Divergent selection and heterogeneous genomic divergence

Introgression of wing pattern alleles and speciation via homoploid hybridization in Heliconius butterflies: a review of evidence from the genome

The diverse Müllerian mimetic wing patterns of neotropical Heliconius (Nymphalidae) have been proposed to be not only aposematic signals to potential predators, but also intra- and interspecific recognition signals that allow the butterflies to maintain their specific identities, and which perhaps drive the process of speciation, as well. Adaptive features under differential selection that also serve as cues for assortative mating have been referred to as 'magic traits', which can drive ecological speciation. Such traits are expected to exhibit allelic differentiation between closely related species with ongoing gene flow, whereas unlinked neutral traits are expected to be homogenized to a greater degree by introgression. However, recent evidence suggests that interspecific hybridization among Heliconius butterflies may have resulted in adaptive introgression of these very same traits across species boundaries, and in the evolution of new species by homoploid hybrid speciation. The theory and data supporting various aspects of the apparent paradox of 'magic trait' introgression are reviewed, with emphasis on population genomic comparisons of Heliconius melpomene and its close relatives.

Widespread yet heterogeneous genomic divergence

Genetic differentiation during adaptive divergence and speciation is heterogeneous among genomic regions. Some regions can be highly differentiated between populations, for example, because they harbour genes under divergent selection or those causing reproductive isolation and thus are resistant to gene flow. Other regions might be homogenized by gene flow and thus weakly differentiated. Debates persist about the number of differentiated regions expected under divergence with gene flow, and their causes, size, and genomic distribution. In this issue of Molecular Ecology, a study of freshwater stickleback used next-generation sequencing to shed novel insight into these issues (Roesti et al. 2012). Many genomic regions distributed across the genome were strongly differentiated, indicating divergence with gene flow can involve a greater number of loci than often thought. Nonetheless, differentiation of some regions, such as those near the centre of chromosomes where recombination is reduced, was strongly accentuated over others. Thus, divergence was widespread yet highly heterogeneous across the genome. Moreover, different population pairs varied in patterns of differentiation, illustrating how genomic divergence builds up across stages of the speciation process. The study demonstrates how variation in different evolutionary processes, such as selection and recombination rate, can combine to result in similar genomic patterns. Future work could focus on teasing apart the contributions of different processes for causing differentiation, a task facilitated by experimental manipulations.

Detecting the footprints of divergent selection in oaks with linked markers

Genome scans are increasingly used to study ecological speciation, providing a useful genome-wide perspective on divergent selection in the presence of gene flow. Here, we compare current approaches to detect footprints of divergent selection in closely related species. We analyzed 192 individuals from two interfertile European temperate oak species using 30 nuclear microsatellites from eight linkage groups. These markers present little intraspecific differentiation and can be used in combination to assign individual genotypes to species. We first show that different outlier detection tests give somewhat different results, possibly due to model constraints. Second, using linkage information for these markers, we further characterize the signature of divergent selection in the presence of gene flow. In particular, we show that recombination estimates for regions with outlier markers are lower than those for a control region, in line with a prediction from ecological speciation theory. Most importantly, we show that analyses at the haplotype level can distinguish between truly divergent (bi-directional) selection and positive selection in one of the two species, offering a new and improved method for characterizing the speciation process.

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.

Outlier loci highlight the direction of introgression in oaks

Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Quercus petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and nonoutlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late-successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with nonoutlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species' contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized.

Reproductive isolation and local adaptation quantified for a chromosome inversion in a malaria mosquito

Chromosome inversions have long been thought to be involved in speciation and local adaptation. We have little quantitative information, however, about the effects that inversion polymorphisms have on reproductive isolation and viability. Here we provide the first estimates from any organism for the total amount of reproductive isolation associated with an inversion segregating in natural populations. We sampled chromosomes from 751 mosquitoes of the malaria vector Anopheles funestus along a 1421 km transect in Cameroon that traverses savannah, highland, and rainforest ecological zones. We then developed a series of population genetic models that account for selection, migration, and assortative mating, and fit the models to the data using likelihood. Results from the best-fit models suggest there is strong local adaptation, with relative viabilities of homozygotes ranging from 25% to 130% compared to heterozygotes. Viabilities vary qualitatively between regions: the inversion is underdominant in the savannah, whereas in the highlands it is overdominant. The inversion is also implicated in strong assortative mating. In the savannah, the two homozygote forms show 92% reproductive isolation, suggesting that this one inversion can generate most of the genetic barriers needed for speciation.

