Comparison of selection methods for improvement of the population hybrid

Summary The objective of this study was to compare several selection procedures with respect to expected genetic gain in the population hybrid across a range of initial allelic frequencies, degrees of dominance, and environmental variances. The methods compared were intrapopulation recurrent selection using full-sib or S₁ families, full-sib and two half-sib reciprocal recurrent selection procedures, and convergent improvement applied to populations. Comparisons were made by calculating expected allelic frequency changes for each method. The optimal selection method for a given set of allelic frequencies and degree of dominance depended little on the environmental variance. Partly because of its short cycle, full-sib intrapopulation selection was the most effective method for the majority of allelic frequency combinations when the degree of dominance was small and an off-season nursery could be used to make recombinations. With larger values for the degree of dominance, S₁ and reciprocal full-sib methods became optimal, the former method especially when favorable alleles had a high frequency and the latter when populations were highly divergent. When off-season nursery use was restricted to making self-pollinations or was absent, S₁ selection was optimal for the majority of allelic frequency combinations. Convergent improvement was superior only for extremely divergent allelic frequencies and then only when the degree of dominance was less than 0.10. Half-sib reciprocal methods were never optimal, although the gain for the standard half-sib reciprocal procedure differed little from that of full-sib reciprocal selection when the degree of dominance was 0.75.     

Molecular correlates of reproductive isolation

Evolution of reproductive isolation as a byproduct of genetic divergence in isolated populations is the dominant (albeit not exclusive) mode of speciation in sexual animals. But little is known about the factors linking speciation to general divergence. Several authors have argued that allopatric speciation should proceed more rapidly if isolated populations also experience divergent selection. Reproductive isolation between allopatric populations is not subject to direct selection; it can accumulate only by random drift or as a fortuitous byproduct of selection on other traits. Here I present a novel analysis of published data, demonstrating that pre- and postmating isolation of Drosophila species are more tightly correlated with allozyme divergence than with silent DNA divergence. Inasmuch as proteins are more subject to the action of natural selection than are silent DNA polymorphisms, this result provides broad support for a model of selection-mediated allopatric speciation.     

Genealogy-Based Methods for Inference of Historical Recombination and Gene Flow and Their Application in Saccharomyces cerevisiae

Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance.     

Characterising functionally important and ecologically meaningful genetic diversity using a candidate gene approach

Over the past two decades the fields of molecular ecology and population genetics have been dominated by the use of putatively neutral DNA markers, primarily to resolve spatio-temporal patterns of genetic variation to inform our understanding of population structure, gene flow and pedigree. Recent emphasis in comparative functional genomics, however, has fuelled a resurgence of interest in functionally important genetic variation that underpins phenotypic traits of adaptive or ecological significance. It may prove a major challenge to transfer genomics information from classical model species to examine functional diversity in non-model species in natural populations, but already multiple gene-targeted candidate loci with major effect on phenotype and fitness have been identified. Here we briefly describe some of the research strategies used for isolating and characterising functional genetic diversity at candidate gene-targeted loci, and illustrate the efficacy of some of these approaches using our own studies on red grouse (Lagopus lagopus scoticus). We then review how candidate gene markers have been used to: (1) quantify genetic diversity among populations to identify those depauperate in genetic diversity and requiring specific management action; (2) identify the strength and mode of selection operating on individuals within natural populations; and (3) understand direct mechanistic links between allelic variation at single genes and variance in individual fitness.     

Genetic Divergence and Signatures of Natural Selection in Marginal Populations of a Keystone,Long-Lived Conifer,Eastern White Pine (Pinus strobus) from Northern Ontario

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (N _e) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and N _e than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and N _e between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.     

