The genes underlying the process of speciation

Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds

The rate at which speciation occurs varies greatly among different kinds of organisms and is frequently assumed to result from species- or clade-specific factors that influence the rate at which populations acquire reproductive isolation. This premise leads to a fundamental prediction that has never been tested: Organisms that quickly evolve prezygotic or postzygotic reproductive isolation should have faster rates of speciation than organisms that slowly acquire reproductive isolation. We combined phylogenetic estimates of speciation rates from Drosophila and birds with a method for analyzing interspecific hybridization data to test whether the rate at which individual lineages evolve reproductive isolation predicts their macroevolutionary rate of species formation. We find that some lineages evolve reproductive isolation much more quickly than others, but this variation is decoupled from rates of speciation as measured on phylogenetic trees. For the clades examined here, reproductive isolation--especially intrinsic, postzygotic isolation--does not seem to be the rate-limiting control on macroevolutionary diversification dynamics. These results suggest that factors associated with intrinsic reproductive isolation may have less to do with the tremendous variation in species diversity across the evolutionary tree of life than is generally assumed.

Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon

Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.

Differential introgression in a mosaic hybrid zone reveals candidate barrier genes

Hybrid zones act as genomic sieves. Although globally advantageous alleles will spread throughout the zone and neutral alleles can be freely exchanged between species, introgression will be restricted for genes that contribute to reproductive barriers or local adaptation. Seminal fluid proteins (SFPs) are known to contribute to reproductive barriers in insects and have been proposed as candidate barrier genes in the hybridizing field crickets Gryllus pennsylvanicus and Gryllus firmus. Here, we have used 125 single nucleotide polymorphisms to characterize patterns of differential introgression and to identify genes that may contribute to prezygotic barriers between these species. Using a transcriptome scan of the male cricket accessory gland (the site of SFP synthesis), we identified genes with major allele frequency differences between the species. We then compared patterns of introgression for genes encoding SFPs with patterns for genes expressed in the same tissue that do not encode SFPs. We find no evidence that SFPs have reduced gene exchange across the cricket hybrid zone. However, a number of genes exhibit dramatically reduced introgression, and many of these genes encode proteins with functional roles consistent with known barriers.

Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology

Ecologically mediated selection has increasingly become recognised as an important driver of speciation. The correlation between neutral genetic differentiation and environmental or phenotypic divergence among populations, to which we collectively refer to as isolation-by-ecology (IBE), is an indicator of ecological speciation. In a meta-analysis framework, we determined the strength and commonality of IBE in nature. On the basis of 106 studies, we calculated a mean effect size of IBE with and without controlling for spatial autocorrelation among populations. Effect sizes were 0.34 (95% CI 0.24-0.42) and 0.26 (95% CI 0.13-0.37), respectively, indicating that an average of 5% of the neutral genetic differentiation among populations was explained purely by ecological contrast. Importantly, spatial autocorrelation reduced IBE correlations for environmental variables, but not for phenotypes. Through simulation, we showed how the influence of isolation-by-distance and spatial autocorrelation of ecological variables can result in false positives or underestimated correlations if not accounted for in the IBE model. Collectively, this meta-analysis showed that ecologically induced genetic divergence is pervasive across time-scales and taxa, and largely independent of the choice of molecular marker. We discuss the importance of these results in the context of adaptation and ecological speciation and suggest future research avenues.

Embryonic lethality leads to hybrid male inviability in hybrids between Drosophila melanogaster and D. santomea

The study of the morphological defects unique to interspecific hybrids can reveal which developmental pathways have diverged between species. Drosophila melanogaster and D. santomea diverged more than 10 million years ago, and when crossed produce sterile adult females. Adult hybrid males are absent from all interspecific crosses. We aimed to determine the fate of these hybrid males. To do so, we tracked the development of hybrid females and males using classic genetic markers and techniques. We found that hybrid males die predominantly as embryos with severe segment-specification defects while a large proportion of hybrid females embryos hatch and survive to adulthood. In particular, we show that most male embryos show a characteristic abdominal ablation phenotype, not observed in either parental species. This suggests that sex-specific embryonic developmental defects eliminate hybrid males in this interspecific cross. The study of the developmental abnormalities that occur in hybrids can lead to the understanding of cryptic molecular divergence between species sharing a conserved body plan.