The role of selection in driving landscape genomic structure of the waterflea Daphnia magna

The combined analysis of neutral and adaptive genetic variation is crucial to reconstruct the processes driving population genetic structure in the wild. However, such combined analysis is challenging because of the complex interaction among neutral and selective processes in the landscape. Overcoming this level of complexity requires an unbiased search for the evidence of selection in the genomes of populations sampled from their natural habitats and the identification of demographic processes that lead to present-day populations' genetic structure. Ecological model species with a suite of genomic tools and well-understood ecologies are best suited to resolve this complexity and elucidate the role of selective and demographic processes in the landscape genomic structure of natural populations. Here we investigate the water flea Daphnia magna, an emerging model system in genomics and a renowned ecological model system. We infer past and recent demographic processes by contrasting patterns of local and regional neutral genetic diversity at markers with different mutation rates. We assess the role of the environment in driving genetic variation in our study system by identifying correlates between biotic and abiotic variables naturally occurring in the landscape and patterns of neutral and adaptive genetic variation. Our results indicate that selection plays a major role in determining the population genomic structure of D. magna. First, environmental selection directly impacts genetic variation at loci hitchhiking with genes under selection. Second, priority effects enhanced by local genetic adaptation (cf. monopolization) affect neutral genetic variation by reducing gene flow among populations and genetic diversity within populations.

Patterns of transcriptome divergence in the male accessory gland of two closely related species of field crickets

One of the central questions in evolutionary genetics is how much of the genome is involved in the early stages of divergence between populations, causing them to be reproductively isolated. In this article, we investigate genomic differentiation in a pair of closely related field crickets (Gryllus firmus and G. pennsylvanicus). These two species are the result of allopatric divergence and now interact along an extensive hybrid zone in eastern North America. Genes encoding seminal fluid proteins (SFPs) are often divergent between species, and it has been hypothesized that these proteins may play a key role in the origin and maintenance of reproductive isolation between diverging lineages. Hence, we chose to scan the accessory gland transcriptome to enable direct comparisons of differentiation for genes known to encode SFPs with differentiation in a much larger set of genes expressed in the same tissue. We have characterized differences in allele frequency between two populations for >6000 SNPs and >26,000 contigs. About 10% of all SNPs showed nearly fixed differences between the two species. Genes encoding SFPs did not have significantly elevated numbers of fixed SNPs per contig, nor did they seem to show larger differences than expected in their average allele frequencies. The distribution of allele frequency differences across the transcriptome is distinctly bimodal, but the relatively high proportion of fixed SNPs does not necessarily imply "ancient" divergence between these two lineages. Further studies of linkage disequilibrium and introgression across the hybrid zone are needed to direct our attention to those genome regions that are important for reproductive isolation.

Characterization of 39 novel EST-SSR markers for Liriodendron tulipifera and cross-species amplification in L. chinense (Magnoliaceae)

PREMISE OF THE STUDY

A novel set of simple sequence repeat (SSR) markers were developed and characterized from the expressed sequence tag (EST) database of Liriodendron tulipifera for application in population genetic studies of Liriodendron.

METHODS AND RESULTS

Thirty-nine polymorphic EST-SSR loci were identified among 27 individuals sampled from a cultivated population of L. tulipifera. The number of alleles per locus ranged from three to 18. The average observed heterozygosity and expected heterozygosity were 0.684 and 0.778, respectively. Of the 39 loci, 32 showed interspecific transferability and polymorphism in a related species, L. chinense. The number of alleles per locus ranged from two to 11, and the average observed heterozygosity and expected heterozygosity were 0.475 and 0.736, respectively.

CONCLUSIONS

The developed EST-SSR markers will be useful for investigating adaptive genetic differentiation in Liriodendron.

