Unravelling genetics at the top: mountain islands or isolated belts?

Background and Aims

In mountain plant populations, local adaptation has been described as one of the main responses to climate warming, allowing plants to persist under stressful conditions. This is especially the case for marginal populations at their lowest elevation, as they are highly vulnerable. Adequate levels of genetic diversity are required for selection to take place, while high levels of altitudinal gene flow are seen as a major limiting factor potentially precluding local adaptation processes. Thus, a compromise between genetic diversity and gene flow seems necessary to guarantee persistence under oncoming conditions. It is therefore critical to determine if gene flow occurs preferentially between mountains at similar altitudinal belts, promoting local adaptation at the lowest populations, or conversely along altitude within each mountain.

Methods

Microsatellite markers were used to unravel genetic diversity and population structure, inbreeding and gene flow of populations at two nearby altitudinal gradients of Silene ciliata, a Mediterranean high-mountain cushion plant.

Key Results

Genetic diversity and inbreeding coefficients were similar in all populations. Substantial gene flow was found both along altitudinal gradients and horizontally within each elevation belt, although greater values were obtained along altitudinal gradients. Gene flow may be responsible for the homogeneous levels of genetic diversity found among populations. Bayesian cluster analyses also suggested that shifts along altitudinal gradients are the most plausible scenario.

Conclusions

Past population shifts associated with glaciations and interglacial periods in temperate mountains may partially explain current distributions of genetic diversity and population structure. In spite of the predominance of gene flow along the altitudinal gradients, local genetic differentiation of one of the lower populations together with the detection of one outlier locus might support the existence of different selection forces at low altitudes.     

Altitudinal and seasonal variation in microsatellite allele frequencies of Drosophila buzzatii

Variation in climate, particularly temperature, is known to affect the genetic composition of populations. Although there have been many studies of latitudinal variation, comparisons of populations across altitudes or seasons, particularly for animal species, are less common. Here, we study genetic variation (microsatellite markers) in populations of Drosophila buzzatii collected along altitudinal gradients and in different seasons. We found no differences in genetic variation between 2 years or between seasons within years. However, there were numerous cases of significant associations between allele frequencies or expected heterozygosities and altitude, with more than half showing nonlinear relationships. While these associations indicate possible selection and local altitudinal adaptation, direct tests gave strong evidence for selection affecting two loci and weaker evidence for five other loci. Two loci that are located within an inversion (including the one with strongest evidence for selection) show a linear increase in genetic diversity with altitude, likely due to thermal selection. Parallel associations with altitude here and with latitude in Australian populations indicate that selection is operating on chromosomal regions marked by some of the loci.     

Adaptive responses for seed and leaf phenology in natural populations of sessile oak along an altitudinal gradient

We assessed the adaptive potential of seed and leaf phenology in 10 natural populations of sessile oak (Quercus petraea) sampled along two altitudinal transects using common garden experiments. Population differentiation for both phenological traits was observed with high-altitude populations germinating and flushing later than low altitude ones. However, high genetic variation and heritability values were also maintained within populations, despite slightly decreasing for dates of leaf unfolding with increasing altitude. We suggest that biotic and abiotic fluctuating selection pressures within populations and high gene flow are the main mechanisms maintaining high genetic variation for these fitness related traits. Moreover, changes in selection intensity and/or selection pressures along the altitudinal gradient can explain the reduction in genetic variation observed for leaf phenology. We anticipate that the maintenance of high genetic variation will be a valuable resource for future adaptation of sessile oak populations undergoing an upslope shift caused by climate change.     