Divergent selection drives genetic differentiation in an R2R3-MYB transcription factor that contributes to incipient speciation in Mimulus aurantiacus

Identifying the molecular genetic basis of traits contributing to speciation is of crucial importance for understanding the ecological and evolutionary mechanisms that generate biodiversity. Despite several examples describing putative "speciation genes," it is often uncertain to what extent these genetic changes have contributed to gene flow reductions in nature. Therefore, considerable interest lies in characterizing the molecular basis of traits that actively confer reproductive isolation during the early stages of speciation, as these loci can be attributed directly to the process of divergence. In Southern California, two ecotypes of Mimulus aurantiacus are parapatric and differ primarily in flower color, with an anthocyanic, red-flowered morph in the west and an anthocyanin-lacking, yellow-flowered morph in the east. Evidence suggests that the genetic changes responsible for this shift in flower color have been essential for divergence and have become fixed in natural populations of each ecotype due to almost complete differences in pollinator preference. In this study, we demonstrate that a cis-regulatory mutation in an R2R3-MYB transcription factor results in differential regulation of enzymes in the anthocyanin biosynthetic pathway and is the major contributor to differences in floral pigmentation. In addition, molecular population genetic data show that, despite gene flow at neutral loci, divergent selection has driven the fixation of alternate alleles at this gene between ecotypes. Therefore, by identifying the genetic basis underlying ecologically based divergent selection in flower color between these ecotypes, we have revealed the ecological and functional mechanisms involved in the evolution of pre-mating isolation at the early stages of incipient speciation.

Rates of molecular evolution and diversification in plants: chloroplast substitution rates correlate with species-richness in the Proteaceae

BACKGROUND

Many factors have been identified as correlates of the rate of molecular evolution, such as body size and generation length. Analysis of many molecular phylogenies has also revealed correlations between substitution rates and clade size, suggesting a link between rates of molecular evolution and the process of diversification. However, it is not known whether this relationship applies to all lineages and all sequences. Here, in order to investigate how widespread this phenomenon is, we investigate patterns of substitution in chloroplast genomes of the diverse angiosperm family Proteaceae. We used DNA sequences from six chloroplast genes (6278bp alignment with 62 taxa) to test for a correlation between diversification and the rate of substitutions.

RESULTS

Using phylogenetically-independent sister pairs, we show that species-rich lineages of Proteaceae tend to have significantly higher chloroplast substitution rates, for both synonymous and non-synonymous substitutions.

CONCLUSIONS

We show that the rate of molecular evolution in chloroplast genomes is correlated with net diversification rates in this large plant family. We discuss the possible causes of this relationship, including molecular evolution driving diversification, speciation increasing the rate of substitutions, or a third factor causing an indirect link between molecular and diversification rates. The link between the synonymous substitution rate and clade size is consistent with a role for the mutation rate of chloroplasts driving the speed of reproductive isolation. We find no significant differences in the ratio of non-synonymous to synonymous substitutions between lineages differing in net diversification rate, therefore we detect no signal of population size changes or alteration in selection pressures that might be causing this relationship.

Differential introgression reveals candidate genes for selection across a spruce (Picea sitchensis × P. glauca) hybrid zone

Differential patterns of introgression between species across ecological gradients provide a fine-scale depiction of extrinsic and intrinsic factors that contribute to the maintenance of species barriers and adaptation across heterogeneous environments. Introgression was examined for 721 individuals collected from the ecological transition zone spanning maritime to continental climates within the Picea sitchensis-Picea glauca contact zone using a panel of 268 candidate gene single nucleotide polymorphisms. Geographic clines showed a strong spatial relationship between allele frequencies and both distance from the ocean along major rivers and mean annual precipitation, indicating a strong role for environmental selection. Interspecific patterns of differentiation using outlier tests revealed three candidate genes that may be targets of long-term divergent selection between the parental species, although contemporary genomic clines within the hybrid zone suggested neutral patterns of introgression for these genes. This study provides a fine-scale analysis of locus-specific introgression, identifying a suite of candidate loci that may be targets of extrinsic or intrinsic selection, with broad application in understanding local adaptation to climate.