Consequences of a poecilogonous life history for genetic structure in coastal populations of the polychaete Streblospio benedicti

In many species, alternative developmental pathways lead to the production of two distinct phenotypes, promoting the evolution of morphological novelty and diversification. Offspring type in marine invertebrates influences transport time by ocean currents, which dictate dispersal potential and gene flow, and thus has sweeping evolutionary effects on the potential for local adaptation and on rates of speciation, extinction and molecular evolution. Here, we use the polychaete Streblospio benedicti to investigate the effects of dimorphic offspring type on gene flow and genetic structure in coastal populations. We use 84 single nucleotide polymorphism (SNP) markers for this species to assay populations on the East and West Coasts of the United States. Using these markers, we found that in their native East Coast distribution, populations of S. benedicti have high-population genetic structure, but this structure is associated primarily with geographic separation rather than developmental differences. Interestingly, very little genetic differentiation is recovered between individuals of different development types when they occur in the same or nearby populations, further supporting that this is a true case of poecilogony. In addition, we were able to demonstrate that the recently introduced (~100 ya) West Coast populations probably originated from a lecithotrophic population near Delaware.

The genomics of adaptation

The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

Ecological proteomics: finding molecular markers that matter

It is becoming increasingly clear that local adaptation can occur even in the face of high gene flow and limited overall genomic differentiation among populations (reviewed by Nosil et al. 2009). Thus, one important task for molecular ecologists is to sift through genomic data to identify the genes that matter for local adaptation (Hoffmann & Willi 2008; Stapley et al. 2010). Recent advances in high-throughput molecular technologies have facilitated this search, and a variety of approaches can be applied, including those grounded in population genetics [e.g. outlier analysis (Pavlidis et al. 2008)], classical and quantitative genetics [e.g. quantitative trait locus analysis (MacKay et al. 2009)], and cellular and molecular biology [e.g. transcriptomics (Larsen et al. 2011)]. However, applying these approaches in nonmodel organisms that lack extensive genetic and genomic resources has been a formidable challenge. In this issue, Papakostas et al. (2012). demonstrate how one such approach – high-throughput label-free proteomics (reviewed by Gstaiger & Aebersold 2009; Domon & Aebersold 2010) – can be applied to detect genes that may be involved in local adaptation in a species with limited genomic resources. Using this approach, they identified genes that may be implicated in local adaptation to salinity in European whitefish (Coregonus lavaretus L.) and provide insight into the mechanisms by which fish cope with changes in this critically important environmental parameter.

Localizing F(ST) outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow

Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence-with-gene-flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing F(ST) outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between-population recombination and gene exchange are reduced over large 'divergence hitchhiking' (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in genomic regions where ongoing gene flow is expected. We use this predicted difference among nonoutliers to perform a critical test of divergence hitchhiking. Results show that nonoutlier markers within clusters of F(ST) outliers and QTL resolve the genetic population structure of the two host races nearly as well as the outliers themselves, while nonoutliers outside DH regions reveal no population structure, as expected if they experience more gene flow. These results provide clear evidence for divergence hitchhiking, a mechanism that may dramatically facilitate the process of speciation-with-gene-flow. They also show the power of integrating genome scans with genetic analyses of the phenotypic traits involved in local adaptation and population divergence.

A genome scan and linkage disequilibrium analysis among chromosomal races of the Australian grasshopper Vandiemenella viatica

In the past decade the interest surrounding the role of recombination in speciation has been re-kindled by a new generation of chromosomal speciation models that invoke the recombination-suppression properties of some types of chromosomal rearrangement. A common prediction of recombination-suppression models is that gene exchange between diverging populations will be more restricted in regions of the genome that experience low recombination. We carried out a genome scan of three chromosomal races of the grasshopper Vandiemenella viatica (Orthoptera: Morabinae), occurring on Kangaroo Island, South Australia, using 1517 AFLP loci, with a view to elucidating the roles that selection and chromosomal variation have played in the formation of these taxa. An analysis of molecular variance demonstrated that chromosomal race accounted for a significant proportion of the genetic variance in the total dataset, which concurred with the findings of an earlier study. Sampling across one previously-identified hybrid zone, and the identification of outlier loci between parental races allowed us to establish that, in admixed populations, outlier loci which potentially pre-date the isolation of populations of races on Kangaroo Island exhibit higher levels of linkage disequilibrium with each other than putatively neutral loci. In turn this suggests that they might reside within genomic regions of low recombination, or be closely linked with each other.

