Locally differentiated cryptic pigmentation in the freshwater isopod Asellus aquaticus

A repeated pattern of background colour matching in animals is an indication that pigmentation may be cryptic. Here, we examine the relationship between pigmentation of the freshwater isopod Asellus aquaticus and background darkness in 29 lakes, wetlands and ponds in Southern Sweden. The results show that Asellus pigmentation was correlated with substrate darkness across all localities. In seven localities, in which two contrasting substrate types were noted, Asellus populations were differentiated with respect to pigmentation. These findings thus provide phenomenological support for cryptic pigmentation in Asellus. Pigmentation generally increased with body size, but the relationship between pigmentation and size differed among localities, possibly as a result of differences in correlational selection on pigmentation and size. Selection thus appears to have resulted in local differentiation over a small spatial scale, even within lakes and wetlands. This differentiation is a likely cause behind elevated phenotype variation noted in localities with two substrate types, suggesting that habitat heterogeneity promotes genetic diversity.     

Modelling contemporary evolution in stickleback

During the past decade, two lines of research have advanced our understanding of micro‐evolution. On the one hand, a number of studies have generated evidence for strong selection on phenotypes ( Kingsolver et al. 2001 ) and the contemporary (sometimes deemed ‘rapid’) evolution of phenotypic traits ( Hendry & Kinnison 1999 ). On the other hand, other studies have sought to identify the genes that underlie ecologically important traits ( Ungerer et al. 2008 ). Over the next decade, micro‐evolutionists might expect considerable progress from the study of contemporary evolution at both the phenotypic and genetic level simultaneously. In this issue of Molecular Ecology, Le Rouzic et al. (2011) present a teaser for this approach. They examined contemporary evolution of an adaptive trait with a well‐studied genetic basis, the number of lateral plates, in threespine stickleback (Gasterosteus aculeatus L.). A time series of 20 years of change for this trait after introduction into a pond in Norway was compared with a similar time series of 12 years following the invasion of a lake in Alaska. Using a modelling approach, the authors then teased apart selection acting upon the phenotype and selection acting on a major effect gene. In both time series, selection was strong and consistent. The models suggested that selection could act directly on the phenotype, or through the gene’s pleiotropic effects.     

Rapid adaptive divergence between ecotypes of an aquatic isopod inferred from FST–QST analysis

Divergent natural selection is often thought to be the principal factor driving phenotypic differentiation between populations. We studied two ecotypes of the aquatic isopod Asellus aquaticus which have diverged in parallel in several Swedish lakes. In these lakes, isopods from reed belts along the shores colonized new stonewort stands in the centre of the lakes and rapid phenotypic changes in size and pigmentation followed after colonization. We investigated if selection was likely to be responsible for these observed phenotypic changes using indirect inferences of selection (F_ST–Q_ST analysis). Average Q_ST for seven quantitative traits were higher than the average F_ST between ecotypes for putatively neutral markers (AFLPs). This suggests that divergent natural selection has played an important role during this rapid diversification. In contrast, the average Q_ST between the different reed ecotype populations was not significantly different from the mean F_ST. Genetic drift could therefore not be excluded as an explanation for the minor differences between allopatric populations inhabiting the same source habitat. We complemented this traditional F_ST–Q_ST approach by comparing the F_ST distributions across all loci (n = 67–71) with the Q_ST for each of the seven traits. This analysis revealed that pigmentation traits had diverged to a greater extent and at higher evolutionary rates than size‐related morphological traits. In conclusion, this extended and detailed type of F_ST–Q_ST analysis provides a powerful method to infer adaptive phenotypic divergence between populations. However, indirect inferences about the operation of divergent selection should be analyzed on a per‐trait basis and complemented with detailed ecological information.     

Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions

Invasive species are predicted to suffer from reductions in genetic diversity during founding events, reducing adaptive potential. Integrating evidence from two literature reviews and two case studies, we address the following questions: How much genetic diversity is lost in invasions? Do multiple introductions ameliorate this loss? Is there evidence for loss of diversity in quantitative traits? Do invaders that have experienced strong bottlenecks show adaptive evolution? How do multiple introductions influence adaptation on a landscape scale? We reviewed studies of 80 species of animals, plants, and fungi that quantified nuclear molecular diversity within introduced and source populations. Overall, there were significant losses of both allelic richness and heterozygosity in introduced populations, and large gains in diversity were rare. Evidence for multiple introductions was associated with increased diversity, and allelic variation appeared to increase over long timescales (~100 years), suggesting a role for gene flow in augmenting diversity over the long‐term. We then reviewed the literature on quantitative trait diversity and found that broad‐sense variation rarely declines in introductions, but direct comparisons of additive variance were lacking. Our studies of Hypericum canariense invasions illustrate how populations with diminished diversity may still evolve rapidly. Given the prevalence of genetic bottlenecks in successful invading populations and the potential for adaptive evolution in quantitative traits, we suggest that the disadvantages associated with founding events may have been overstated. However, our work on the successful invader Verbascum thapsus illustrates how multiple introductions may take time to commingle, instead persisting as a ‘mosaic of maladaptation’ where traits are not distributed in a pattern consistent with adaptation. We conclude that management limiting gene flow among introduced populations may reduce adaptive potential but is unlikely to prevent expansion or the evolution of novel invasive behaviour.     

Influence of genetic architecture on contemporary local evolution in the soapberry bug,Jadera haematoloma: artificial selection on beak length

Little is known about the influence of genetic architecture on local adaptation. We investigated the genetic architecture of the rapid contemporary evolution of mouthparts, the flight polymorphism and life history traits in the soapberry bug Jadera haematoloma (Hemiptera) using laboratory selection. The mouthparts of these seed‐feeding bugs have adapted in 40–50 years by decreasing in length following novel natural selection induced by a host switch to the seeds of an introduced tree with smaller fruits than those of the native host vine. Laboratory selection on beak length in both an ancestral population feeding on the native host and a derived population feeding on the introduced host reveals genetic variance allowing a rapid response (heritabilities of 0.51–0.87) to selection for either longer or shorter beaks. This selection resulted in reverse evolution by restoring long beaks in the derived population and forward evolution by re‐creating short beaks in the ancestral bugs. There were strong genetic correlations (0.68–0.84) in both populations between beak lengths and the frequency of flight morphs, with short beaks associated with short wings. The results reveal a genetically interrelated set of adaptive multivariate traits including both beak length and flight morph. This suite of traits reflects host plant patchiness and seeding phenology. Weaker evidence suggests that egg mass and early egg production may be elements of the same suite. Reversible or forward evolution thus may occur in a broad set of genetically correlated multivariate traits undergoing rapid contemporary adaptation to altered local environments.     

Standing genetic variation as a potential mechanism of novel cave phenotype evolution in the freshwater isopod,Asellus aquaticus

Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F₂ crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the orange eye phenotype and therefore the orange eye phenotype is hidden within the cave populations. Our goal was to investigate the origin of the orange eye alleles within the Slovenian cave populations by examining A. aquaticus individuals from Slovenian and Romanian surface populations and Asellus aquaticus infernus individuals from a Romanian cave population. We found orange eye individuals present in lab raised surface populations of A. aquaticus from both Slovenia and Romania. Using a mapping approach with crosses between individuals of two surface populations, we found that the region known to be responsible for the orange eye phenotype within the two previously examined Slovenian cave populations was also responsible within both the Slovenian and the Romanian surface populations. Complementation crosses between orange eye Slovenian and orange eye Romanian surface individuals suggest that the same gene is responsible for the orange eye phenotype in both surface populations. Additionally, we observed a low frequency phenotype of eye loss in crosses generated between the two surface populations and also in the Romanian surface population. Finally, in a cave population from Romania, A. aquaticus infernus, we found that the same region is also responsible for the orange eye phenotype as the Slovenian cave populations and the Slovenian and Romanian surface populations. Therefore, we present evidence that variation present in the cave populations could originate from standing variation present in the surface populations and/or transgressive hybridization of different surface phylogenetic lineages rather than de novo mutations.     

Uncovering adaptive evolution in the human lineage

Background

The recent increase in human polymorphism data, together with the availability of genome sequences from several primate species, provides an unprecedented opportunity to investigate how natural selection has shaped human evolution.

Results

We compared human branch-specific substitutions with variation data in the current human population to measure the impact of adaptive evolution on human protein coding genes. The use of single nucleotide polymorphisms (SNPs) with high derived allele frequencies (DAFs) minimized the influence of segregating slightly deleterious mutations and improved the estimation of the number of adaptive sites. Using DAF ≥ 60% we showed that the proportion of adaptive substitutions is 0.2% in the complete gene set. However, the percentage rose to 40% when we focused on genes that are specifically accelerated in the human branch with respect to the chimpanzee branch, or on genes that show signatures of adaptive selection at the codon level by the maximum likelihood based branch-site test. In general, neural genes are enriched in positive selection signatures. Genes with multiple lines of evidence of positive selection include taxilin beta, which is involved in motor nerve regeneration and syntabulin, and is required for the formation of new presynaptic boutons.