Evidence of neutral and adaptive genetic divergence between European trout populations sampled along altitudinal gradients

Species with a wide geographical distribution are often composed of distinct subgroups which may be adapted to their local environment. European trout (Salmo trutta species complex) provide an example of such a complex consisting of several genetically and ecologically distinct forms. However, trout populations are strongly influenced by human activities, and it is unclear to what extent neutral and adaptive genetic differences have persisted. We sampled 30 Swiss trout populations from heterogeneous environments along replicated altitudinal gradients in three major European drainages. More than 850 individuals were genotyped at 18 microsatellite loci which included loci diagnostic for evolutionary lineages and candidate markers associated with temperature tolerance, reproductive timing and immune defence. We find that the phylogeographic structure of Swiss trout populations has not been completely erased by stocking. Distinct genetic clusters corresponding to the different drainages could be identified, although nonindigenous alleles were clearly present, especially in the two Mediterranean drainages. We also still detected neutral genetic differentiation within rivers which was often associated with the geographical distance between populations. Five loci showed evidence of divergent selection between populations with several drainage-specific patterns. Lineage-diagnostic markers, a marker linked to a quantitative trait locus for upper temperature tolerance in other salmonids and a marker linked to the major histocompatibility class I gene were implicated in local adaptation and some patterns were associated with altitude. In contrast, tentative evidence suggests a signal of balancing selection at a second immune relevant gene (TAP2). Our results confirm the persistence of both neutral and potentially adaptive genetic differences between trout populations in the face of massive human-mediated dispersal.     

Limits to local adaptation in six populations of the annual plant Diodia teres

* Local adaptation is common, but tests for adaptive differentiation frequently compare populations from strongly divergent environments, making it unlikely that any influence of stochastic processes such as drift or mutation on local adaptation will be detected. Here, the hypothesis that local adaptation is more likely to develop when the native environments of populations are more distinct than when they are similar was tested. * A reciprocal transplant experiment including two populations from each of three habitats was conducted to determine the pattern of local adaptation. In addition to testing for local adaptation at the population level, the hypothesis was tested that local adaptation is more common between populations from different habitats than between populations from the same habitat. * Local adaptation was not common, but more evidence was found of local adaptation between populations from different habitats than between populations from the same habitat. Two instances of foreign genotype fitness advantage confirm that stochastic processes such as drift can limit local adaptation. * These results are consistent with the hypothesis that stochastic processes can inhibit local adaptation but are more likely to be overwhelmed by natural selection when populations occur in divergent environments.     

Toxic hydrogen sulfide and dark caves: phenotypic and genetic divergence across two abiotic environmental gradients in Poecilia mexicana

Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system.     

Thermal adaptation and ecological speciation

Ecological speciation is defined as the emergence of reproductive isolation as a direct or indirect consequence of divergent ecological adaptation. Several empirical examples of ecological speciation have been reported in the literature which very often involve adaptation to biotic resources. In this review, we investigate whether adaptation to different thermal habitats could also promote speciation and try to assess the importance of such processes in nature. Our survey of the literature identified 16 animal and plant systems where divergent thermal adaptation may underlie (partial) reproductive isolation between populations or may allow the stable coexistence of sibling taxa. In many of the systems, the differentially adapted populations have a parapatric distribution along an environmental gradient. Isolation often involves extrinsic selection against locally maladapted parental or hybrid genotypes, and additional pre- or postzygotic barriers may be important. Together, the identified examples strongly suggest that divergent selection between thermal environments is often strong enough to maintain a bimodal genotype distribution upon secondary contact. What is less clear from the available data is whether it can also be strong enough to allow ecological speciation in the face of gene flow through reinforcement-like processes. It is possible that intrinsic features of thermal gradients or the genetic basis of thermal adaptation make such reinforcement-like processes unlikely but it is equally possible that pertinent systems are understudied. Overall, our literature survey highlights (once again) the dearth of studies that investigate similar incipient species along the continuum from initial divergence to full reproductive isolation and studies that investigate all possible reproductive barriers in a given system.     

Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi

Recent studies of humans, dogs and rodents have started to discover the genetic underpinnings of high altitude adaptations, yet amphibians have received little attention in this respect. To identify possible signatures of adaptation to altitude, we performed a genome scan of 15 557 single nucleotide polymorphisms (SNPs) obtained with restriction site‐associated DNA sequencing of pooled samples from 11 populations of Andrew's toad (Bufo andrewsi) from the edge of the Tibetan Plateau, spanning an altitudinal gradient from 1690 to 2768 m.a.s.l. We discovered significant geographic differentiation among all sites, with an average F_ST = 0.023 across all SNPs. Apart from clear patterns of isolation by distance, we discovered numerous outlier SNPs showing strong associations with variation in altitude (1394 SNPs), average annual temperature (1859 SNPs) or both (1051 SNPs). Levels and patterns of genetic differentiation in these SNPs were consistent with the hypothesis that they have been subject to directional selection and reflect adaptation to altitudinal variation among the study sites. Genes with footprints of selection were significantly enriched in binding and metabolic processes. Several genes potentially related to high altitude adaptation were identified, although the identity and functional significance of most genomic targets of selection remain unknown. In general, the results provide genomic support for results of earlier common garden and low coverage genetic studies that have uncovered substantial adaptive differentiation along altitudinal and latitudinal gradients in amphibians.     

PLANT RESPONSES TO CLIMATE IN THE CAPE FLORISTIC REGION OF SOUTH AFRICA: EVIDENCE FOR ADAPTIVE DIFFERENTIATION IN THE PROTEACEAE

Local adaptation along environmental gradients may drive plant species radiation within the Cape Floristic Region (CFR), yet few studies examine the role of ecologically based divergent selection within CFR clades. In this study, we ask whether populations within the monophyletic white protea clade (Protea section Exsertae, Proteaceae) differ in key functional traits along environmental gradients and whether differences are consistent with local adaptation. Using seven taxa, we measured trait–environment associations and selection gradients across 35 populations of wild adults and their offspring grown in two common gardens. Focal traits were leaf size and shape, specific leaf area (SLA), stomatal density, growth, and photosynthetic rate. Analyses on wild and common garden plants revealed heritable trait differences that were associated with gradients in rainfall seasonality, drought stress, cold stress, and less frequently, soil fertility. Divergent selection between gardens generally matched trait–environment correlations and literature‐based predictions, yet variation in selection regimes among wild populations generally did not. Thus, selection via seedling survival may promote gradient‐wide differences in SLA and leaf area more than does selection via adult fecundity. By focusing on the traits, life stages, and environmental clines that drive divergent selection, our study uniquely demonstrates adaptive differentiation among plant populations in the CFR.     

Conceptual issues in local adaptation

Studies of local adaptation provide important insights into the power of natural selection relative to gene flow and other evolutionary forces. They are a paradigm for testing evolutionary hypotheses about traits favoured by particular environmental factors. This paper is an attempt to summarize the conceptual framework for local adaptation studies. We first review theoretical work relevant for local adaptation. Then we discuss reciprocal transplant and common garden experiments designed to detect local adaptation in the pattern of deme × habitat interaction for fitness. Finally, we review research questions and approaches to studying the processes of local adaptation – divergent natural selection, dispersal and gene flow, and other processes affecting adaptive differentiation of local demes. We advocate multifaceted approaches to the study of local adaptation, and stress the need for experiments explicitly addressing hypotheses about the role of particular ecological and genetic factors that promote or hinder local adaptation. Experimental evolution of replicated populations in controlled spatially heterogeneous environments allow direct tests of such hypotheses, and thus would be a valuable way to complement research on natural populations.     

Local adaptation and ecological differentiation under selection,migration, and drift in Arabidopsis lyrata*

How the balance between selection, migration, and drift influences the evolution of local adaptation has been under intense theoretical scrutiny. Yet, empirical studies that relate estimates of local adaptation to quantification of gene flow and effective population sizes have been rare. Here, we conducted a reciprocal transplant trial, a common garden trial, and a whole‐genome‐based demography analysis to examine these effects among Arabidopsis lyrata populations from two altitudinal gradients in Norway. Demography simulations indicated that populations within the two gradients are connected by gene flow (0.1 < 4N_em < 11) and have small effective population sizes (N_e < 6000), suggesting that both migration and drift can counteract local selection. However, the three‐year field experiments showed evidence of local adaptation at the level of hierarchical multiyear fitness, attesting to the strength of differential selection. In the lowland habitat, local superiority was associated with greater fecundity, while viability accounted for fitness differences in the alpine habitat. We also demonstrate that flowering time differentiation has contributed to adaptive divergence between these locally adapted populations. Our results show that despite the estimated potential of gene flow and drift to hinder differentiation, selection among these A. lyrata populations has resulted in local adaptation.     