Phylogenetic footprinting: a boost for microbial regulatory genomics

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the best conserved motifs in those homologous regions. There are two popular sets of methods-alignment-based and motif-based, which are generally employed for phylogenetic methods. However, serious efforts have lacked to develop a tool exclusively for phylogenetic footprinting, based on either of these methods. Nevertheless, a number of software and tools exist that can be applied for prediction of phylogenetic footprinting with variable degree of success. The output from these tools may get affected by a number of factors associated with current state of knowledge, techniques and other resources available. We here present a critical apprehension of various phylogenetic approaches with reference to prokaryotes outlining the available resources and also discussing various factors affecting footprinting in order to make a clear idea about the proper use of this approach on prokaryotes.

The language of speciation

The literature on speciation has expanded dramatically in recent years, catalyzed by the emergence of new conceptual frameworks, new theoretical approaches, and new methods for characterizing pattern and inferring process. As a consequence, the language used to describe the speciation process has become more complex. Increasing complexity may be an accurate reflection of current thinking with respect to how phenotypic differences limit gene flow, how selection results in the evolution of reproductive isolation, and genetic changes that contribute to speciation. However, increased language complexity has come at a cost; old definitions have been reconfigured and new terms have been introduced. In some instances, the introduction of new terminology has failed to recognize historical usage, leading to unnecessary ambiguity and redundancy. Although the writings of Mayr and Dobzhansky remain a reference point in the language of speciation, the last decades of the 20th century saw substantial changes in our thinking about the speciation process. During that period, the language of speciation remained relatively stable. In contrast, the first decade of the 21st century has witnessed a remarkable expansion of the language of speciation. Here, the origin and evolution of ideas about speciation are viewed through the lens of changing language use.

Historical demographic dynamics underlying local adaptation in the presence of gene flow

The range of a species is the result of the relative contribution of spatial tracking of environmental requirements and adaptation to ecological conditions outside the ancestral niche. The appearance of novel habitats caused by climatic oscillation can promote range expansion and accompanying demographic growth. The demographic dynamics of populations leave a signal in \ patterns. We modeled three competing scenarios pertaining to the circumstance of a range expansion by the Karoo Scrub-Robin into newly available habitat resulting from the increasing aridification of southern Africa. Genetic variation was contrasted with the theoretical expectations of a spatial range expansion, and compared with data of a putative adaptive trait. We infer that this bird likely colonized the arid zone, as a consequence of adaptive evolution in a small peripheral population, followed by an expansion with recurrent exchange of migrants with the ancestral populations.

Population-genetic analysis of HvABCG31 promoter sequence in wild barley (Hordeum vulgare ssp. spontaneum)

Background

The cuticle is an important adaptive structure whose origin played a crucial role in the transition of plants from aqueous to terrestrial conditions. HvABCG31/Eibi1 is an ABCG transporter gene, involved in cuticle formation that was recently identified in wild barley (Hordeum vulgare ssp. spontaneum). To study the genetic variation of HvABCG31 in different habitats, its 2 kb promoter region was sequenced from 112 wild barley accessions collected from five natural populations from southern and northern Israel. The sites included three mesic and two xeric habitats, and differed in annual rainfall, soil type, and soil water capacity.

Results

Phylogenetic analysis of the aligned HvABCG31 promoter sequences clustered the majority of accessions (69 out of 71) from the three northern mesic populations into one cluster, while all 21 accessions from the Dead Sea area, a xeric southern population, and two isolated accessions (one from a xeric population at Mitzpe Ramon and one from the xeric ‘African Slope’ of “Evolution Canyon”) formed the second cluster. The southern arid populations included six haplotypes, but they differed from the consensus sequence at a large number of positions, while the northern mesic populations included 15 haplotypes that were, on average, more similar to the consensus sequence. Most of the haplotypes (20 of 22) were unique to a population. Interestingly, higher genetic variation occurred within populations (54.2%) than among populations (45.8%). Analysis of the promoter region detected a large number of transcription factor binding sites: 121–128 and 121–134 sites in the two southern arid populations, and 123–128,125–128, and 123–125 sites in the three northern mesic populations. Three types of TFBSs were significantly enriched: those related to GA (gibberellin), Dof (DNA binding with one finger), and light.

