Microgeographic countergradient variation in the wood frog, Rana sylvatica

Prior studies have shown that macrogeographic gradients in temperature associated with latitude and altitude can lead to countergradient patterns of variation in a number of taxa: individuals from colder environments are known to grow or develop faster than their conspecifics from warmer environments when placed in a common setting. In this study, I hypothesized that countergradient variation also is important at microgeographic scales. The wood frog, Rana sylvatica, breeds in open-canopied, temporary wetlands as well as those heavily shaded by vegetation. Shading leads to cooler thermal environments that are associated with embryonic development rates as much as 50% slower than those in unshaded wetlands. Wetlands with contrasting canopy environments are often found within tens or hundreds of meters of each other. In a common garden experiment, embryos from nearby natural wetlands displayed countergradient variation: individuals collected from shaded wetlands developed up to 12% faster than those collected from relatively unshaded wetlands. The results of this study suggest that the concept of countergradient variation may be extended to small scales of space. In addition, the rate and scale of vegetation dynamics (the agent of wetland shading) imply that divergence in development among residents of nearby wetlands may be relatively rapid, on the order of decades.     

Local selection modifies phenotypic divergence among Rana temporaria populations in the presence of gene flow

In ectotherms, variation in life history traits among populations is common and suggests local adaptation. However, geographic variation itself is not a proof for local adaptation, as genetic drift and gene flow may also shape patterns of quantitative variation. We studied local and regional variation in means and phenotypic plasticity of larval life history traits in the common frog Rana temporaria using six populations from central Sweden, breeding in either open‐canopy or partially closed‐canopy ponds. To separate local adaptation from genetic drift, we compared differentiation in quantitative genetic traits (Q_ST) obtained from a common garden experiment with differentiation in presumably neutral microsatellite markers (F_ST). We found that R. temporaria populations differ in means and plasticities of life history traits in different temperatures at local, and in F_ST at regional scale. Comparisons of differentiation in quantitative traits and in molecular markers suggested that natural selection was responsible for the divergence in growth and development rates as well as in temperature‐induced plasticity, indicating local adaptation. However, at low temperature, the role of genetic drift could not be separated from selection. Phenotypes were correlated with forest canopy closure, but not with geographical or genetic distance. These results indicate that local adaptation can evolve in the presence of ongoing gene flow among the populations, and that natural selection is strong in this system.     

Gene flow does not prevent personality and morphological differentiation between two blue tit populations

Understanding the causes and consequences of population phenotypic divergence is a central goal in ecology and evolution. Phenotypic divergence among populations can result from genetic divergence, phenotypic plasticity or a combination of the two. However, few studies have deciphered these mechanisms for populations geographically close and connected by gene flow, especially in the case of personality traits. In this study, we used a common garden experiment to explore the genetic basis of the phenotypic divergence observed between two blue tit (Cyanistes caeruleus) populations inhabiting contrasting habitats separated by 25 km, for two personality traits (exploration speed and handling aggression), one physiological trait (heart rate during restraint) and two morphological traits (tarsus length and body mass). Blue tit nestlings were removed from their population and raised in a common garden for up to 5 years. We then compared adult phenotypes between the two populations, as well as trait‐specific Q_st and F_st. Our results revealed differences between populations similar to those found in the wild, suggesting a genetic divergence for all traits. Q_st–F_st comparisons revealed that the trait divergences likely result from dissimilar selection patterns rather than from genetic drift. Our study is one of the first to report a Q_st–F_st comparison for personality traits and adds to the growing body of evidence that population genetic divergence is possible at a small scale for a variety of traits including behavioural traits.     

Exploring genomic variation associated with drought stress in Picea mariana populations

Predicted increases in drought and heat stress will likely induce shifts in species bioclimatic envelopes. Genetic variants adapted to water limitation may prove pivotal for species response under scenarios of increasing drought. In this study, we aimed to explore this hypothesis by investigating genetic variation in 16 populations of black spruce (Picea mariana) in relation to climate variables in Alaska. A total of 520 single nucleotide polymorphisms (SNPs) were genotyped for 158 trees sampled from areas of contrasting climate regimes. We used multivariate and univariate genotype‐by‐environment approaches along with available gene annotations to investigate the relationship between climate and genetic variation among sampled populations. Nine SNPs were identified as having a significant association with climate, of which five were related to drought stress response. Outlier SNPs with respect to the overall environment were significantly overrepresented for several biological functions relevant for coping with variable hydric regimes, including osmotic stress response. This genomic imprint is consistent with local adaptation of black spruce to drought stress. These results suggest that natural selection acting on standing variation prompts local adaptation in forest stands facing water limitation. Improved understanding of possible adaptive responses could inform our projections about future forest dynamics and help prioritize populations that harbor valuable genetic diversity for conservation.     