A hybrid genetic linkage map of two ecologically and morphologically divergent Midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq)

Cichlid fishes are an excellent model system for studying speciation and the formation of adaptive radiations because of their tremendous species richness and astonishing phenotypic diversity. Most research has focused on African rift lake fishes, although Neotropical cichlid species display much variability as well. Almost one dozen species of the Midas cichlid species complex (Amphilophus spp.) have been described so far and have formed repeated adaptive radiations in several Nicaraguan crater lakes. Here we apply double-digest restriction-site associated DNA sequencing to obtain a high-density linkage map of an interspecific cross between the benthic Amphilophus astorquii and the limnetic Amphilophus zaliosus, which are sympatric species endemic to Crater Lake Apoyo, Nicaragua. A total of 755 RAD markers were genotyped in 343 F₂ hybrids. The map resolved 25 linkage groups and spans a total distance of 1427 cM with an average marker spacing distance of 1.95 cM, almost matching the total number of chromosomes (n = 24) in these species. Regions of segregation distortion were identified in five linkage groups. Based on the pedigree of parents to F₂ offspring, we calculated a genome-wide mutation rate of 6.6 × 10⁻⁸ mutations per nucleotide per generation. This genetic map will facilitate the mapping of ecomorphologically relevant adaptive traits in the repeated phenotypes that evolved within the Midas cichlid lineage and, as the first linkage map of a Neotropical cichlid, facilitate comparative genomic analyses between African cichlids, Neotropical cichlids and other teleost fishes.

The genomic landscape of species divergence in Ficedula flycatchers

Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.

Quantitative traits and mode of speciation in Martinique anoles

We investigate extensive quantitative trait variation (dewlap hue, colour pattern, dorsum hue, body proportions and scalation) in the Martinique anole across eight transects representing nascent parapatric ecological speciation, nascent allopatric speciation and allopatric divergence without sufficient genetic structure to suggest speciation. Quantitative trait divergence can be extremely large between adjacent sets of populations, but with one exception that this is associated with difference in habitat rather than past allopatry. Nascent ecological speciation shows the greatest level of quantitative trait divergence across all character sets including those implicated in natural, as well as sexual selection. The sole example of nascent allopatric speciation is associated with fairly strong quantitative trait divergence among most character sets, but not the set most implicated in natural (rather than sexual) selection. The role of sexual selection in ecological speciation is discussed, both in terms of female choice with assortative mating and male-male competition with condition-dependant sexual signals.

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.

A complex speciation-richness relationship in a simple neutral model

Speciation is the “elephant in the room” of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities. We focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. We use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations.

Time scales of divergence and speciation among natural populations and subspecies of Arabidopsis lyrata (Brassicaceae)

PREMISE OF THE STUDY

Plant populations that face new environments adapt and diverge simultaneously, and both processes leave footprints in their genetic diversity. Arabidopsis lyrata is an excellent species for studying these processes. Pairs of populations and subspecies of A. lyrata represent different stages of divergence. These populations are also known to be locally adapted and display various stages of emerging reproductive isolation.

METHODS

We used nucleotide diversity data from 19 loci to estimate divergence times and levels of diversity among nine A. lyrata populations. Traditional distance-based methods and model-based clustering analysis were used to supplement pairwise coalescence-based analysis of divergence.