Conclusions

Drought stress and adaptive natural selection may have been important determinants in the observed sequence variation of HvABCG31 promoter. Abiotic stresses may be involved in the HvABCG31 gene transcription regulations, generating more protective cuticles in plants under stresses.

Recombinant hybrids retain heterozygosity at many loci: new insights into the genomics of reproductive isolation in Populus

The maintenance of species barriers in the face of gene flow is often thought to result from strong selection against intermediate genotypes, thereby preserving genetic differentiation. Most speciation genomic studies thus aim to identify exceptionally divergent loci between populations, but divergence will be affected by many processes other than reproductive isolation (RI) and speciation. Through genomic studies of recombinant hybrids sampled in the wild, genetic variation associated with RI can be observed in situ, because selection against incompatible genotypes will leave detectable patterns of variation in the hybrid genomes. To better understand the mechanisms directly involved in RI, we investigated three natural 'replicate' hybrid zones between two divergent Populus species via locus-specific patterns of ancestry across recombinant hybrid genomes. As expected, genomic patterns in hybrids and their parental species were consistent with the presence of underdominant selection at several genomic regions. Surprisingly, many loci displayed greatly increased between-species heterozygosity in recombinant hybrids despite striking genetic differentiation between the parental genomes, the opposite of what would be expected with selection against intermediate genotypes. Only a limited, reproducible set of genotypic combinations was present in hybrid genomes across localities. In the absence of clearly delimited 'hybrid habitats', our results suggest that complex epistatic interactions within genomes play an important role in advanced stages of RI between these ecologically divergent forest trees. This calls for more genomic studies that test for unusual patterns of genomic ancestry in hybridizing species.

Do highly divergent loci reside in genomic regions affecting reproductive isolation? A test using next-generation sequence data in Timema stick insects

Background

Genetic divergence during speciation with gene flow is heterogeneous across the genome, with some regions exhibiting stronger differentiation than others. Exceptionally differentiated regions are often assumed to experience reduced introgression, i.e., reduced flow of alleles from one population into another because such regions are affected by divergent selection or cause reproductive isolation. In contrast, the remainder of the genome can be homogenized by high introgression. Although many studies have documented variation across the genome in genetic differentiation, there are few tests of this hypothesis that explicitly quantify introgression. Here, we provide such a test using 38,304 SNPs in populations of Timema cristinae stick insects. We quantify whether loci that are highly divergent between geographically separated (‘allopatric’) populations exhibit unusual patterns of introgression in admixed populations. To the extent this is true, highly divergent loci between allopatric populations contribute to reproductive isolation in admixed populations.

Results

As predicted, we find a substantial association between locus-specific divergence between allopatric populations and locus-specific introgression in admixed populations. However, many loci depart from this relationship, sometimes strongly so. We also report evidence for selection against foreign alleles due to local adaptation.

Conclusions

Loci that are strongly differentiated between allopatric populations sometimes contribute to reproductive isolation in admixed populations. However, geographic variation in selection and local adaptation, in aspects of genetic architecture (such as organization of genes, recombination rate variation, number and effect size of variants contributing to adaptation, etc.), and in stochastic evolutionary processes such as drift can cause strong differentiation of loci that do not always contribute to reproductive isolation. The results have implications for the theory of ‘genomic islands of speciation’.

Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship

In Drosophila, male flies perform innate, stereotyped courtship behavior. This innate behavior evolves rapidly between fly species, and is likely to have contributed to reproductive isolation and species divergence. We currently understand little about the neurobiological and genetic mechanisms that contributed to the evolution of courtship behavior. Here we describe a novel behavioral difference between the two closely related species D. yakuba and D. santomea: the frequency of wing rowing during courtship. During courtship, D. santomea males repeatedly rotate their wing blades to face forward and then back (rowing), while D. yakuba males rarely row their wings. We found little intraspecific variation in the frequency of wing rowing for both species. We exploited multiplexed shotgun genotyping (MSG) to genotype two backcross populations with a single lane of Illumina sequencing. We performed quantitative trait locus (QTL) mapping using the ancestry information estimated by MSG and found that the species difference in wing rowing mapped to four or five genetically separable regions. We found no evidence that these loci display epistasis. The identified loci all act in the same direction and can account for most of the species difference.

Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica

Local adaptation is important in evolutionary processes and speciation. We used multiple tests to identify several candidate genes that may be involved in local adaptation from 1026 loci in 14 natural populations of Cryptomeria japonica, the most economically important forestry tree in Japan. We also studied the relationships between genotypes and environmental variables to obtain information on the selective pressures acting on individual populations. Outlier loci were mapped onto a linkage map, and the positions of loci associated with specific environmental variables are considered. The outlier loci were not randomly distributed on the linkage map; linkage group 11 was identified as a genomic island of divergence. Three loci in this region were also associated with environmental variables such as mean annual temperature, daily maximum temperature, maximum snow depth, and so on. Outlier loci identified with high significance levels will be essential for conservation purposes and for future work on molecular breeding.

Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America

Understanding the genetic underpinnings of adaptive change is a fundamental but largely unresolved problem in evolutionary biology. Drosophila melanogaster, an ancestrally tropical insect that has spread to temperate regions and become cosmopolitan, offers a powerful opportunity for identifying the molecular polymorphisms underlying clinal adaptation. Here, we use genome-wide next-generation sequencing of DNA pools ('pool-seq') from three populations collected along the North American east coast to examine patterns of latitudinal differentiation. Comparing the genomes of these populations is particularly interesting since they exhibit clinal variation in a number of important life history traits. We find extensive latitudinal differentiation, with many of the most strongly differentiated genes involved in major functional pathways such as the insulin/TOR, ecdysone, torso, EGFR, TGFβ/BMP, JAK/STAT, immunity and circadian rhythm pathways. We observe particularly strong differentiation on chromosome 3R, especially within the cosmopolitan inversion In(3R)Payne, which contains a large number of clinally varying genes. While much of the differentiation might be driven by clinal differences in the frequency of In(3R)P, we also identify genes that are likely independent of this inversion. Our results provide genome-wide evidence consistent with pervasive spatially variable selection acting on numerous loci and pathways along the well-known North American cline, with many candidates implicated in life history regulation and exhibiting parallel differentiation along the previously investigated Australian cline.

AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha

Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.

Parallel and lineage-specific molecular adaptation to climate in boreal black spruce

In response to selective pressure, adaptation may follow different genetic pathways throughout the natural range of a species due to historical differentiation in standing genetic variation. Using 41 populations of black spruce (Picea mariana), the objectives of this study were to identify adaptive genetic polymorphisms related to temperature and precipitation variation across the transcontinental range of the species, and to evaluate the potential influence of historical events on their geographic distribution. Population structure was first inferred using 50 control nuclear markers. Then, 47 candidate gene SNPs identified in previous genome scans were tested for relationship with climatic factors using an F(ST) -based outlier method and regressions between allele frequencies and climatic variations. Two main intraspecific lineages related to glacial vicariance were detected at the transcontinental scale. Within-lineage analyses of allele frequencies allowed the identification of 23 candidate SNPs significantly related to precipitation and/or temperature variation, among which seven were common to both lineages, eight were specific to the eastern lineage and eight were specific to the western lineage. The implication of these candidate SNPs in adaptive processes was further supported by gene functional annotations. Multiple evidences indicated that the occurrence of lineage-specific adaptive SNPs was better explained by selection acting on historically differentiated gene pools rather than differential selection due to heterogeneity of interacting environmental factors and pleiotropic effects. Taken together, these findings suggest that standing genetic variation of potentially adaptive nature has been modified by historical events, hence affecting the outcome of recent selection and leading to different adaptive routes between intraspecific lineages.

