautus. We found that a genomic region consistently governs variation in several of the traits that distinguish these contrasting forms. Additionally, some of the taxon‐specific traits controlled by this QTL cluster have evolved repeatedly during the adaptation to the same habitats, suggesting that it could mediate divergence between locally adapted forms. This cluster contains footprints of divergent natural selection across the range of S. lautus, which suggests that it could have been instrumental for the rapid diversification of this species.     

The Genetics of Evolutionary Change in Senecio vulgaris L.: A QTL Mapping Approach

Abstract: The cosmopolitan weed Senecio vulgaris var. vulgaris is likely to have originated from the non-weedy S. vulgaris ssp. denticulatus from which it differs by showing no seed dormancy, by completing its life cycle from germination to seed formation much faster and by lacking ray florets. An F2 generation of 120 individuals obtained through selfing of one hybrid individual between var. vulgaris and ssp. denticulatus was used to construct a linkage map based on RAPD polymorphisms and the presence or absence of ray florets. This linkage map was used for a QTL analysis of 12 characters distinguishing the two taxa. For seven of these 12 characters, three significant QTLs could be found. One of these QTLs controls the speed of development, height of plants, leaf number, number of lateral branches and number of outer involucral bracts. A second QTL, located in the same linkage group, coincides with the ray floret locus and controls the number of disc florets. Plant height and leaf number are controlled by a third QTL in a different linkage group. Considering earlier evidence on the genetics of seed dormancy, it is argued that probably only three chromosomal regions, or even genetic loci, control seed dormancy, speed of development and presence or absence of ray florets as the ecologically most important differences between var. vulgaris and ssp. denticulatus. These findings have important implications for the genetics of evolutionary change and speciation.     

Different Sources of Allelic Variation Drove Repeated Color Pattern Divergence in Cichlid Fishes

The adaptive radiations of East African cichlid fish in the Great Lakes Victoria, Malawi, and Tanganyika are well known for their diversity and repeatedly evolved phenotypes. Convergent evolution of melanic horizontal stripes has been linked to a single locus harboring the gene agouti-related peptide 2 (agrp2). However, where and when the causal variants underlying this trait evolved and how they drove phenotypic divergence remained unknown. To test the alternative hypotheses of standing genetic variation versus de novo mutations (independently originating in each radiation), we searched for shared signals of genomic divergence at the agrp2 locus. Although we discovered similar signatures of differentiation at the locus level, the haplotypes associated with stripe patterns are surprisingly different. In Lake Malawi, the highest associated alleles are located within and close to the 5′ untranslated region of agrp2 and likely evolved through recent de novo mutations. In the younger Lake Victoria radiation, stripes are associated with two intronic regions overlapping with a previously reported cis-regulatory interval. The origin of these segregating haplotypes predates the Lake Victoria radiation because they are also found in more basal riverine and Lake Kivu species. This suggests that both segregating haplotypes were present as standing genetic variation at the onset of the Lake Victoria adaptive radiation with its more than 500 species and drove phenotypic divergence within the species flock. Therefore, both new (Lake Malawi) and ancient (Lake Victoria) allelic variation at the same locus fueled rapid and convergent phenotypic evolution.     

水稻籽粒镉积累QTL定位及候选基因分析

水稻(Oryza sativa)是全世界重要的经济作物之一, 稻田镉(Cd)污染和镉积累问题严重威胁世界水稻的产量和品质以及人类健康, 如何降低水稻中镉积累已成为热点问题。以籼稻品种华占(HZ)为父本、粳稻品种热研2号(Nekken2)为母本, 连续自交多代后得到120个重组自交系群体, 对其镉积累进行检测和分析, 同时利用遗传图谱进行QTL作图。结果共检测到7个QTLs, 分别位于水稻第2、3、9和12号染色体上, 其中1个LOD值高达4.97。对这些QTL区间内与耐金属离子胁迫相关的候选基因进行定量分析, 发现LOC_Os02g50240、LOC_Os02g52780、LOC_Os09g31200、LOC_Os09g35030和LOC_Os09g37949这5个基因在双亲间的表达量差异显著, 结合亲本对不同金属离子的浓度积累数据, 推测LOC_ Os02g50240、LOC_Os09g31200及LOC_Os09g35030的高表达可能极大地提高了水稻对镉离子的吸收和胁迫耐受能力。通过QTL挖掘和分析, 发现这些基因与水稻籽粒的镉积累有关, 可能影响水稻耐镉胁迫的能力。研究结果为进一步筛选和培育耐镉胁迫的水稻品种创造了条件, 为阐明水稻镉积累的分子调控机制奠定了基础。     

Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit

Kiwifruit (Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwifruit, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high-throughput genotyping platform for genome-wide DNA polymorphisms. In this study, we developed a high-density SNP genotyping array to facilitate genetic studies and breeding applications in kiwifruit. SNP discovery was performed by genome-wide DNA sequencing of 40 kiwifruit genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance and distribution over the available Actinidia chinensis genome. A total of 134 729 unique SNPs were put on the array. The array was evaluated by genotyping 400 kiwifruit individuals. We performed a multidimensional scaling analysis to assess the diversity of kiwifruit germplasm, showing that the array was effective to distinguish kiwifruit accessions. Using a tetraploid F1 population, we constructed an integrated linkage map covering 3060.9 cM across 29 linkage groups and performed QTL analysis for the sex locus that has been identified on Linkage Group 3 (LG3) in Actinidia arguta. Finally, our dataset presented evidence of tetrasomic inheritance with partial preferential pairing in A. arguta. In conclusion, we developed and evaluated a 135K SNP genotyping array for kiwifruit. It has the advantage of a comprehensive design that can be an effective tool in genetic studies and breeding applications in this high-value crop.     

南瓜遗传连锁图谱的构建及粒宽性状的QTL定位

以印度南瓜纯系大粒材料‘0515-1’和小粒材料‘0460-1-1’为亲本,获得193个南瓜F2单株群体,应用AFLP和SSR分子标记技术进行多态性筛选,构建了含84个标记位点的遗传连锁图谱。结果表明,整个图谱包含12个连锁群,全长683.50cM,标记平均间距为8.13cM。采用复合区间定位分析,共检测到控制南瓜籽粒宽度的4个数量性状位点(QTL),分别位于3个连锁群上,各QTL的贡献率在2.87%～29.68%之间。     

Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide‐toxic habitats of a neotropical fish (Poecilia mexicana)

Replicated ecological gradients are prime systems to study processes of molecular evolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H₂S) and compared two population pairs of sulphide‐adapted and ancestral fish by sequencing population pools of >200 individuals (Pool‐Seq). We inferred the evolutionary processes shaping divergence and tested the hypothesis of increase of parallelism from SNPs to molecular pathways. Coalescence analyses showed that the divergence occurred in the face of substantial bidirectional gene flow. Population divergence involved many short, widely dispersed regions across the genome. Analyses of allele frequency spectra suggest that differentiation at most loci was driven by divergent selection, followed by a selection‐mediated reduction of gene flow. Reconstructing allelic state changes suggested that selection acted mainly upon de novo mutations in the sulphide‐adapted populations. Using a corrected Jaccard index to quantify parallel evolution, we found a negligible proportion of statistically significant parallel evolution of J_corr = 0.0032 at the level of SNPs, divergent genome regions (J_corr = 0.0061) and genes therein (J_corr = 0.0091). At the level of metabolic pathways, the overlap was J_corr = 0.2545, indicating increasing parallelism with increasing level of biological integration. The majority of pathways contained positively selected genes in both sulphide populations. Hence, adaptation to sulphidic habitats necessitated adjustments throughout the genome. The largely unique evolutionary trajectories may be explained by a high proportion of de novo mutations driving the divergence. Our findings favour Gould's view that evolution is often the unrepeatable result of stochastic events with highly contingent effects.     

Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population

Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade‐off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker‐based approaches – chromosome partitioning, quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome‐wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait.     

Repeated and predictable patterns of ecotypic differentiation during a biological invasion: lake–stream divergence in parapatric Swiss stickleback

The relative importance of ecological selection and geographical isolation in promoting and constraining genetic and phenotypic differentiation among populations is not always obvious. Interacting with divergent selection, restricted opportunity for gene flow may in some cases be as much a cause as a consequence of adaptation, with the latter being a hallmark of ecological speciation. Ecological speciation is well studied in parts of the native range of the three‐spined stickleback. Here, we study this process in a recently invaded part of its range. Switzerland was colonized within the past 140 years from at least three different colonization events involving different stickleback lineages. They now occupy diverse habitats, ranging from small streams to the pelagic zone of large lakes. We use replicated systems of parapatric lake and stream populations, some of which trace their origins to different invasive lineages, to ask (i) whether phenotypic divergence occurred among populations inhabiting distinct habitats, (ii) whether trajectories of phenotypic divergence follow predictable parallel patterns and (iii) whether gene flow constrains divergent adaptation or vice versa. We find consistent phenotypic divergence between populations occupying distinct habitats. This involves parallel evolution in several traits with known ecological relevance in independent evolutionary lineages. Adaptive divergence supersedes homogenizing gene flow even at a small spatial scale. We find evidence that adaptive phenotypic divergence places constraints on gene flow over and above that imposed by geographical distance, signalling the early onset of ecological speciation.