KEY RESULTS

Estimated divergence times varied from 130,000 generations between North American and European subspecies to 39,000 generations between central European and Scandinavian populations. In concordance with previous studies, the highest level of diversity was found in Central Europe and the lowest in North America and a diverged Russian Karhumäki population. Local adaptation among Northern and central European populations has emerged during the last 39,000 generations. Populations that are reproductively isolated by prezygotic mechanisms have been separated for a longer time period of ∼70,000 generations but still have shared nucleotide polymorphism.

CONCLUSIONS

In A. lyrata, reproductively isolated populations started to diverge ∼70,000 generations ago and more closely related, locally adapted populations have been separate lineages for ∼39,000 generations. However, based on the posterior distribution of divergence times, the processes leading to reproductive isolation and local adaptation are likely to temporally coincide.

Extraordinarily rapid life-history divergence between Cryptasterina sea star species

Life history plays a critical role in governing microevolutionary processes such as gene flow and adaptation, as well as macroevolutionary processes such speciation. Here, we use multilocus phylogeographic analyses to examine a speciation event involving spectacular life-history differences between sister species of sea stars. Cryptasterina hystera has evolved a suite of derived life-history traits (including internal self-fertilization and brood protection) that differ from its sister species Cryptasterina pentagona, a gonochoric broadcast spawner. We show that these species have only been reproductively isolated for approximately 6000 years (95% highest posterior density of 905-22 628), and that this life-history change may be responsible for dramatic genetic consequences, including low nucleotide diversity, zero heterozygosity and no gene flow. The rapid divergence of these species rules out some mechanisms of isolation such as adaptation to microhabitats in sympatry, or slow divergence by genetic drift during prolonged isolation. We hypothesize that the large phenotypic differences between species relative to the short divergence time suggests that the life-history differences observed may be direct responses to disruptive selection between populations. We speculate that local environmental or demographic differences at the southern range margin are possible mechanisms of selection driving one of the fastest known marine speciation events.

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.

Genomics of isolation in hybrids

Hybrid zones are common in nature and can offer critical insights into the dynamics and components of reproductive isolation. Hybrids between diverged lineages are particularly informative about the genetic architecture of reproductive isolation, because introgression in an admixed population is a direct measure of isolation. In this paper, we combine simulations and a new statistical model to determine the extent to which different genetic architectures of isolation leave different signatures on genome-level patterns of introgression. We found that reproductive isolation caused by one or several loci of large effect caused greater heterogeneity in patterns of introgression than architectures involving many loci with small fitness effects, particularly when isolating factors were closely linked. The same conditions that led to heterogeneous introgression often resulted in a reasonable correspondence between outlier loci and the genetic loci that contributed to isolation. However, demographic conditions affected both of these results, highlighting potential limitations to the study of the speciation genomics. Further progress in understanding the genomics of speciation will require large-scale empirical studies of introgression in hybrid zones and model-based analyses, as well as more comprehensive modelling of the expected levels of isolation with different demographies and genetic architectures of isolation.

Genomic divergence during speciation: causes and consequences

Speciation is a fundamental process responsible for the diversity of life. Progress has been made in detecting individual 'speciation genes' that cause reproductive isolation. In contrast, until recently, less attention has been given to genome-wide patterns of divergence during speciation. Thus, major questions remain concerning how individual speciation genes are arrayed within the genome, and how this affects speciation. This theme issue is dedicated to exploring this genomic perspective of speciation. Given recent sequencing and computational advances that now allow genomic analyses in most organisms, the goal is to help move the field towards a more integrative approach. This issue draws upon empirical studies in plants and animals, and theoretical work, to review and further document patterns of genomic divergence. In turn, these studies begin to disentangle the role that different processes, such as natural selection, gene flow and recombination rate, play in generating observed patterns. These factors are considered in the context of how genomes diverge as speciation unfolds, from beginning to end. The collective results point to how experimental work is now required, in conjunction with theory and sequencing studies, to move the field from descriptive studies of patterns of divergence towards a predictive framework that tackles the causes and consequences of genome-wide patterns.