A comparison of four methods for detecting weak genetic structure from marker data

Genetic structure is ubiquitous in wild populations and is the result of the processes of natural selection, genetic drift, mutation, and gene flow. Genetic drift and divergent selection promotes the generation of genetic structure, while gene flow homogenizes the subpopulations. The ability to detect genetic structure from marker data diminishes rapidly with a decreasing level of differentiation among subpopulations. Weak genetic structure may be unimportant over evolutionary time scales but could have important implications in ecology and conservation biology. In this paper we examine methods for detecting and quantifying weak genetic structures using simulated data. We simulated populations consisting of two putative subpopulations evolving for up to 50 generations with varying degrees of gene flow (migration), and varying amounts of information (allelic diversity). There are a number of techniques available to detect and quantify genetic structure but here we concentrate on four methods: F(ST), population assignment, relatedness, and sibship assignment. Under the simple mating system simulated here, the four methods produce qualitatively similar results. However, the assignment method performed relatively poorly when genetic structure was weak and we therefore caution against using this method when the analytical aim is to detect fine-scale patterns. Further work should examine situations with different mating systems, for example where a few individuals dominate reproductive output of the population. This study will help workers to design their experiments (e.g., sample sizes of markers and individuals), and to decide which methods are likely to be most appropriate for their particular data.     

Genetic and Morphological Divergence in Three Strains of Brook Trout Salvelinus fontinalis Commonly Stocked in Lake Superior

Fitness related traits often show spatial variation across populations of widely distributed species. Comparisons of genetic variation among populations in putatively neutral DNA markers and in phenotypic traits susceptible to selection (Q_ST F_ST analysis) can be used to determine to what degree differentiation among populations can be attributed to selection or genetic drift. Traditionally, Q_ST F_ST analyses require a large number of populations to achieve sufficient statistical power; however, new methods have been developed that allow Q_ST F_ST comparisons to be conducted on as few as two populations if their pedigrees are informative. This study compared genetic and morphological divergence in three strains of brook trout Salvelinus fontinalis that were historically or currently used for stocking in the Lake Superior Basin. Herein we examined if morphological divergence among populations showed temporal variation, and if divergence could be attributed to selection or was indistinguishable from genetic drift. Multivariate Q_ST F_ST analysis showed evidence for divergent selection between populations. Univariate analyses suggests that the pattern observed in the multivariate analyses was largely driven by divergent selection for length and weight, and moreover by divergence between the Assinica strain and each of the Iron River and Siskiwit strains rather than divergent selection between each population pair. While it could not be determined if divergence was due to natural selection or inadvertent artificial selection in hatcheries, selected differences were consistent with patterns of domestication commonly found in salmonids.     

Balancing selection at a frog antimicrobial peptide locus: fluctuating immune effector alleles?

Balancing selection is common on many defense genes, but it has rarely been reported for immune effector proteins such as antimicrobial peptides (AMPs). We describe genetic diversity at a brevinin-1 AMP locus in three species of leopard frogs (Rana pipiens, Rana blairi, and Rana palustris). Several highly divergent allelic lineages are segregating at this locus. That this unusual pattern results from balancing selection is demonstrated by multiple lines of evidence, including a ratio of nonsynonymous/synonymous polymorphism significantly higher than 1, the ZnS test, incongruence between the number of segregating sites and haplotype diversity, and significant Tajima's D values. Our data are more consistent with a model of fluctuating selection in which alleles change frequencies over time than with a model of stable balancing selection such as overdominance. Evidence for fluctuating selection includes skewed allele frequencies, low levels of synonymous variation, nonneutral values of Tajima's D within allelic lineages, an inverse relationship between the frequency of an allelic lineage and its degree of polymorphism, and divergent allele frequencies among populations. AMP loci could be important sites of adaptive genetic diversity, with consequences for host-pathogen coevolution and the ability of species to resist disease epidemics.     

Ecological niche dimensionality and the evolutionary diversification of stick insects

The degree of phenotypic divergence and reproductive isolation between taxon pairs can vary quantitatively, and often increases as evolutionary divergence proceeds through various stages, from polymorphism to population differentiation, ecotype and race formation, speciation, and post-speciational divergence. Although divergent natural selection promotes divergence, it does not always result in strong differentiation. For example, divergent selection can fail to complete speciation, and distinct species pairs sometimes collapse ('speciation in reverse'). Widely-discussed explanations for this variability concern genetic architecture, and the geographic arrangement of populations. A less-explored possibility is that the degree of phenotypic and reproductive divergence between taxon pairs is positively related to the number of ecological niche dimensions (i.e., traits) subject to divergent selection. Some data supporting this idea stem from laboratory experimental evolution studies using Drosophila, but tests from nature are lacking. Here we report results from manipulative field experiments in natural populations of herbivorous Timema stick insects that are consistent with this 'niche dimensionality' hypothesis. In such insects, divergent selection between host plants might occur for cryptic colouration (camouflage to evade visual predation), physiology (to detoxify plant chemicals), or both of these niche dimensions. We show that divergent selection on the single niche dimension of cryptic colouration can result in ecotype formation and intermediate levels of phenotypic and reproductive divergence between populations feeding on different hosts. However, greater divergence between a species pair involved divergent selection on both niche dimensions. Although further replication of the trends reported here is required, the results suggest that dimensionality of selection may complement genetic and geographic explanations for the degree of diversification in nature.     