Incompatibility and competitive exclusion of genomic segments between sibling Drosophila species

The extent and nature of genetic incompatibilities between incipient races and sibling species is of fundamental importance to our view of speciation. However, with the exception of hybrid inviability and sterility factors, little is known about the extent of other, more subtle genetic incompatibilities between incipient species. Here we experimentally demonstrate the prevalence of such genetic incompatibilities between two young allopatric sibling species, Drosophila simulans and D. sechellia. Our experiments took advantage of 12 introgression lines that carried random introgressed D. sechellia segments in different parts of the D. simulans genome. First, we found that these introgression lines did not show any measurable sterility or inviability effects. To study if these sechellia introgressions in a simulans background contained other fitness consequences, we competed and genetically tracked the marked alleles within each introgression against the wild-type alleles for 20 generations. Strikingly, all marked D. sechellia introgression alleles rapidly decreased in frequency in only 6 to 7 generations. We then developed computer simulations to model our competition results. These simulations indicated that selection against D. sechellia introgression alleles was high (average s = 0.43) and that the marker alleles and the incompatible alleles did not separate in 78% of the introgressions. The latter result likely implies that most introgressions contain multiple genetic incompatibilities. Thus, this study reveals that, even at early stages of speciation, many parts of the genome diverge to a point where introducing foreign elements has detrimental fitness consequences, but which cannot be seen using standard sterility and inviability assays.

Determining the extent of genomic incompatibilities is a pivotal issue in understanding the process of speciation. A controversial topic that has recently sparked debate is whether there are few isolated genetic regions (so-called “genomic islands of speciation”) or extensive genetic regions (“genomic continents of speciation”) responsible for species divergence. To answer this question, most work has focused on species divergence at the DNA sequence level. Here, we present a new perspective by shifting the focus to the fitness and functional aspects of foreign genomic introgression. To illustrate our point, we performed an introgression experiment on two sibling species, D. sechellia and D. simulans. After introgressing random genomic segments of D. sechellia into D. simulans genetic background, a 20-generation competition experiment revealed that, even at the early stages of speciation, there are virtually always detrimental fitness consequences to introducing random foreign elements from one genome to another. This implies that incipient speciation may be characterized by widespread accumulation of genomic incompatibilities rather than a few isolated genes. This study shows that we should move beyond the sterility and inviability assays in order to understand the full extent of genetic incompatibilities during speciation.

Uninformative polymorphisms bias genome scans for signatures of selection

Background

With the establishment of high-throughput sequencing technologies and new methods for rapid and extensive single nucleotide (SNP) discovery, marker-based genome scans in search of signatures of divergent selection between populations occupying ecologically distinct environments are becoming increasingly popular.

Methods and Results

On the basis of genome-wide SNP marker data generated by RAD sequencing of lake and stream stickleback populations, we show that the outcome of such studies can be systematically biased if markers with a low minor allele frequency are included in the analysis. The reason is that these ‘uninformative’ polymorphisms lack the adequate potential to capture signatures of drift and hitchhiking, the focal processes in ecological genome scans. Bias associated with uninformative polymorphisms is not eliminated by just avoiding technical artifacts in the data (PCR and sequencing errors), as a high proportion of SNPs with a low minor allele frequency is a general biological feature of natural populations.

Conclusions

We suggest that uninformative markers should be excluded from genome scans based on empirical criteria derived from careful inspection of the data, and that these criteria should be reported explicitly. Together, this should increase the quality and comparability of genome scans, and hence promote our understanding of the processes driving genomic differentiation.

Genomic consequences of multiple speciation processes in a stick insect

Diverse geographical modes and mechanisms of speciation are known, and individual speciation genes have now been identified. Despite this progress, genome-wide outcomes of different evolutionary processes during speciation are less understood. Here, we integrate ecological and spatial information, mating trials, transplantation data and analysis of 86 130 single nucleotide polymorphisms (SNPs) in eight populations (28 pairwise comparisons) of Timema cristinae stick insects to test the effects of different factors on genomic divergence in a system undergoing ecological speciation. We find patterns consistent with effects of numerous factors, including geographical distance, gene flow, divergence in host plant use and climate, and selection against maladaptive hybridization (i.e. reinforcement). For example, the number of highly differentiated ‘outlier loci’, allele-frequency clines and the overall distribution of genomic differentiation were recognizably affected by these factors. Although host use has strong effects on phenotypic divergence and reproductive isolation, its effects on genomic divergence were subtler and other factors had pronounced effects. The results demonstrate how genomic data can provide new insights into speciation and how genomic divergence can be complex, yet predictable. Future work could adopt experimental, mapping and functional approaches to directly test which genetic regions are affected by selection and determine their physical location in the genome.