Natural selection drives altitudinal divergence at the albumin locus in deer mice, Peromyscus maniculatus

In populations that are distributed across steep environmental gradients, the potential for local adaptation is largely determined by the spatial scale of fitness variation relative to dispersal distance. Since altitudinal gradients are generally characterized by dramatic ecological transitions over relatively short linear distances, adaptive divergence across such gradients will typically require especially strong selection to counterbalance the homogenizing effect of gene flow. Here we report the results of a study that was designed to test for evidence of adaptive divergence across an altitudinal gradient in a natural population of deer mice, Peromyscus maniculatus. We conducted a multilocus survey of allozyme variation across a steep altitudinal gradient in the southern Rocky Mountains that spanned several distinct biomes, from prairie grassland to alpine tundra. As a control for the effects of altitude, we also surveyed the same loci in mice sampled along a latitudinal transect through the prairie grassland that ran perpendicular to the east-west altitudinal transect. We used a coalescent-based simulation model to identify loci that deviated from neutral expectations, and we then assessed whether locus-specific patterns of variation were nonrandom with respect to altitude. Results indicated that the albumin locus (Alb) reflects a history of diversifying selection across the altitudinal gradient. This conclusion is supported by two main lines of evidence: (1) Alb was characterized by levels of divergence across the altitudinal transect that exceeded neutral expectations in two consecutive years of sampling (in contrast to the spatial pattern of variation across the latitudinal transect), and (2) levels of divergence at the Alb locus exhibited a positive association with altitudinal distance in both years (in contrast to the pattern observed at unlinked loci). We conclude that clinal variation at the Alb locus reflects a balance between gene flow and diversifying selection that results from elevational changes in fitness rankings among alternative genotypes.     

Machine‐learning‐based detection of adaptive divergence of the stream mayfly Ephemera strigata populations

Adaptive divergence is a key mechanism shaping the genetic variation of natural populations. A central question linking ecology with evolutionary biology is how spatial environmental heterogeneity can lead to adaptive divergence among local populations within a species. In this study, using a genome scan approach to detect candidate loci under selection, we examined adaptive divergence of the stream mayfly Ephemera strigata in the Natori River Basin in northeastern Japan. We applied a new machine‐learning method (i.e., random forest) besides traditional distance‐based redundancy analysis (dbRDA) to examine relationships between environmental factors and adaptive divergence at non‐neutral loci. Spatial autocorrelation analysis based on neutral loci was employed to examine the dispersal ability of this species. We conclude the following: (a) E. strigata show altitudinal adaptive divergence among the populations in the Natori River Basin; (b) random forest showed higher resolution for detecting adaptive divergence than traditional statistical analysis; and (c) separating all markers into neutral and non‐neutral loci could provide full insight into parameters such as genetic diversity, local adaptation, and dispersal ability.     

Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata

The molecular genetic basis of adaptive variation is of fundamental importance for evolutionary dynamics, but is still poorly known. Only in very few cases has the relationship between genetic variation at the molecular level, phenotype and function been established in natural populations. We examined the functional significance and genetic basis of a polymorphism in production of leaf hairs, trichomes, in the perennial herb Arabidopsis lyrata. Earlier studies suggested that trichome production is subject to divergent selection. Here we show that the production of trichomes is correlated with reduced damage from insect herbivores in natural populations, and using statistical methods developed for medical genetics we document an association between loss of trichome production and mutations in the regulatory gene GLABROUS1. Sequence data suggest that independent mutations in this regulatory gene have provided the basis for parallel evolution of reduced resistance to insect herbivores in different populations of A. lyrata and in the closely related Arabidopsis thaliana. The results show that candidate genes identified in model organisms provide a valuable starting point for analysis of the genetic basis of phenotypic variation in natural populations.     

Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex

A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result in adaptive population differentiation and reproductive isolation and affect differentially the level of genetic divergence along the genome. Genome‐wide scan of large sets of individuals from multiple populations is a powerful approach to identify loci or genomic regions under ecologically divergent selection. Here, we focused on the pea aphid, a species complex of divergent host races, to explore the organization of the genomic divergence associated with host plant adaptation and ecological speciation. We analysed 390 microsatellite markers located at variable distances from predicted genes in replicate samples of sympatric populations of the pea aphid collected on alfalfa, red clover and pea, which correspond to three common host‐adapted races reported in this species complex. Using a method that accounts for the hierarchical structure of our data set, we found a set of 11 outlier loci that show higher genetic differentiation between host races than expected under the null hypothesis of neutral evolution. Two of the outliers are close to olfactory receptor genes and three other nearby genes encoding salivary proteins. The remaining outliers are located in regions with genes of unknown functions, or which functions are unlikely to be involved in interactions with the host plant. This study reveals genetic signatures of divergent selection across the genome and provides an inventory of candidate genes responsible for plant specialization in the pea aphid, thereby setting the stage for future functional studies.     

Local adaptation enhances seedling recruitment along an altitudinal gradient in a high mountain mediterranean plant

BACKGROUND AND AIMS: Germination and seedling establishment, which are critical stages in the regeneration process of plant populations, may be subjected to natural selection and adaptive evolution. The aims of this work were to assess the main limitations on offspring performance of Silene ciliata, a high mountain Mediterranean plant, and to test whether local adaptation at small spatial scales has a significant effect on the success of establishment. METHODS: Reciprocal sowing experiments were carried out among three populations of the species to test for evidence of local adaptation on seedling emergence, survival and size. Studied populations were located at the southernmost margin of the species' range, along the local elevation gradient that leads to a drought stress gradient. KEY RESULTS: Drought stress in summer was the main cause of seedling mortality even though germination mainly occurred immediately after snowmelt to make the best use of soil moisture. The results support the hypothesis that species perform better at the centre of their altitudinal range than at the boundaries. Evidence was also found of local adaptation in seedling survival and growth along the whole gradient. CONCLUSIONS: The local adaptation acting on seedling emergence and survival favours the persistence of remnant populations on the altitudinal and latitudinal margins of mountain species. In a global warming context, such processes may help to counteract the contraction of this species' ranges and the consequent loss of habitat area.     

Plant reproductive systems and evolution during biological invasion

Recent biological invasions provide opportunities to investigate microevolution during contemporary timescales. The tempo and scope of local adaptation will be determined by the intensity of natural selection and the amounts and kinds of genetic variation within populations. In flowering plants, genetic diversity is strongly affected by interactions between reproductive systems and stochastic forces associated with immigration history and range expansion. Here, we explore the significance of reproductive system diversity for contemporary evolution during plant invasion. We focus in particular on how reproductive modes influence the genetic consequences of long-distance colonization and determine the likelihood of adaptive responses during invasion. In many clonal invaders, strong founder effects and restrictions on sexual reproduction limit opportunities for local adaptation. In contrast, adaptive changes to life-history traits should be a general expectation in both outbreeding and inbreeding species. We provide evidence that evolutionary modifications to reproductive systems promote the colonizing ability of invading populations and that reproductive timing is an important target of selection during range expansion. Knowledge of the likelihood and speed at which local adaptation evolves in invasive plants will be particularly important for management practices when evolutionary changes enhance ecological opportunities and invasive spread.     