Host environment and local genetic adaptation determine phenotype in parasitic Rhinanthus angustifolius

Plants have a remarkable capacity to adapt to local environmental conditions, which can result in ecotypic differentiation. Patterns of differentiation can, however, also be influenced by the extensive phenotypic plasticity exhibited by many plant species. In this study, we evaluated the distinctness of two putative ecotypes of the parasitic herb Rhinanthus angustifolius. We compared population means of characters commonly used to distinguish between the putative ecotypes after growing individuals of R. angustifolius with a variety of host species in a common garden. Resulting data were also pooled over environments to study how phenotypic plasticity affects the distinctness of ecotypes and individual populations. Except for node number, most of the characters were plastic. The pattern of differentiation was consistent with the existence of two, or possibly three, habitat‐related groups of populations; however, we observed considerable overlap in flowering time and morphological characters after pooling data across host environments. The results show that the complex phenological and morphological variation in R. angustifolius is caused by a combination of genetically determined ecotypic differentiation and plastic responses to the host environment and other factors. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 89–103.     

Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations

Drought is a major stress for plants, creating a strong selection pressure for traits that enable plant growth and survival in dry environments. Many drought responses are conserved species‐wide responses, while others vary among populations distributed across heterogeneous environments. We tested how six populations of the widely distributed California valley oak (Quercus lobata) sampled from contrasting climates would differ in their response to soil drying relative to well‐watered controls in a common environment by measuring ecophysiological traits in 93 individuals and gene expression (RNA‐seq) in 42 individuals. Populations did not differ in their adjustment of turgor loss point during soil drying, suggesting a generalized species‐wide response. Differential expression analysis identified 689 genes with a common response to treatment across populations and 470 genes with population‐specific responses. Weighted gene co‐expression network analysis (WGCNA) identified groups of genes with similar expression patterns that may be regulated together (gene modules). Several gene modules responded differently to water stress among populations, suggesting regional differences in gene network regulation. Populations from sites with a high mean annual temperature responded to the imposed water stress with significantly greater changes in gene module expression, indicating that these populations may be locally adapted to respond to drought. We propose that this variation among valley oak populations provides a mechanism for differential tolerance to the increasingly frequent and severe droughts in California.     

Adaptation,ancestral variation and gene flow in a ‘Sky Island’ Drosophila species

Over time, populations of species can expand, contract, fragment and become isolated, creating subpopulations that must adapt to local conditions. Understanding how species maintain variation after divergence as well as adapt to these changes in the face of gene flow is of great interest, especially as the current climate crisis has caused range shifts and frequent migrations for many species. Here, we characterize how a mycophageous fly species, Drosophila innubila, came to inhabit and adapt to its current range which includes mountain forests in south‐western USA separated by large expanses of desert. Using population genomic data from more than 300 wild‐caught individuals, we examine four populations to determine their population history in these mountain forests, looking for signatures of local adaptation. In this first extensive study, establishing D. innubila as a key genomic "Sky Island" model, we find D. innubila spread northwards during the previous glaciation period (30–100 KYA) and have recently expanded even further (0.2–2 KYA). D. innubila shows little evidence of population structure, consistent with a recent establishment and genetic variation maintained since before geographic stratification. We also find some signatures of recent selective sweeps in chorion proteins and population differentiation in antifungal immune genes suggesting differences in the environments to which flies are adapting. However, we find little support for long‐term recurrent selection in these genes. In contrast, we find evidence of long‐term recurrent positive selection in immune pathways such as the Toll signalling system and the Toll‐regulated antimicrobial peptides.     

