The genetic basis of evolution, adaptation and speciation

A primary question in biology concerns the genetic basis of the evolution of novel traits, often in response to environmental changes, and how this can subsequently cause species isolation. This topic was the focus of the symposium on the Genetics of Speciation and Evolution at the annual meeting of the Canadian Society for Ecology and Evolution, held in Banff in May 2011. The presentations revealed some of the rapid advances being made in understanding the genetic basis of adaptation and speciation, as well as the elegant interplay between an organism's genetic complement and the environment that organism experiences.     

Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry.     

Evolutionary potential in the wild: more than meets the eye

The genus Aquilegia consists of 60–70 perennial plant species widely distributed throughout the northern hemisphere. Its flowers have a delicate and ornamental appearance that makes them a favourite of gardeners. In this genus, adaptive radiations for both floral and vegetative traits have occurred. These adaptive radiations, and the key phylogenetic placement of Aquilegia between Arabidopsis and rice, make this genus a ‘model system’ for plant evolution ( Kramer 2009 ). In this issue, Castellanos et al. (2011) use a marker‐based method to infer heritability for floral and vegetative traits in two Aquilegia species. Layered on top of this are estimates of the strength of natural selection. This novel joint estimation of heritability and selection in the wild showed that vegetative traits, compared to floral traits, have the highest evolutionarily potential. Evolutionary potential is the most important quantity to measure in wild populations. It combines inheritance and strength of selection and predicts the potential for populations to adapt to changing environments. The combination of molecular techniques with species in natural environments makes this work a model for molecular ecological investigations.     

Familiarity adds to attractiveness in matters of siskin mate choice

There is currently considerable controversy in evolutionary ecology revolving around whether social familiarity brings attraction when a female chooses a mate. The topic of familiarity is significant because by avoiding or preferring familiar individuals as mates, the potential for local adaptation may be reduced or favoured. The topic becomes even more interesting if we simultaneously analyse preferences for familiarity and sexual ornaments, because when familiarity influences female mating preferences, this could very significantly affect the strength of sexual selection on male ornamentation. Here, we have used mate-choice experiments in siskins Carduelis spinus to analyse how familiarity and patterns of ornamentation (i.e. the size of wing patches) interact to influence mating success. Our results show that females clearly prefer familiar individuals when choosing between familiar and unfamiliar males with similar-sized wing patches. Furthermore, when females were given the choice between a highly ornamented unfamiliar male and a less ornamented familiar male, half of the females still preferred the socially familiar birds as mates. Our finding suggests that male familiarity may be as important as sexual ornaments in affecting female behaviour in mate choice. Given that the potential for local adaptation may be favoured by preferring familiar individuals as mates, social familiarity as a mate-choice criterion may become a potential area of fruitful research on sympatric speciation processes.     

Making inferences about speciation using sophisticated statistical genetics methods: look before you leap

Understanding speciation is a fundamental aim of evolutionary biology and a very challenging one. Speciation can be viewed as the dynamics of genetic differentiation between populations resulting in substantial reproductive isolation (Gavrilets 2003). It was generally accepted that very small levels of migration prevent genetic differentiation among populations and, therefore, speciation. However, recent theoretical work showed that sympatric speciation is possible (Gavrilets 2003). Nevertheless, providing empirical evidence that gene flow occurred during speciation is challenging because several gene flow scenarios can explain observed patterns of genetic differentiation. Positive migration rate estimates alone do not prove ongoing gene flow during divergence. We also need to know whether migration took place before, during or after speciation. There is no statistical method specifically aimed at estimating gene flow timing, but several studies used the isolation with migration model (Hey & Nielsen 2004, 2007; Hey 2010b) to estimate this parameter and make inferences about speciation scenarios. It is tempting to use statistical methods to estimate important evolutionary parameters even if they do not appear explicitly in the inference model. Nevertheless, before doing so, we need to determine whether they can provide reliable results. In this issue of Molecular Ecology, Strasburg and Rieseberg (2011) present a simulation study that examines the degree to which gene flow timing estimates obtained from IMa2 (Hey 2010b) can be used to make inferences about speciation mode. Their results are sobering; gene flow timing estimates obtained in this way are not reliable and cannot be used to unequivocally establish if gene flow was ongoing during speciation.     