Ecotype differentiation in the face of gene flow within the diving beetle Agabus bipustulatus (Linnaeus, 1767) in northern Scandinavia

The repeated occurrence of habitat-specific polyphyletic evolved ecotypes throughout the ranges of widely distributed species implies that multiple, independent and parallel selection events have taken place. Ecological transitions across altitudinal gradients over short geographical distances are often associated with variation in habitat-related fitness, these patterns suggest the action of strong selective forces. Genetic markers will therefore contribute differently to differences between ecotypes in local hybrid zones. Here we have studied the adaptive divergence between ecotypes of the water beetle Agabus bipustulatus along several parallel altitudinal gradients in northern Scandinavia. This water beetle is well known for its remarkable morphological variation associated with mountain regions throughout the western Palaearctic. Two morphological ecotypes are recognised: a montane type with reduced flight muscles and a lowland type with fully developed muscles. Using a multilocus survey of allozyme variation and a morphological analysis with landmark-based morphometrics, across thirty-three populations and seven altitudinal gradients, we studied the local adaptive process of gene flow and selection in detail. Populations were sampled at three different elevations: below, at and above the tree line. The results indicate that the levels of divergence observed between ecotypes in morphology and allele frequencies at α-Glycerophosphate dehydrogenase relative to those shown by neutral molecular markers reflects local diversifying selection in situ. Four main lines of evidence are shown here: (1) A repeated morphological pattern of differentiation is observed across all altitudinal transects, with high reclassification probabilities. (2) Allele and genotype frequencies at the α-Gpdh locus are strongly correlated with altitude, in sharp contrast to the presumable neutral markers. (3) Genetic differentiation is two to three times higher among populations across the tree line than among populations at or below. (4) Genetic differentiation between ecotypes within independent mountain areas is reflected by different sets of allozymes.     

Divergence with gene flow and fine-scale phylogeographical structure in the wedge-billed woodcreeper, Glyphorynchus spirurus, a Neotropical rainforest bird

Determining the relative roles of vicariance and selection in restricting gene flow between populations is of central importance to the evolutionary process of population divergence and speciation. Here we use molecular and morphological data to contrast the effect of isolation (by mountains and geographical distance) with that of ecological factors (altitudinal gradients) in promoting differentiation in the wedge-billed woodcreeper, Glyphorynchus spirurus , a tropical forest bird, in Ecuador. Tarsus length and beak size increased relative to body size with altitude on both sides of the Andes, and were correlated with the amount of moss on tree trunks, suggesting the role of selection in driving adaptive divergence. In contrast, molecular data revealed a considerable degree of admixture along these altitudinal gradients, suggesting that adaptive divergence in morphological traits has occurred in the presence of gene flow. As suggested by mitochondrial DNA sequence data, the Andes act as a barrier to gene flow between ancient subspecific lineages. Genome-wide amplified fragment length polymorphism markers reflected more recent patterns of gene flow and revealed fine-scale patterns of population differentiation that were not detectable with mitochondrial DNA, including the differentiation of isolated coastal populations west of the Andes. Our results support the predominant role of geographical isolation in driving genetic differentiation in G. spirurus , yet suggest the role of selection in driving parallel morphological divergence along ecological gradients.     

RECENT ECOLOGICAL SELECTION ON REGULATORY DIVERGENCE IS SHAPING CLINAL VARIATION IN SENECIO ON MOUNT ETNA

The hybrid zone on Mount Etna (Sicily) between Senecio aethnensis and Senecio chrysanthemifolius (two morphologically and physiologically distinct species) is a classic example of an altitudinal cline. Hybridization at intermediate altitudes and gradients in phenotypic and life‐history traits occur along altitudinal transects of the volcano. The cline is considered to be a good example of ecological selection with species differences arising by divergent selection opposing gene flow. However, the possibility that the cline formed from recent secondary contact following an allopatric phase is difficult to exclude. We demonstrate a recent split between S. aethnensis and S. chrysanthemifolius (as recent as ～32,000 years ago) and sufficient gene flow (2Nm > 1) to have prevented divergence (implicating a role for diversifying selection in the maintenance of the cline). Differentially expressed genes between S. aethnensis and S. chrysanthemifolius exhibit significantly higher genetic divergence relative to “expression invariant” controls, suggesting that species differences may in part be mediated by divergent selection on differentially expressed genes involved with altitude‐related adaptation. The recent split time and the absence of fixed differences between these two ecologically distinct species suggest the rapid evolution to an altitudinal cline involving selection on both sequence and expression variation.