Admixture mapping of male nuptial colour and body shape in a recently formed hybrid population of threespine stickleback

Despite recent progress, we still know relatively little about the genetic architecture that underlies adaptation to divergent environments. Determining whether the genetic architecture of phenotypic adaptation follows any predictable patterns requires data from a wide variety of species. However, in many organisms, genetic studies are hindered by the inability to perform genetic crosses in the laboratory or by long generation times. Admixture mapping is an approach that circumvents these issues by taking advantage of hybridization that occurs between populations or species in the wild. Here, we demonstrate the utility of admixture mapping in a naturally occurring hybrid population of threespine sticklebacks (Gasterosteus aculeatus) from Enos Lake, British Columbia. Until recently, this lake contained two species of sticklebacks adapted to divergent habitats within the lake. This benthic-limnetic species pair diverged in a number of phenotypes, including male nuptial coloration and body shape, which were previously shown to contribute to reproductive isolation between them. However, recent ecological disturbance has contributed to extensive hybridization between the species, and there is now a single, admixed population within Enos Lake. We collected over 500 males from Enos Lake and found that most had intermediate nuptial colour and body shape. By genotyping males with nuptial colour at the two extremes of the phenotypic distribution, we identified seven genomic regions on three chromosomes associated with divergence in male nuptial colour. These genomic regions are also associated with variation in body shape, suggesting that tight linkage and/or pleiotropy facilitated adaptation to divergent environments in benthic-limnetic species pairs.

Footprints of natural and artificial selection for photoperiod pathway genes in Oryza

Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31°N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.

Genome-wide architecture of reproductive isolation in a naturally occurring hybrid zone between Mus musculus musculus and M. m. domesticus

Studies of a hybrid zone between two house mouse subspecies (Mus musculus musculus and M. m. domesticus) along with studies using laboratory crosses reveal a large role for the X chromosome and multiple autosomal regions in reproductive isolation as a consequence of disrupted epistasis in hybrids. One limitation of previous work has been that most of the identified genomic regions have been large. The goal here is to detect and characterize precise genomic regions underlying reproductive isolation. We surveyed 1401 markers evenly spaced across the genome in 679 mice collected from two different transects. Comparisons between transects provide a means for identifying common patterns that likely reflect intrinsic incompatibilities. We used a genomic cline approach to identify patterns that correspond to epistasis. From both transects, we identified contiguous regions on the X chromosome in which markers were inferred to be involved in epistatic interactions. We then searched for autosomal regions showing the same patterns and found they constitute about 5% of autosomal markers. We discovered substantial overlap between these candidate regions underlying reproductive isolation and QTL for hybrid sterility identified in laboratory crosses. Analysis of gene content in these regions suggests a key role for several mechanisms, including the regulation of transcription, sexual conflict and sexual selection operating at both the postmating prezygotic and postzygotic stages of reproductive isolation. Taken together, these results indicate that speciation in two recently diverged (c. 0.5 Ma) house mouse subspecies is complex, involving many genes dispersed throughout the genome and associated with distinct functions.

Genomics of adaptation and speciation in cichlid fishes: recent advances and analyses in African and Neotropical lineages

Cichlid fishes are remarkably phenotypically diverse and species-rich. Therefore, they provide an exciting opportunity for the study of the genetics of adaptation and speciation by natural and sexual selection. Here, we review advances in the genomics and transcriptomics of cichlids, particularly regarding ecologically relevant differences in body shape, trophic apparatus, coloration and patterning, and sex determination. Research conducted so far has focused almost exclusively on African cichlids. To analyse genomic diversity and selection in a Neotropical radiation, we conducted a comparative transcriptomic analysis between sympatric, ecologically divergent crater-lake Midas cichlids (Lake Xiloá Amphilophus amarillo and Amphilophus sagittae). We pyrosequenced (Roche 454) expressed sequence tag (EST) libraries and generated more than 178 000 000 ESTs and identified nine ESTs under positive selection between these sister species (Ka/Ks > 1). None of these ESTs were found to be under selection in African cichlids. Of 11 candidate genes for ecomorphological differentiation in African cichlids, none showed signs of selection between A. amarillo and A. sagittae. Although more population-level studies are now needed to thoroughly document patterns of divergence during speciation of cichlids, available information so far suggests that adaptive phenotypic diversification in Neotropical and African cichlids may be evolving through non-parallel genetic bases.