Establishment of new mutations under divergence and genome hitchhiking

Theoretical models addressing genome-wide patterns of divergence during speciation are needed to help us understand the evolutionary processes generating empirical patterns. Here, we examine a critical issue concerning speciation-with-gene flow: to what degree does physical linkage (r < 0.5) of new mutations to already diverged genes aid the build-up of genomic islands of differentiation? We used simulation and analytical approaches to partition the probability of establishment for a new divergently selected mutation when the mutation (i) is the first to arise in an undifferentiated genome (the direct effect of selection), (ii) arises unlinked to any selected loci (r = 0.5), but within a genome that has some already diverged genes (the effect of genome-wide reductions in gene flow for facilitating divergence, which we term 'genome hitchhiking'), and (iii) arises in physical linkage to a diverged locus (divergence hitchhiking). We find that the strength of selection acting directly on a new mutation is generally the most important predictor for establishment, with divergence and genomic hitchhiking having smaller effects. We outline the specific conditions under which divergence and genome hitchhiking can aid mutation establishment. The results generate predictions about genome divergence at different points in the speciation process and avenues for further work.

Identification of novel single nucleotide polymorphisms (SNPs) in deer (Odocoileus spp.) using the BovineSNP50 BeadChip

Single nucleotide polymorphisms (SNPs) are growing in popularity as a genetic marker for investigating evolutionary processes. A panel of SNPs is often developed by comparing large quantities of DNA sequence data across multiple individuals to identify polymorphic sites. For non-model species, this is particularly difficult, as performing the necessary large-scale genomic sequencing often exceeds the resources available for the project. In this study, we trial the Bovine SNP50 BeadChip developed in cattle (Bos taurus) for identifying polymorphic SNPs in cervids Odocoileus hemionus (mule deer and black-tailed deer) and O. virginianus (white-tailed deer) in the Pacific Northwest. We found that 38.7% of loci could be genotyped, of which 5% (n = 1068) were polymorphic. Of these 1068 polymorphic SNPs, a mixture of putatively neutral loci (n = 878) and loci under selection (n = 190) were identified with the F_ST-outlier method. A range of population genetic analyses were implemented using these SNPs and a panel of 10 microsatellite loci. The three types of deer could readily be distinguished with both the SNP and microsatellite datasets. This study demonstrates that commercially developed SNP chips are a viable means of SNP discovery for non-model organisms, even when used between very distantly related species (the Bovidae and Cervidae families diverged some 25.1−30.1 million years before present).

The genomics of speciation-with-gene-flow

The emerging field of speciation genomics is advancing our understanding of the evolution of reproductive isolation from the individual gene to a whole-genome perspective. In this new view it is important to understand the conditions under which 'divergence hitchhiking' associated with the physical linkage of gene regions, versus 'genome hitchhiking' associated with reductions in genome-wide rates of gene flow caused by selection, can enhance speciation-with-gene-flow. We describe here a theory predicting four phases of speciation, defined by changes in the relative effectiveness of divergence and genome hitchhiking, and review empirical data in light of the theory. We outline future directions, emphasizing the need to couple next-generation sequencing with selection, transplant, functional genomics, and mapping studies. This will permit a natural history of speciation genomics that will help to elucidate the factors responsible for population divergence and the roles that genome structure and different forms of hitchhiking play in facilitating the genesis of new biodiversity.

Large-scale candidate gene scan reveals the role of chemoreceptor genes in host plant specialization and speciation in the pea aphid

Understanding the drivers of speciation is critical to interpreting patterns of biodiversity. The identification of the genetic changes underlying adaptation and reproductive isolation is necessary to link barriers to gene flow to the causal origins of divergence. Here, we present a novel approach to the genetics of speciation, which should complement the commonly used approaches of quantitative trait locus mapping and genome-wide scans for selection. We present a large-scale candidate gene approach by means of sequence capture, applied to identifying the genetic changes underlying reproductive isolation in the pea aphid, a model system for the study of ecological speciation. Targeted resequencing enabled us to scale up the candidate gene approach, specifically testing for the role of chemosensory gene families in host plant specialization. Screening for the signature of divergence under selection at 172 candidate and noncandidate loci, we revealed a handful of loci that show high levels of differentiation among host races, which almost all correspond to odorant and gustatory receptor genes. This study offers the first indication that some chemoreceptor genes, often tightly linked together in the genome, could play a key role in local adaptation and reproductive isolation in the pea aphid and potentially other phytophagous insects. Our approach opens a new route toward the functional genomics of ecological speciation.