Spatial and temporal population genetic structure of four northeastern Pacific littorinid gastropods: the effect of mode of larval development on variation at one mitochondrial and two nuclear DNA markers

We investigated the effect of development mode on the spatial and temporal population genetic structure of four littorinid gastropod species. Snails were collected from the same three sites on the west coast of Vancouver Island, Canada in 1997 and again in 2007. DNA sequences were obtained for one mitochondrial gene, cytochrome b ( Cyt b ), and for up to two nuclear genes, heat shock cognate 70 ( HSC70 ) and aminopeptidase N intron ( APN54 ). We found that the mean level of genetic diversity and long-term effective population sizes ( N _e) were significantly greater for two species, Littorina scutulata and L. plena , that had a planktotrophic larval stage than for two species, Littorina sitkana and L. subrotundata , that laid benthic egg masses which hatched directly into crawl-away juveniles. Predictably, two poorly dispersing species, L. sitkana and L. subrotundata , showed significant spatial genetic structure at an 11- to 65-km geographical scale that was not observed in the two planktotrophic species. Conversely, the two planktotrophic species had more temporal genetic structure over a 10-year interval than did the two direct-developing species and showed highly significant temporal structure for spatially pooled samples. The greater temporal genetic variation of the two planktotrophic species may have been caused by their high fecundity, high larval dispersal, and low but spatially correlated early survivorship. The sweepstakes-like reproductive success of the planktotrophic species could allow a few related females to populate hundreds of kilometres of coastline and may explain their substantially larger temporal genetic variance but lower spatial genetic variance relative to the direct-developing species.     

Comparing geographical genetic differentiation between candidate and noncandidate loci for adaptation strengthens support for parallel ecological divergence in the marine snail Littorina saxatilis

The Galician sympatric ecotypes of Littorina saxatilis have been proposed as a model system for studying parallel ecological speciation. Such a model system makes a clear prediction: candidate loci (for divergent adaptation) should present a higher level of geographical differentiation than noncandidate (neutral) loci. We used 2356 amplified fragment length polymorphisms (AFLPs) and four microsatellite loci to identify candidate loci for ecological adaptation using the F _ST outlier method. Three per cent of the studied AFLP loci were identified as candidate loci associated with adaptation, after multitest adjustments, thus contributing to ecotype differentiation (candidate loci were not detected within ecotypes). Candidate and noncandidate loci were analysed separately at four different F _ST partitions: differences between ecotypes (overall and local), differences between localities and micro-geographical differences within ecotypes. The magnitude of F _ST differed between candidate and noncandidate loci for all partitions except in the case of microgeographical differentiation within ecotypes, and the microsatellites (putatively neutral) showed an identical pattern to noncandidate loci. Thus, variation in candidate loci is determined partially independent by divergent natural selection (in addition to stochastic forces) at each locality, while noncandidate loci are exclusively driven by stochastic forces. These results support the evolutionary history described for these particular populations, considered to be a clear example of incomplete sympatric ecological speciation.     

The evolution from females to hermaphrodites results in a sexual conflict over mating in androdioecious nematode worms and clam shrimp

The nematode worm Caenorhabditis elegans and the clam shrimp Eulimnadia texana are two well‐studied androdioecious species consisting mostly of self‐fertilizing hermaphrodites and few males. To understand how androdioecy can evolve, a simple two‐step mathematical model of the evolutionary pathway from a male–female species to a selfing‐hermaphrodite species is constructed. First, the frequency of mutant females capable of facultative self‐fertilization increases if the benefits of reproductive assurance exceed the cost. Second, hermaphrodites become obligate self‐fertilizers if the fitness of selfed offspring exceeds one‐half the fitness of outcrossed offspring. Genetic considerations specific to C. elegans and E. texana show that males may endure as descendants of the ancestral male–female species. These models combined with an extensive literature review suggest a sexual conflict over mating in these androdioecious species: selection favours hermaphrodites that self and males that outcross. The strength of selection on hermaphrodites and males differs, however. Males that fail to outcross suffer a genetic death. Hermaphrodites may never encounter a rare male, and those that do and outcross only bear less fecund offspring. This asymmetric sexual conflict results in an evolutionary stand‐off: rare, but persistent males occasionally fertilize common, but reluctant hermaphrodites. A consequence of this stand‐off may be an increase in the longevity of the androdioecious mating system.     