Evolution and ecology of MHC molecules: from genomics to sexual selection

In the past few years the DNA sequence database for molecules of the MHC (major histocompatibility complex) has expanded greatly, yielding a more complete picture of the long-term rates and patterns of evolution of the MHC in vertebrates. Sharing of MHC allelic lineages between long-diverged species (trans-species evolution) has been detected virtually wherever it is sought, but new analyses of linked neutral regions and the complexities of sequence convergence and microrecombination in the peptide binding region challenge traditional phylogenetic analyses. Methods for estimating the intensity of selection on MHC genes suggest that viability is important, but recent studies in natural populations of mammals give inconsistent results concerning mate choice. The complex and interacting roles of microrecombination, parasite-mediated selection and mating preferences for maintaining the extraordinary levels of MHC polymorphism observed are still difficult to evaluate.     

Isolation and characterization of major histocompatibility class IIβ genes in an endangered North American cyprinid fish, the Rio Grande silvery minnow (Hybognathus amarus)

The major histocompatibility complex (MHC) is a critical component of the adaptive immune response in vertebrates. Due to the role that MHC plays in immunity, absence of variation within these genes may cause species to be vulnerable to emerging diseases. The freshwater fish family Cyprinidae comprises the most diverse and species-rich group of freshwater fish in the world, but some are imperiled. Despite considerable species richness and the long evolutionary history of the family, there are very few reports of MHC sequences (apart from a few model species), and no sequences are reported from endemic North American cyprinids (subfamily Leuciscinae). Here we isolate and characterize the MH Class II beta genes from complementary DNA and genomic DNA of the non-model, endangered Rio Grande silvery minnow (Hybognathus amarus), a North American cyprinid. Phylogenetic reconstruction revealed two groups of divergent MH alleles that are paralogous to previously described loci found in deeply divergent cyprinid taxa including common carp, zebrafish, African large barb and bream. Both groups of alleles were under the influence of diversifying selection yet not all individuals had alleles belonging to both allelic groups. We concluded that the general organization and pattern of variation of MH class II genes in Rio Grande silvery minnow is similar to that identified in other cyprinid fishes studied to date, despite distant evolutionary relationships and evidence of a severe genetic bottleneck.     

Effects of natural and sexual selection on adaptive population divergence and premating isolation in a damselfly

The relative strength of different types of directional selection has seldom been compared directly in natural populations. A recent meta-analysis of phenotypic selection studies in natural populations suggested that directional sexual selection may be stronger in magnitude than directional natural selection, although this pattern may have partly been confounded by the different time scales over which selection was estimated. Knowledge about the strength of different types of selection is of general interest for understanding how selective forces affect adaptive population divergence and how they may influence speciation. We studied divergent selection on morphology in parapatric, natural damselfly (Calopteryx splendens) populations. Sexual selection was stronger than natural selection measured on the same traits, irrespective of the time scale over which sexual selection was measured. Visualization of the fitness surfaces indicated that population divergence in overall morphology is more strongly influenced by divergent sexual selection rather than natural selection. Courtship success of experimental immigrant males was lower than that of resident males, indicating incipient sexual isolation between these populations. We conclude that current and strong sexual selection promotes adaptive population divergence in this species and that premating sexual isolation may have arisen as a correlated response to divergent sexual selection. Our results highlight the importance of sexual selection, rather than natural selection in the adaptive radiation of odonates, and supports previous suggestions that divergent sexual selection promotes speciation in this group.     

Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples

BACKGROUND AND AIMS: The main aim of this study was to use an amplified fragment length polymorphism (AFLP)-based, large-scale screening of the whole genome of Phaseolus vulgaris to determine the effects of selection on the structure of the genetic diversity in wild and domesticated populations. METHODS: Using pooled DNA samples, seven each of wild and domesticated populations of P. vulgaris were studied using 2506 AFLP markers (on average, one every 250 kb). About 10 % of the markers were also analysed on individual genotypes and were used to infer allelic frequencies empirically from bulk data. In both data sets, tests were made to determine the departure from neutral expectation for each marker using an F(ST)-based method. KEY RESULTS: The most important outcome is that a large fraction of the genome of the common bean (16 %; P < 0.01) appears to have been subjected to effects of selection during domestication. Markers obtained in individual genotypes were also mapped and classified according to their proximities to known genes and quantitative trait loci (QTLs) of the domestication syndrome. Most of the markers that were found to be potentially under the effects of selection were located in the proximity of previously mapped genes and QTLs related to the domestication syndrome. CONCLUSIONS: Overall, the results indicate that in P. vulgaris a large portion of the genome appears to have been subjected to the effects of selection, probably because of linkage to the loci selected during domestication. As most of the markers that are under the effects of selection are linked to known loci related to the domestication syndrome, it is concluded that population genomics approaches are very efficient in detecting QTLs. A method based on bulk DNA samples is presented that is effective in pre-screening for a large number of markers to determine selection signatures.     

The evolutionary ecology of the major histocompatibility complex

The major histocompatibility complex (MHC) has become a paradigm for how selection can act to maintain adaptively important genetic diversity in natural populations. Here, we review the contribution of studies on the MHC in non-model species to our understanding of how selection affects MHC diversity, emphasising how ecological and ethological processes influence the tempo and mode of evolution at the MHC, and conversely, how variability at the MHC affects individual fitness, population dynamics and viability. We focus on three main areas: the types of information that have been used to detect the action of selection on MHC genes; the relative contributions of parasite-mediated and sexual selection on the maintenance of MHC diversity; and possible future lines of research that may help resolve some of the unanswered issues associated with MHC evolution.     

Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus aculeatus

Adaptation is driven by natural selection; however, many adaptations are caused by weak selection acting over large timescales, complicating its study. Therefore, it is rarely possible to study selection comprehensively in natural environments. The threespine stickleback (Gasterosteus aculeatus) is a well-studied model organism with a short generation time, small genome size, and many genetic and genomic tools available. Within this originally marine species, populations have recurrently adapted to freshwater all over its range. This evolution involved extensive parallelism: pre-existing alleles that adapt sticklebacks to freshwater habitats, but are also present at low frequencies in marine populations, have been recruited repeatedly. While a number of genomic regions responsible for this adaptation have been identified, the details of selection remain poorly understood. Using whole-genome resequencing, we compare pooled genomic samples from marine and freshwater populations of the White Sea basin, and identify 19 short genomic regions that are highly divergent between them, including three known inversions. 17 of these regions overlap protein-coding genes, including a number of genes with predicted functions that are relevant for adaptation to the freshwater environment. We then analyze four additional independently derived young freshwater populations of known ages, two natural and two artificially established, and use the observed shifts of allelic frequencies to estimate the strength of positive selection. Adaptation turns out to be quite rapid, indicating strong selection acting simultaneously at multiple regions of the genome, with selection coefficients of up to 0.27. High divergence between marine and freshwater genotypes, lack of reduction in polymorphism in regions responsible for adaptation, and high frequencies of freshwater alleles observed even in young freshwater populations are all consistent with rapid assembly of G. aculeatus freshwater genotypes from pre-existing genomic regions of adaptive variation, with strong selection that favors this assembly acting simultaneously at multiple loci.     

When can ecological speciation be detected with neutral loci?