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

Evolutionary diversification is often initiated by adaptive divergence between populations occupying ecologically distinct environments while still exchanging genes. The genetic foundations of this divergence process are largely unknown and are here explored through genome scans in multiple independent lake-stream population pairs of threespine stickleback. We find that across the pairs, overall genomic divergence is associated with the magnitude of divergence in phenotypes known to be under divergent selection. Along this same axis of increasing diversification, genomic divergence becomes increasingly biased towards the centre of chromosomes as opposed to the peripheries. We explain this pattern by within-chromosome variation in the physical extent of hitchhiking, as recombination is greatly reduced in chromosome centres. Correcting for this effect suggests that a great number of genes distributed widely across the genome are involved in the divergence into lake vs. stream habitats. Analyzing additional allopatric population pairs, however, reveals that strong divergence in some genomic regions has been driven by selection unrelated to lake-stream ecology. Our study highlights a major contribution of large-scale variation in recombination rate to generating heterogeneous genomic divergence and indicates that elucidating the genetic basis of adaptive divergence might be more challenging than currently recognized.

Sex pheromone evolution is associated with differential regulation of the same desaturase gene in two genera of leafroller moths

Chemical signals are prevalent in sexual communication systems. Mate recognition has been extensively studied within the Lepidoptera, where the production and recognition of species-specific sex pheromone signals are typically the defining character. While the specific blend of compounds that makes up the sex pheromones of many species has been characterized, the molecular mechanisms underpinning the evolution of pheromone-based mate recognition systems remain largely unknown. We have focused on two sets of sibling species within the leafroller moth genera Ctenopseustis and Planotortrix that have rapidly evolved the use of distinct sex pheromone blends. The compounds within these blends differ almost exclusively in the relative position of double bonds that are introduced by desaturase enzymes. Of the six desaturase orthologs isolated from all four species, functional analyses in yeast and gene expression in pheromone glands implicate three in pheromone biosynthesis, two Δ9-desaturases, and a Δ10-desaturase, while the remaining three desaturases include a Δ6-desaturase, a terminal desaturase, and a non-functional desaturase. Comparative quantitative real-time PCR reveals that the Δ10-desaturase is differentially expressed in the pheromone glands of the two sets of sibling species, consistent with differences in the pheromone blend in both species pairs. In the pheromone glands of species that utilize (Z)-8-tetradecenyl acetate as sex pheromone component (Ctenopseustis obliquana and Planotortrix octo), the expression levels of the Δ10-desaturase are significantly higher than in the pheromone glands of their respective sibling species (C. herana and P. excessana). Our results demonstrate that interspecific sex pheromone differences are associated with differential regulation of the same desaturase gene in two genera of moths. We suggest that differential gene regulation among members of a multigene family may be an important mechanism of molecular innovation in sex pheromone evolution and speciation.

Chemical signals are prevalent in sexual communication systems, especially within the Lepidoptera where sex pheromones are typically one of the defining characteristics of species. We have isolated six desaturases from two groups of sibling species of leafroller moths belonging to the genera Ctenopseustis and Planotortrix. Functional analyses in yeast and quantitative RT–PCR indicate that three of the desaturases are involved in the biosynthesis of sex pheromone components in these species. One of three enzymes is a Δ10-desaturase that is differentially expressed in the pheromone glands of the two sets of sibling species, consistent with differences in the pheromone blend in both species pairs. In the pheromone glands of species that utilize (Z)-8-tetradecenyl acetate as sex pheromone component (C. obliquana and P. octo), the expression levels of the Δ10-desaturase are significantly higher than pheromone gland expression levels in their sibling species (C. herana and P. excessana). Our results demonstrate that interspecific sex pheromone differences are associated with differential regulation of the same desaturase gene in these two genera of moths. Based on these findings differential gene regulation among members of a multigene family may be an important mechanism of molecular innovation in sex pheromone evolution and speciation.