Conclusions

We combined several methods to detect adaptive evolution in human coding sequences at a genome-wide level. The use of variation data, in addition to sequence divergence information, uncovered previously undetected positive selection signatures in neural genes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-599) contains supplementary material, which is available to authorized users.     

Variability selection in hominid evolution

Variability selection (abbreviated as VS) is a process considered to link adaptive change to large degrees of environment variability. Its application to hominid evolution is based, in part, on the pronounced rise in environmental remodeling that took place over the past several million years. The VS hypothesis differs from prior views of hominid evolution, which stress the consistent selective effects associated with specific habitats or directional trends (e.g., woodland, savanna expansion, cooling). According to the VS hypothesis, wide fluctuations over time created a growing disparity in adaptive conditions. Inconsistency in selection eventually caused habitat-specific adaptations to be replaced by structures and behaviors responsive to complex environmental change. Key hominid adaptations, in fact, emerged during times of heightened variability. Early bipedality, encephalized brains, and complex human sociality appear to signify a sequence of VS adaptations—i.e., a ratcheting up of versatility and responsiveness to novel environments experienced over the past 6 million years. The adaptive results of VS cannot be extrapolated from selection within a single environmental shift or relatively stable habitat. If some complex traits indeed require disparities in adaptive setting (and relative fitness) in order to evolve, the VS idea counters the prevailing view that adaptive change necessitates long-term, directional consistency in selection. © 1998 Wiley-Liss, Inc.     

Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa

The adaptive potential of tree species to cope with climate change has important ecological and economic implications. Many temperate tree species experience a wide range of environmental conditions, suggesting high adaptability to new environmental conditions. We investigated adaptation to regional climate in the drought‐sensitive tree species Alnus glutinosa (Black alder), using a complementary approach that integrates genomic, phenotypic and landscape data. A total of 24 European populations were studied in a common garden and through landscape genomic approaches. Genotyping‐by‐sequencing was used to identify SNPs across the genome, resulting in 1990 SNPs. Although a relatively low percentage of putative adaptive SNPs was detected (2.86% outlier SNPs), we observed clear associations among outlier allele frequencies, temperature and plant traits. In line with the typical drought avoiding nature of A. glutinosa, leaf size varied according to a temperature gradient and significant associations with multiple outlier loci were observed, corroborating the ecological relevance of the observed outlier SNPs. Moreover, the lack of isolation by distance, the very low genetic differentiation among populations and the high intrapopulation genetic variation all support the notion that high gene exchange combined with strong environmental selection promotes adaptation to environmental cues.     

Molecular population genetics and the search for adaptive evolution in plants

The first papers on plant molecular population genetics were published approximately 10 years ago. Since that time, well over 50 additional studies of plant nucleotide polymorphism have been published, and many of these studies focused on detecting the signature of balancing or positive selection at a locus. In this review, we discuss some of the theoretical and statistical issues surrounding the detection of selection, with focus on plant populations, and we also summarize the empirical plant molecular population genetics literature. At face value, the literature suggests that a history of balancing or positive selection in plant genes is rampant. In two well-studied taxa (maize and Arabidopsis) over 20% of studied genes have been interpreted as containing the signature of selection. We argue that this is probably an overstatement of the prevalence of natural selection in plant genomes, for two reasons. First, demographic effects are difficult to incorporate and have generally not been well integrated into the plant population genetics literature. Second, the genes studied to date are not a random sample, so selected genes may be overrepresented. The next generation of studies in plant molecular population genetics requires additional sampling of local populations, explicit comparisons among loci, and improved theoretical methods to control for demography. Eventually, candidate loci should be confirmed by explicit consideration of phenotypic effects.     