It is not yet clear under what conditions empirical studies can reliably detect progress toward ecological speciation through the analysis of allelic variation at neutral loci. We use a simulation approach to investigate the range of parameter space under which such detection is, and is not, likely. We specifically test for the conditions under which divergent natural selection can cause a ‘generalized barrier to gene flow’ that is present across the genome. Our individual‐based numerical simulations focus on how population divergence at neutral loci varies in relation to recombination rate with a selected locus, divergent selection on that locus, migration rate and population size. We specifically test whether genetic differences at neutral markers are greater between populations in different environments than between populations in similar environments. We find that this expected signature of ecological speciation can be detected under part of the parameter space, most consistently when divergent selection is strong and migration is intermediate. By contrast, the expected signature of ecological speciation is not reliably detected when divergent selection is weak or migration is low or high. These findings provide insights into the strengths and weaknesses of using neutral markers to infer ecological speciation in natural systems.     

The status of AFLP in the genomics era and a pipeline for converting AFLPs into single-locus markers

Even though next-generation sequencing (NGS) has now become the predominant state-of-the-art technique for genotyping populations, amplified fragment length polymorphism (AFLP) DNA fingerprinting is still a relevant method, thanks to its versatility, cost-effectiveness, independence of prior sequence information and broad applicability. Even though the number of AFLP studies reached its peak in 2012, it is still applied extensively for phylogenetic analysis, genotyping or identifying non-model species, which often feature complex and large genomes. For these purposes, tools continue to be developed for designing AFLP studies, scoring AFLPs or handling AFLP data. Moreover, AFLP studies embrace the NGS technology; for example, the whole-genome sequence of model species is used to design more efficient AFLP studies for non-model species. Conversely, in complexity reduction of polymorphic sequences and restriction site-associated DNA sequencing studies, polymorphisms are often found to be present in many restriction sites, which can still be studied as AFLPs. We discuss the latest advances in AFLP-based studies in the era of NGS and anticipate that AFLP will remain a relevant method in the near future, even for species with a known genome, owing to its many promising new features such as methylation-sensitive-AFLP. Here, we also present an optimized pipeline for converting AFLP markers into single-locus markers, which can be applied in both traditional AFLP and NGS studies.     

Mate preference across the speciation continuum in a clade of mimetic butterflies

Premating behavioral isolation is increasingly recognized as an important part of ecological speciation, where divergent natural selection causes the evolution of reproductive barriers. A number of studies have now demonstrated that traits under divergent natural selection also affect mate preferences. However, studies of single species pairs only capture a snapshot of the speciation process, making it difficult to assess the role of mate preferences throughout the entire process. Heliconius butterflies are well known for their brightly colored mimetic warning patterns, and previous studies have shown that these patterns are also used as mate recognition cues. Here, we present mate preference data for four pairs of sister taxa, representing different stages of divergence, which together allow us to compare diverging mate preferences across the continuum of Heliconius speciation. Using a novel Bayesian approach, our results support a model of ecological speciation in which strong premating isolation arises early, but continues to increase throughout the continuum from polymorphic populations through to "good," sympatric ecologically divergent species.     

Decoupling of differentiation between traits and their underlying genes in response to divergent selection

We dissected the relationship between genetic differentiation (Q(ST)) for a trait and its underlying genes (G(STq), differentiation for a quantitative locus) in an evolutionary context, with the aim of identifying the conditions in which these two measurements are decoupled. We used two parameters (θ(B) and θ(W)) scaling the contributions of inter- and intrapopulation allelic covariation between genes controlling the trait of interest. We monitored the changes in θ(B) and θ(W), Q(ST) and G(STq) over successive generations of divergent and stabilizing selection, in simulations for an outcrossing species with extensive gene flow. The dynamics of these parameters are characterized by two phases. Initially, during the earliest generations, differentiation of the trait increases very rapidly and the principal and immediate driver of Q(ST) is θ(B). During subsequent generations, G(STq) increases steadily and makes an equal contribution to Q(ST). These results show that selection first captures beneficial allelic associations at different loci at different populations, and then targets changes in allelic frequencies. The same patterns are observed when environmental change modifies divergent selection, as shown by the very rapid response of θ(B) to the changes of selection regimes. We compare our results with previous experimental findings and consider their relevance to the detection of molecular signatures of natural selection.     

Gene Frequency Distributions as a Test of Selective Neutrality

The analysis of differences between loci in the variance of gene frequency over populations within a species has been suggested as a method of detecting natural selection. It is shown that, in the absence of selection, the expected variation over loci depends strongly on the pattern of relationships between populations. The effect of structure within a species is always to increase the variation and therefore to reduce the power of the method.