The Role of Parasitism in Adaptive Radiations—When Might Parasites Promote and When Might They Constrain Ecological Speciation?

Research on speciation and adaptive radiation has flourished during the past decades, yet factors underlying initiation of reproductive isolation often remain unknown. Parasites represent important selective agents and have received renewed attention in speciation research. We review the literature on parasite-mediated divergent selection in context of ecological speciation and present empirical evidence for three nonexclusive mechanisms by which parasites might facilitate speciation: reduced viability or fecundity of immigrants and hybrids, assortative mating as a pleiotropic by-product of host adaptation, and ecologically-based sexual selection. We emphasise the lack of research on speciation continuums, which is why no study has yet made a convincing case for parasite driven divergent evolution to initiate the emergence of reproductive isolation. We also point interest towards selection imposed by single versus multiple parasite species, conceptually linking this to strength and multifariousness of selection. Moreover, we discuss how parasites, by manipulating behaviour or impairing sensory abilities of hosts, may change the form of selection that underlies speciation. We conclude that future studies should consider host populations at variable stages of the speciation process, and explore recurrent patterns of parasitism and resistance that could pinpoint the role of parasites in imposing the divergent selection that initiates ecological speciation.

Chromatin evolution and molecular drive in speciation

Are there biological generalities that underlie hybrid sterility or inviability? Recently, around a dozen "speciation genes" have been identified mainly in Drosophila, and the biological functions of these genes are revealing molecular generalities. Major cases of hybrid sterility and inviability seem to result from chromatin evolution and molecular drive in speciation. Repetitive satellite DNAs within heterochromatin, especially at centromeres, evolve rapidly through molecular drive mechanisms (both meiotic and centromeric). Chromatin-binding proteins, therefore, must also evolve rapidly to maintain binding capability. As a result, chromatin binding proteins may not be able to interact with chromosomes from another species in a hybrid, causing hybrid sterility and inviability.

Biogeography of species richness gradients: linking adaptive traits, demography and diversification

Here we review how adaptive traits contribute to the emergence and maintenance of species richness gradients through their influence on demographic and diversification processes. We start by reviewing how demographic dynamics change along species richness gradients. Empirical studies show that geographical clines in population parameters and measures of demographic variability are frequent along latitudinal and altitudinal gradients. Demographic variability often increases at the extremes of regional species richness gradients and contributes to shape these gradients. Available studies suggest that adaptive traits significantly influence demographic dynamics, and set the limits of species distributions. Traits related to thermal tolerance, resource use, phenology and dispersal seem to play a significant role. For many traits affecting demography and/or diversification processes, complex mechanistic approaches linking genotype, phenotype and fitness are becoming progressively available. In several taxa, species can be distributed along adaptive trait continuums, i.e. a main axis accounting for the bulk of inter-specific variation in some correlated adaptive traits. It is shown that adaptive trait continuums can provide useful mechanistic frameworks to explain demographic dynamics and diversification in species richness gradients. Finally, we review the existence of sequences of adaptive traits in phylogenies, the interactions of adaptive traits and community context, the clinal variation of traits across geographical gradients, and the role of adaptive traits in determining the history of dispersal and diversification of clades. Overall, we show that the study of demographic and evolutionary mechanisms that shape species richness gradients clearly requires the explicit consideration of adaptive traits. To conclude, future research lines and trends in the field are briefly outlined.