Microclimate predicts frost hardiness of alpine Arabidopsis thaliana populations better than elevation

In mountain regions, topological differences on the microscale can strongly affect microclimate and may counteract the average effects of elevation, such as decreasing temperatures. While these interactions are well understood, their effect on plant adaptation is understudied. We investigated winter frost hardiness of Arabidopsis thaliana accessions originating from 13 sites along altitudinal gradients in the Southern Alps during three winters on an experimental field station on the Swabian Jura and compared levels of frost damage with the observed number of frost days and the lowest temperature in eight collection sites. We found that frost hardiness increased with elevation in a log‐linear fashion. This is consistent with adaptation to a higher frequency of frost conditions, but also indicates a decreasing rate of change in frost hardiness with increasing elevation. Moreover, the number of frost days measured with temperature loggers at the collection sites correlated much better with frost hardiness than the elevation of collection sites, suggesting that populations were adapted to their local microclimate. Notably, the variance in frost days across sites increased exponentially with elevation. Together, our results suggest that strong microclimate heterogeneity of high alpine environments can preserve functional genetic diversity among small populations. Synthesis: Here, we tested how plant populations differed in their adaptation to frost exposure along an elevation gradient and whether microsite temperatures improve the prediction of frost hardiness. We found that local temperatures, particularly the number of frost days, are a better predictor of the frost hardiness of plants than elevation. This reflects a substantial variance in frost frequency between sites at similar high elevations. We conclude that high mountain regions harbor microsites that differ in their local microclimate and thereby can preserve a high functional genetic diversity among them. Therefore, high mountain regions have the potential to function as a refugium in times of global change.     

Microgeographic variation in early fitness traits of Pinus sylvestris from contrasting soils

Premise

The possibility of fine-scale intraspecific adaptive divergence under gene flow is established by theoretical models and has been confirmed empirically in tree populations distributed along steep altitudinal clines or across extreme edaphic discontinuities. However, the possibility of microgeographic adaptive divergence due to less severe but more frequent kinds of soil variation is unclear.

Methods

In this study, we looked for evidence of local adaptation to calcareous versus siliceous soil types in two nearby Mediterranean Pinus sylvestris populations connected via pollen flow. Using a greenhouse experiment, we tested for variation in early (up to three years of age) seedling performance among open-pollinated maternal families originating from each edaphic provenance when experimentally grown on both types of natural local substrate.

Results

Although seedlings were clearly affected by the edaphic environment, exhibiting lower and slower emergence as well as higher mortality on the calcareous than in the siliceous substrate, neither the performance on each substrate nor the plasticity among substrates varied significantly with seedling edaphic provenance.

Conclusions

We found no evidence of local adaptation to a non-extreme edaphic discontinuity over a small spatial scale, at least during early stages of seedling establishment. Future studies on microgeographic soil-driven adaptation should consider long-term experiments to minimize maternal effects and allow a potentially delayed expression of edaphic adaptive divergence.     

Additive impacts of experimental climate change increase risk to an ectotherm at the Arctic's edge

Globally, Arctic and Subarctic regions have experienced the greatest temperature increases during the last 30 years. These extreme changes have amplified threats to the freshwater ecosystems that dominate the landscape in many areas by altering water budgets. Several studies in temperate environments have examined the adaptive capacity of organisms to enhance our understanding of the potential repercussions of warming and associated accelerated drying for freshwater ecosystems. However, few experiments have examined these impacts in Arctic or Subarctic freshwater ecosystems, where the climate is changing most rapidly. To evaluate the capacity of a widespread ectotherm to anticipated environmental changes, we conducted a mesocosm experiment with wood frogs (Rana sylvatica) in the Canadian Subarctic. Three warming treatments were fully crossed with three drying treatments to simulate a range of predicted changes in wetland environments. We predicted wetland warming and drying would act synergistically, with water temperature partially compensating for some of the negative effects of accelerated drying. Across all drying regimes, a 1 °C increase in water temperature increased the odds of survival by 1.79, and tadpoles in 52‐day and 64‐day hydroperiod mesocosms were 4.1–4.3 times more likely to survive to metamorphosis than tadpoles in 45‐day mesocosms. For individuals who survived to metamorphosis, there was only a weak negative effect of temperature on size. As expected, increased temperatures accelerated tadpole growth through day 30 of the experiment. Our results reveal that one of the dominant herbivores in Subarctic wetlands, wood frog tadpoles, are capable of increasing their developmental rates in response to increased temperature and accelerated drying, but only in an additive manner. The strong negative effects of drying on survival, combined with lack of compensation between these two environmental drivers, suggest changes in the aquatic environment that are expected in this ecosystem will reduce mean fitness of populations across the landscape.     