嘉陵江下游蛇鮈的两性异形与雌性个体生殖力

为了解蛇鮈雌雄间是否存在显著的外部形态差异及雌性个体生殖力情况, 在繁殖期对嘉陵江下游(合川江段)共76尾蛇鮈样本的两性异形、性比及雌性个体生殖力进行分析.结果表明: 嘉陵江下游蛇鮈繁殖群体的性比接近1∶1,且蛇鮈两性的体型大小相同,但局部特征(如头部和躯干部等)呈现出显著的两性异形,如成体雄性蛇鮈的头部、胸鳍和腹鳍均较雌性蛇鮈大,而躯干部的体宽、体高和躯干长则是雌性蛇鮈大于雄性蛇鮈,这可能是性选择长期作用的结果.主成分分析显示,前3个主成分的累积贡献率达75.2%,但雌雄个体间形态特征相互重叠,无法将两者截然分开;利用判别函数对蛇鮈性别进行回判,综合判别准确率为92.1%.蛇鮈雌性个体绝对生殖力在979～19979粒;且与体长和去内脏体质量均呈显著正相关.同历史资料相比,本研究中嘉陵江蛇鮈的生殖力增大显著,这可能是蛇鮈对种群资源量下降和水环境变化主动适应的结果.     

Parallel genotypic adaptation: when evolution repeats itself

Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together.     

The genic view of the process of speciation

The unit of adaptation is usually thought to be a gene or set of interacting genes, rather than the whole genome, and this may be true of species differentiation. Defining species on the basis of reproductive isolation (RI), on the other hand, is a concept best applied to the entire genome. The biological species concept (BSC; 84 ) stresses the isolation aspect of speciation on the basis of two fundamental genetic assumptions – the number of loci underlying species differentiation is large and the whole genome behaves as a cohesive, or coadapted genetic unit. Under these tenets, the exchange of any part of the genomes between diverging groups is thought to destroy their integrity. Hence, the maintenance of each species’ genome cohesiveness by isolating mechanisms has become the central concept of species. In contrast, the Darwinian view of speciation is about differential adaptation to different natural or sexual environments. RI is viewed as an important by product of differential adaptation and complete RI across the whole genome need not be considered as the most central criterion of speciation. The emphasis on natural and sexual selection thus makes the Darwinian view compatible with the modern genic concept of evolution. Genetic and molecular analyses of speciation in the last decade have yielded surprisingly strong support for the neo‐Darwinian view of extensive genetic differentiation and epistasis during speciation. However, the extent falls short of what BSC requires in order to achieve whole‐genome ‘cohesiveness’. Empirical observations suggest that the gene is the unit of species differentiation. Significantly, the genetic architecture underlying RI, the patterns of species hybridization and the molecular signature of speciation genes all appear to support the view that RI is one of the manifestations of differential adaptation, as 34 , Chap. 8) suggested. The nature of this adaptation may be as much the result of sexual selection as natural selection. In the light of studies since its early days, BSC may now need a major revision by shifting the emphasis from isolation at the level of whole genome to differential adaptation at the genic level. With this revision, BSC would in fact be close to Darwin’s original concept of speciation.     

Sympatric host races of the European corn borer: adaptation to host plants and hybrid performance

The European corn borer (ECB), Ostrinia nubilalis, is a major pest of maize crops. In Europe, two sympatric host races are found: one feeds on maize (Zea mays) and the other mainly on mugwort (Artemisia vulgaris). The two host races are genetically differentiated, seldom crossing in the laboratory or in the field, and females preferentially lay eggs on their native host species. We conducted two independent experiments, in field and greenhouse conditions, to determine whether the two host races are locally adapted to their host species. The effect of larval density and the performance of hybrids were also investigated. Despite some differences in overall larval feeding performance, both experiments revealed consistent patterns of local adaptation for survival and for larval weight in males. In females the same trend was observed but with weaker statistical support. F1 hybrids did not seem to be disadvantaged compared with the two parental races. Overall, our results showed that both host races are physiologically adapted to their native host. The fitness trade-off between the two host plants provides a potential driving force for ecological speciation in this species.     

