Genetic adaptations in the population history of Arabidopsis thaliana

A population encounters a variety of environmental stresses, so the full source of its resilience can only be captured by collecting all the signatures of adaptation to the selection of the local environment in its population history. Based on the multiomic data of Arabidopsis thaliana, we constructed a database of phenotypic adaptations (p-adaptations) and gene expression (e-adaptations) adaptations in the population. Through the enrichment analysis of the identified adaptations, we inferred a likely scenario of adaptation that is consistent with the biological evidence from experimental work. We analyzed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes and identified 650 p-adaptations and 3,925 e-adaptations [false discovery rate (FDR) = 0.05]. The population underwent large-scale p-adaptations and e-adaptations along 4 lineages. Extremely cold winters and short summers prolonged seed dormancy and expanded the root system architecture. Low temperatures prolonged the growing season, and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected alleles for lower heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The p-adaptations are directly interpretable, while the coadapted gene expressions reflect the physiological requirements for the adaptation. The integration of this information characterizes when and where the population has experienced environmental stress and how the population responded at the molecular level.

Evidence for coloration plasticity in the yellow-bellied toad, Bombina variegata

Phenotypic adaptation in terms of background color matching to the local habitat is an important mechanism for survival in prey species. Thus, intraspecific variation in cryptic coloration is expected among localities with dissimilar habitat features (e.g., soil, vegetation). Yellow-bellied toads (Bombina variegata) display a dark dorsal coloration that varies between populations, assumed to convey crypsis. In this study, we explored I) geographic variation in dorsal coloration and II) coloration plasticity in B. variegata from three localities differing in substrate coloration. Using avian visual modeling, we found that the brightness contrasts of the cryptic dorsa were significantly lower on the local substrates than substrates of other localities. In experiments, individuals from one population were able to quickly change the dorsal coloration to match a lighter substrate. We conclude that the environment mediates an adaptation in cryptic dorsal coloration. We suggest further studies to test the mechanisms by which the color change occurs and explore the adaptive potential of coloration plasticity on substrates of varying brightness in B. variegata and other species.

Mycobacterium vaccae Adaptation to Disinfectants and Hand Sanitisers, and Evaluation of Cross-Tolerance with Antimicrobials

Mycobacterium vaccae is being considered as an adjuvant to antituberculosis therapy, tested for the treatment of autoimmune diseases, and as an anti-depressive agent. This bacterium is ubiquitous in the environment and the widespread use of disinfectants and sanitisers may lead to its adaptation to these compounds. In the present study, M. vaccae cells adapted to these compounds mainly by making adjustments in their lipid composition and net surface charge. The modifications in the lipid composition led to changes in membrane permeability which resulted in increased tolerance towards levofloxacin, thioridazine, and omeprazole.

Highlighting convergent evolution in morphological traits in response to climatic gradient in African tropical tree species: The case of genus Guibourtia Benn

Adaptive evolution is a major driver of organism diversification, but the links between phenotypic traits and environmental niche remain little documented in tropical trees. Moreover, trait-niche relationships are complex because a correlation between the traits and environmental niches displayed by a sample of species may result from (a) convergent evolution if different environmental conditions have selected different sets of traits, and/or (b) phylogenetic inertia if niche and morphological differences between species are simply function of their phylogenetic divergence, in which case the trait-niche correlation does not imply any direct causal link. Here, we aim to assess the respective roles of phylogenetic inertia and convergent evolution in shaping the differences of botanical traits and environmental niches among congeneric African tree species that evolved in different biomes.This issue was addressed with the tree genus Guibourtia Benn. (Leguminosae and Detarioideae), which contains 13 African species occupying various forest habitat types, from rain forest to dry woodlands, with different climate and soil conditions. To this end, we combined morphological data with ecological niche modelling and used a highly resolved plastid phylogeny of the 13 African Guibourtia species.First, we demonstrated phylogenetic signals in both morphological traits (Mantel test between phylogenetic and morphological distances between species: r = .24, p = .031) and environmental niches (Mantel test between phylogenetic and niche distances between species: r = .23, p = .025). Second, we found a significant correlation between morphology and niche, at least between some of their respective dimensions (Mantel's r = .32, p = .013), even after accounting for phylogenetic inertia (Phylogenetic Independent Contrast: r = .69, p = .018). This correlation occurred between some leaflet and flower traits and solar radiation, relative humidity, precipitations, and temperature range.Our results demonstrate the convergent evolution of some morphological traits in response to climatic factors in congeneric tree species and highlight the action of selective forces, along with neutral ones, in shaping the divergence between congeneric tropical plants.

Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments

Natural selection has shaped the strategies for survival and growth of microorganisms. The success of microorganisms depends not only on slow evolutionary tuning but also on the ability to adapt to unpredictable changes in their environment. In principle, adaptive strategies range from purely deterministic mechanisms to those that exploit the randomness intrinsic to many cellular and molecular processes. Depending on the environment and selective pressures, particular strategies can lie somewhere along this continuum. In recent years, non-genetic cell-to-cell differences have received a lot of attention, not least because of their potential impact on the ability of microbial populations to survive in dynamic environments. Using several examples, we describe the origins of spontaneous and induced mechanisms of phenotypic adaptation. We identify some of the commonalities of these examples and consider the potential role of chance and constraints in microbial phenotypic adaptation.

Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish Leucoraja ocellata (Rajidae)

The relative importance of genetic versus epigenetic changes in adaptive evolution is a hotly debated topic, with studies showing that some species appear to be able to adapt rapidly without significant genetic change. Epigenetic mechanisms may be particularly important for the evolutionary potential of species with long maturation times and low reproductive potential ('K-strategists'), particularly when faced with rapidly changing environmental conditions. Here we study the transcriptome of two populations of the winter skate (Leucoraja ocellata), a typical 'K-strategist', in Atlantic Canada; an endemic population in the southern Gulf of St Lawrence and a large population on the Scotian Shelf. The endemic population has been able to adapt to a 10°C higher water temperature over short evolutionary time (7000 years), dramatically reducing its body size (by 45%) significantly below the minimum maturation size of Scotian Shelf and other populations of winter skate, as well as exhibiting other adaptations in life history and physiology. We demonstrate that the adaptive response to selection has an epigenetic basis, cataloguing 3653 changes in gene expression that may have enabled this species to rapidly respond to the novel environment. We argue that the epigenetic augmentation of species evolutionary potential (its regulation though gene expression) can enable K-strategists to survive and adapt to different environments, and this mechanism may be particularly important for the persistence of sharks, skates and rays in the light of future climate change.

Chlorella: 125 years of the green survivalist

Chlorella, the archetype of unicellular green algae, is a high-performance primary producer in aquatic and terrestrial ecosystems. Under the simple spherical morphology of Chlorella, many other 'green balls' unfolded as independent phylogenetic lineages as a result of convergent evolution. By contrast, green algae with strikingly different phenotypes were unmasked as close relatives of Chlorella by modern molecular techniques. Here, we point to the increasing impact of these diverse protists on ecology, evolution, and biotechnology in the light of integrative taxonomy.

The role of calcium and predation on plate morph evolution in the three-spined stickleback (Gasterosteus aculeatus)

While the genetic basis to plate morph evolution of the three-spined stickleback (Gasterosteus aculeatus) is well described, the environmental variables that select for different plate and spine morphs are incompletely understood. Using replicate populations of three-spined sticklebacks on North Uist, Scotland, we previously investigated the role of predation pressure and calcium limitation on the adaptive evolution of stickleback morphology and behavior. While dissolved calcium proved a significant predictor of plate and spine morph, predator abundance did not. Ecol. Evol., xxx, 2014 and xxx performed a comparable analysis to our own to address the same question. They failed to detect a significant effect of dissolved calcium on morphological evolution, but did establish a significant effect of predation; albeit in the opposite direction to their prediction.

Synthetic biology of phenotypic adaptation in vertebrates: the next frontier

For over the last 2 decades, positively selected amino acid sites have been inferred almost exclusively by showing that the number of nonsynonymous substitutions per nonsynonymous site (dn) is greater than that of synonymous substitutions per synonymous site (ds). However, virtually none of these statistical results have been experimentally tested and remain as hypotheses. To perform such experimental tests, we must connect genotype and phenotype and relate the phenotypic changes to the environmental and behavioral changes of the organism. The genotype-phenotype relationship can be established only by synthesizing and manipulating "proper" ancestral phenotypes, whereas the actual functions of adaptive mutations can be learned by studying their chemical roles in phenotypic changes.

Ecological causes of morphological evolution in the three-spined stickleback

The central assumption of evolutionary theory is that natural selection drives the adaptation of populations to local environmental conditions, resulting in the evolution of adaptive phenotypes. The three-spined stickleback (Gasterosteus aculeatus) displays remarkable phenotypic variation, offering an unusually tractable model for understanding the ecological mechanisms underpinning adaptive evolutionary change. Using populations on North Uist, Scotland we investigated the role of predation pressure and calcium limitation on the adaptive evolution of stickleback morphology and behavior. Dissolved calcium was a significant predictor of plate and spine morph, while predator abundance was not. Stickleback latency to emerge from a refuge varied with morph, with populations with highly reduced plates and spines and high predation risk less bold. Our findings support strong directional selection in three-spined stickleback evolution, driven by multiple selective agents.

Synthesis of Experimental Molecular Biology and Evolutionary Biology: An Example from the World of Vision

Natural selection has played an important role in establishing various phenotypes, but the molecular mechanisms of phenotypic adaptation are not well understood. The slow progress is a consequence of mutagenesis experiments in which present-day molecules were used and of the limited scope of statistical methods used to detect adaptive evolution. To fully appreciate phenotypic adaptation, the precise roles of adaptive mutations during phenotypic evolution must be elucidated through the engineering and manipulation of ancestral phenotypes. Experimental and quantum chemical analyses of dim-light vision reveal some surprising results and provide a foundation for a productive study of the adaptive evolution of various phenotypes.