Spatial analyses of two color polymorphisms in an alpine grasshopper reveal a role of small‐scale heterogeneity

Discrete color polymorphisms represent a fascinating aspect of intraspecific diversity. Color morph ratios often vary clinally, but in some cases, there are no marked clines and mixes of different morphs occur at appreciable frequencies in most populations. This poses the questions of how polymorphisms are maintained. We here study the spatial and temporal distribution of a very conspicuous color polymorphism in the club‐legged grasshopper Gomphocerus sibiricus. The species occurs in a green and a nongreen (predominately brown) morph, a green–brown polymorphism that is common among Orthopteran insects. We sampled color morph ratios at 42 sites across the alpine range of the species and related color morph ratios to local habitat parameters and climatic conditions. Green morphs occurred in both sexes, and their morph ratios were highly correlated among sites, suggesting shared control of the polymorphism in females and males. We found that in at least 40 of 42 sites green and brown morphs co‐occurred with proportions of green ranging from 0% to 70% with significant spatial heterogeneity. The proportion of green individuals tended to increase with decreasing summer and winter precipitations. Nongreen individuals can be further distinguished into brown and pied individuals, and again, this polymorphism is shared with other grasshopper species. We found pied individuals at all sites with proportions ranging from 3% to 75%, with slight, but significant variation between years. Pied morphs show a clinal increase in frequency from east to west and decreased with altitude and lower temperatures and were more common on grazed sites. The results suggest that both small‐scale and large‐scale spatial heterogeneity affects color morph ratios. The almost universal co‐occurrence of all three color morphs argues against strong effects of genetic drift. Instead, the data suggest that small‐scale migration–selection balance and/or local balancing selection maintain populations polymorphic.     

体内连续进化技术的研究进展

实验室进化是遗传育种、提高微生物性能的重要方式.近几十年来,实验室进化的方法快速发展,应用也越来越广泛,但是常见的菌株进化策略以及针对特定蛋白的进化存在突变过程不连续,需要多轮操作、工作量大等缺点.微生物突变和筛选技术的进步促进了体内连续进化的发展,大大提高了实验室进化的效率.体内连续进化技术实现了体内突变,完美地把突...     

Quantifying hummingbird preference for floral trait combinations: The role of selection on trait interactions in the evolution of pollination syndromes

Darwin recognized the flower's importance for the study of adaptation and emphasized that the flower's functionality reflects the coordinated action of multiple traits. Here we use a multitrait manipulative approach to quantify the potential role of selection acting on floral trait combinations underlying the divergence and maintenance of three related North American species of Silene (Caryophyllaceae). We artificially generated 48 plant phenotypes corresponding to all combinations of key attractive traits differing among the three Silene species (color, height, inflorescence architecture, flower orientation, and corolla‐tube width). We quantified main and interaction effects of trait manipulation on hummingbird visitation preference using experimental arrays. The main effects of floral display height and floral orientation strongly influenced hummingbird visitation, with hummingbirds preferring flowers held high above the ground and vertically to the sky. Hummingbirds also prefer traits in a nonadditive manner as multiple two‐way and higher order interaction effects were important predictors of hummingbird visitation. Contemporary trait combinations found in hummingbird pollinated S. virginica are mostly preferred. Our study demonstrates the likelihood of pollination syndromes evolving due to selection on trait combinations and highlights the importance of trait interactions in understanding the evolution of complex adaptations.     

The adaptive legacy of human evolution: A search for the environment of evolutionary adaptedness

The growth of evolutionary psychology has led to renewed interest in what might be the significant evolutionary heritage of people living today, and in the extent to which humans are suited to a particular adaptive environment—the EEA. The EEA, though, is a new tool in the battery of evolutionary concepts, and it is important both that it is scrutinized for its utility, and that the actual reconstructions of the environments in which humans and hominids evolved are based on sound palaeobiological inference and an appropriate use of the phylogenetic context of primate evolution.     

Pollinator-dependent evolution of floral trait combinations in an orchid herb

作为驱动花性状进化的重要媒介之一,传粉者塑造了被子植物多样的花部特征。目前,大部分研究集中于传粉者驱动被子植物单个性状的进化,而较少涉及对传粉者驱动被子植物组合性状进化的研究。本研究以兰科植物绶草(Spiranthes sinensis)为材料,分别鉴别和估算了传粉者对植物单个性状和组合性状施加的定向选择和关联选择压力。研究结果表明,传粉者对开花时间和花大小施加定向选择压力,传粉者选择早开花、花更大的个体。传粉者对绶草花展示的组合性状(花大小与花数目)施加正向的关联选择压力,而对开花时间与花展示的组合性状(开花时间与株高、开花时间与花数目)施加负向的关联选择压力。同时,传粉者的选择强度在年际间存在差异。该研究证实了传粉者在驱动植物组合性状进化过程中的作用,同时强调在认识和理解被子植物表型性状进化轨迹时,需要考虑植物组合性状的影响。