Using genetic variation to infer associations with climate in the common frog,Rana temporaria

Recent and historical species' associations with climate can be inferred using molecular markers. This knowledge of population and species‐level responses to climatic variables can then be used to predict the potential consequences of ongoing climate change. The aim of this study was to predict responses of Rana temporaria to environmental change in Scotland by inferring historical and contemporary patterns of gene flow in relation to current variation in local thermal conditions. We first inferred colonization patterns within Europe following the last glacial maximum by combining new and previously published mitochondrial DNA sequences. We found that sequences from our Scottish samples were identical to (92%), or clustered with, the common haplotype previously identified from Western Europe. This clade showed very low mitochondrial variation, which did not allow inference of historical colonization routes but did allow interpretation of patterns of current fine‐scale population structure without consideration of confounding historical variation. Second, we assessed fine‐scale microsatellite‐based patterns of genetic variation in relation to current altitudinal temperature gradients. No population structure was found within altitudinal gradients (average F_ST = 0.02), despite a mean annual temperature difference of 4.5 °C between low‐ and high‐altitude sites. Levels of genetic diversity were considerable and did not vary between sites. The panmictic population structure observed, even along temperature gradients, is a potentially positive sign for R. temporaria persistence in Scotland in the face of a changing climate. This study demonstrates that within taxonomic groups, thought to be at high risk from environmental change, levels of vulnerability can vary, even within species.     

Microgeographic genetic structure and gene flow in Hibiscus moscheutos (Malvaceae) populations

Microgeographic genetic variation in populations of a wetland macrophyte, Hibiscus moscheutos L. (Malvaceae), was investigated using allozyme polymorphism. The species is a self-compatible insect-pollinated perennial, and seeds are water dispersed (hydrochory). Six hundred plants were analyzed from eight brackish and two freshwater populations within the Rhode River watershed/estuarine system. The genetic structure of the populations was assessed by fixation indices and spatial autocorrelation analyses. The degree of genetic differentiation among sites and gene flow between all paired combinations of sites (M ) was analyzed using three hypothetical gene flow models. Fixation indices indicated almost complete panmixia within populations, and spatial autocorrelations showed that genotypes were randomly distributed within sites, most likely the result of water dispersal of seeds. Allele frequencies were significantly different among sites, and estimated FST indicated moderate genetic differentiation (_ = 0.062). Genetic differences between populations were mostly explained by a gene flow model that accounted for the location of populations relative to the tidal stream. The importance of hydrochory in affecting spatial genetic structure was thus suggested both within and among H. moscheutos populations.     

Restricted gene flow and local adaptation highlight the vulnerability of high‐latitude reefs to rapid environmental change

Global climate change poses a serious threat to the future health of coral reef ecosystems. This calls for management strategies that are focused on maximizing the evolutionary potential of coral reefs. Fundamental to this is an accurate understanding of the spatial genetic structure in dominant reef‐building coral species. In this study, we apply a genotyping‐by‐sequencing approach to investigate genome‐wide patterns of genetic diversity, gene flow, and local adaptation in a reef‐building coral, Pocillopora damicornis, across 10 degrees of latitude and a transition from temperate to tropical waters. We identified strong patterns of differentiation and reduced genetic diversity in high‐latitude populations. In addition, genome‐wide scans for selection identified a number of outlier loci putatively under directional selection with homology to proteins previously known to be involved in heat tolerance in corals and associated with processes such as photoprotection, protein degradation, and immunity. This study provides genomic evidence for both restricted gene flow and local adaptation in a widely distributed coral species, and highlights the potential vulnerability of leading‐edge populations to rapid environmental change as they are locally adapted, reproductively isolated, and have reduced levels of genetic diversity.     