Strength, diversity and plasticity of postmating reproductive barriers between two hybridizing oak species (Quercus robur L. and Quercus petraea (Matt) Liebl.)

Very little is known about the nature and strength of reproductive isolation (RI) in Quercus species, despite extensive research on the estimation and evolutionary significance of hybridization rates. We characterized postmating pre- and postzygotic RI between two hybridizing oak species, Quercus robur and Quercus petraea, using a large set of controlled crosses between different genotypes. Various traits potentially associated with reproductive barriers were quantified at several life history stages, from pollen-pistil interactions to seed set and progeny fitness-related traits. Results indicate strong intrinsic postmating prezygotic barriers, with significant barriers also at the postzygotic level, but relatively weaker extrinsic barriers on early hybrid fitness measures assessed in controlled conditions. Using general linear modelling of common garden data with clonal replicates, we showed that most traits exhibited important genotypic differences, as well as different levels of sensitivity to micro-environmental heterogeneity. These new findings suggest a large potential genetic diversity and plasticity of reproductive barriers and are confronted with hybridization evidence in these oak species.

What do we need to know about speciation?

Speciation has been a major focus of evolutionary biology research in recent years, with many important advances. However, some of the traditional organising principles of the subject area no longer provide a satisfactory framework, such as the classification of speciation mechanisms by geographical context into allopatric, parapatric and sympatry classes. Therefore, we have asked where speciation research should be directed in the coming years. Here, we present a distillation of questions about the mechanisms of speciation, the genetic basis of speciation and the relationship between speciation and diversity. Our list of topics is not exhaustive; rather we aim to promote discussion on research priorities and on the common themes that underlie disparate speciation processes.

Signatures of selection and sex-specific expression variation of a novel duplicate during the evolution of the Drosophila desaturase gene family

The tempo and mode of evolution of loci with a large effect on adaptation and reproductive isolation will influence the rate of evolutionary divergence and speciation. Desaturase loci are involved in key biochemical changes in long-chain fatty acids. In insects, these have been shown to influence adaptation to starvation or desiccation resistance and in some cases act as important pheromones. The desaturase gene family of Drosophila is known to have evolved by gene duplication and diversification, and at least one locus shows rapid evolution of sex-specific expression variation. Here, we examine the evolution of the gene family in species representing the Drosophila phylogeny. We find that the family includes more loci than have been previously described. Most are represented as single-copy loci, but we also find additional examples of duplications in loci which influence pheromone blends. Most loci show patterns of variation associated with purifying selection, but there are strong signatures of diversifying selection in new duplicates. In the case of a new duplicate of desat1 in the obscura group species, we show that strong selection on the coding sequence is associated with the evolution of sex-specific expression variation. It seems likely that both sexual selection and ecological adaptation have influenced the evolution of this gene family in Drosophila.

Ecological Divergence and the Origins of Intrinsic Postmating Isolation with Gene Flow

The evolution of intrinsic postmating isolation has received much attention, both historically and in recent studies of speciation genes. Intrinsic isolation often stems from between-locus genetic incompatibilities, where alleles that function well within species are incompatible with one another when brought together in the genome of a hybrid. It can be difficult for such incompatibilities to originate when populations diverge with gene flow, because deleterious genotypic combinations will be created and then purged by selection. However, it has been argued that if genes underlying incompatibilities are themselves subject to divergent selection, then they might overcome gene flow to diverge between populations, resulting in the origin of incompatibilities. Nonetheless, there has been little explicit mathematical exploration of such scenarios for the origin of intrinsic incompatibilities during ecological speciation with gene flow. Here we explore theoretical models for the origin of intrinsic isolation where genes subject to divergent natural selection also affect intrinsic isolation, either directly or via linkage disequilibrium with other loci. Such genes indeed overcome gene flow, diverge between populations, and thus result in the evolution of intrinsic isolation. We also examine barriers to neutral gene flow. Surprisingly, we find that intrinsic isolation sometimes weakens this barrier, by impeding differentiation via ecologically based divergent selection.