蒲河流域河流生境质量综合评价及其与水质响应关系

河流生境是河流生物赖以生存的环境,是维持河流生态完整性、维护河流健康的重要因素。本文结合蒲河流域环境特点,运用层次分析法建立了蒲河流域河流生境质量评价体系,对流域内25个河段的生境质量状况进行了综合评价,并进一步分析了河流生境综合评价指数与河流水质的相关关系。结果表明:(1)蒲河流域25个河段的生境质量状况差异显著,其中1个河段的生境质量等级为好,5个河段为较好等级,16个河段为一般等级,3个河段为较差等级。(2)生境综合评价指数与TP、NH4+-N、CODCr呈负相关,生境质量评价体系中其他指标也与水质指标具有相关性,表明生境质量是影响水质的重要因素。     

Natural selection and the genetics of adaptation in threespine stickleback

Growing knowledge of the molecular basis of adaptation in wild populations is expanding the study of natural selection. We summarize ongoing efforts to infer three aspects of natural selection—mechanism, form and history—from the genetics of adaptive evolution in threespine stickleback that colonized freshwater after the last ice age. We tested a mechanism of selection for reduced bony armour in freshwater by tracking genotype and allele frequency changes at an underlying major locus (Ectodysplasin) in transplanted stickleback populations. We inferred disruptive selection on genotypes at the same locus in a population polymorphic for bony armour. Finally, we compared the distribution of phenotypic effect sizes of genes underlying changes in body shape with that predicted by models of adaptive peak shifts following colonization of freshwater. Studies of the effects of selection on genes complement efforts to identify the molecular basis of adaptive differences, and improve our understanding of phenotypic evolution.     

Mechanisms of incomplete prezygotic reproductive isolation in an intertidal snail: testing behavioural models in wild populations

Two morphs (ecotypes) of the marine snail Littorina saxatilis coexist along Galician exposed rocky shores. They hybridize, but gene flow is impeded by a partial prezygotic reproductive barrier, and we have earlier suggested that this is a case of incipient sympatric speciation. To assess the mechanisms of prezygotic reproductive isolation, we estimated deviations from random mating (sexual selection and sexual isolation) of sympatric snails in 13 localities on the shore, and performed mate choice experiments in the laboratory. We also investigated the microdistribution of both morphs over patches of barnacles and blue mussels in the hybridization zone. We used computer simulations to separate the mechanisms contributing to reproductive isolation. On the shores sampled, male–female pairs were strongly assortative both with respect to morphs (mean Yule's V = 0.77) and size (mean Pearson's r = 0.47). In the laboratory, males of both morphs mounted other snails and mated other males and juveniles at random. However, mature females of equal sizes mated assortatively with respect to morph. The two morphs were nonrandomly distributed over barnacle and mussel patches in the hybridization zone. Monte Carlo simulations showed that this microdistribution could explain about half the morph and size relationships in male–female pairs, while a simple rejection mechanism, rejecting the first 1–3 mates if they were of contrasting morphs, accounted for the remaining part of the reproductive isolation, and for parts of the size relationships found between mates. A size discriminant mate choice mechanism may also, to a lesser extent, contribute to the sexual isolation. Sexual selection was observed for female size (larger ones being favoured) and among certain morphs, but distinct biological mechanisms may cause these processes.     

Convergent exaptation and adaptation in solitary island lizards

Independent evolutionary lineages often display similar characteristics in comparable environments. Three kinds of historical hypotheses could explain this convergence. The first is adaptive and evolutionary: nonrandom patterns may result from analogous evolutionary responses to shared conditions. The second explanation is exaptive and ecological: species may be filtered by their suitability for a particular type of environment. The third potential explanation is a null hypothesis of random colonization from a historically nonrandom source pool. Here we demonstrate that both exaptation and adaptation have produced convergent similarity in different size-related characters of solitary island lizards. Large sexual size dimorphism results from adaptive response to solitary existence; uniform, intermediate size results from ecological filtering of potential colonizers. These results demonstrate the existence of deterministic exaptive convergence and suggest that convergent phenomena may require historical explanations that are ecological as well as evolutionary.