Geographical variation of Plutella xylostella (Lepidoptera: Plutellidae) populations revealed by mitochondrial COI gene in China

The diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), is one of the most serious pests for cruciferous vegetable growers worldwide. To determine the relations of local and regional populations, we performed a mitochondrial COI gene analysis of eight P. xylostella populations from different locations in or around the Qinling Mountains and two other populations, one from Beijing and the other from Guangdong. The mtDNA divergences among the 10 populations were high, and 32 haplotypes were detected in 149 adults. The mean haplotype divergence was 1.7% (range 0.04–4.1%). Haplotype diversity in the 10 populations varied from 0.571 (AK) to 0.885 (HZ), and the nucleotide diversity varied from 0.00286 (AK) to 0.0117 (HZ). The results also did not show significant correlation between genetic and geographical distance. Also, the effective number of migrants between populations (Nm) ranged from 1.43 to infinite, suggesting that population exchange and gene flow among the P. xylostella populations occurred. However, principal component analysis (PCA) showed that the TB and TC populations were differentiated from other populations, indicating possible across‐mountain barrier to migration and gene flow.     

Immigrant inviability promotes reproductive isolation among host‐associated populations of the gall wasp Belonocnema treatae

Ecological speciation describes the evolutionary process whereby divergent natural selection between environments generates reproductive isolation. Studying the magnitude of sequential reproductive barriers between ecologically divergent populations improves our understanding of the way these barriers evolve and how each contributes to the speciation process. Immigrant inviability describes the lower fitness of immigrants in non‐native environments and is an important, but long underexplored, reproductive barrier. In this study, we test the role of immigrant inviability among host‐associated populations of the gall wasp Belonocnema treataeMayr (Hymenoptera: Cynipini: Cynipidae) by measuring the ability of gall wasps to initiate and complete gall formation, while avoiding host immune responses, on closely related native and non‐native live oaks, Quercus virginianaMill., Quercus fusiformisSmall, and Quercus geminataSmall (Fagaceae). In general, we found evidence for immigrant inviability when B. treatae populations colonized non‐native host species. However, patterns were variable among years, suggesting that episodic events may play an important role in connecting ecologically divergent populations.     

No geographic variation in thermoregulatory colour plasticity and limited variation in heat‐avoidance behaviour in Battus philenor caterpillars

Phenotypic plasticity can help organisms cope with variation in their current environment, including temperature variation, but not all environments are equally variable. In the least variable or extreme environments, plasticity may no longer be used. In this case, the plasticity could be lost altogether, or it could persist with either the same or an altered reaction norm, depending on factors such as the plasticity's costs. In the pipevine swallowtail caterpillar (Battus philenor), I tested for changes in two forms of heat‐avoidance plasticity, colour change and refuge‐seeking behaviour, across the species’ range in the United states, including the cooler eastern parts of its range where colour change has not been observed and is unlikely to be needed. I found that both heat‐avoidance behaviour and colour change persisted in all surveyed populations. Indeed, the reaction norm for colour change remained nearly unaltered, whereas the threshold for refuge‐seeking only changed slightly across populations. These results suggest that the costs of these plastic traits are low enough for them to be maintained by whatever minimal gene flow the population receives. I show that plasticity can be maintained unaltered in populations where it is not used and discuss the potential consequences of this persistence for both the ecology and evolution of plasticity.     

Adaptation with gene flow across the landscape in a dune sunflower

Isolation by adaptation increases divergence at neutral loci when natural selection against immigrants reduces the rate of gene flow between different habitats. This can occur early in the process of adaptive divergence and is a key feature of ecological speciation. Despite the ability of isolation by distance (IBD) and other forms of landscape resistance to produce similar patterns of neutral divergence within species, few studies have used landscape genetics to control for these other forces. We have studied the divergence of Helianthus petiolaris ecotypes living in active sand dunes and adjacent non-dune habitat, using landscape genetics approaches, such as circuit theory and multiple regression of distance matrices, in addition to coalescent modelling. Divergence between habitats was significant, but not strong, and was shaped by IBD. We expected that increased resistance owing to patchy and unfavourable habitat in the dunes would contribute to divergence. Instead, we found that landscape resistance models with lower resistance in the dunes performed well as predictors of genetic distances among subpopulations. Nevertheless, habitat class remained a strong predictor of genetic distance when controlling for isolation by resistance and IBD. We also measured environmental variables at each site and confirmed that specific variables, especially soil nitrogen and vegetation cover, explained a greater proportion of variance in genetic distance than did landscape or the habitat classification alone. Asymmetry in effective population sizes and numbers of migrants per generation was detected using coalescent modelling with Bayesian inference, which is consistent with incipient ecological speciation being driven by the dune habitat.     

Variation in thermal niche of a declining river‐breeding frog: From counter‐gradient responses to population distribution patterns

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