Evolutionary Responses Research Articles

Genome-wide identification of potassium channels in maize showed evolutionary patterns and variable functional responses to abiotic stresses

Potassium (K) channels are essential components of plant biology, mediating not only K ion (K+) homeostasis but also regulating several physiological processes and stress tolerance. In the current investigation, we identified 27 K+ channels in maize and deciphered the evolution and divergence pattern with four monocots and five dicot species. Chromosomal localization and expansion of K+ channel genes showed uneven distribution and were independent of genome size. The dispersed duplication is the major force in expanding K+ channels in the target genomes. The mean Ka/Ks ratio of <0.5 in paralogs and orthologs indicates horizontal and vertical expansions of K+ channel genes under strong purifying selection. The one-to-one K+ channel orthologs were prominent among the closely related species, with higher synteny between maize and the rest of the monocots. Comprehensive K+ channels promoter analysis revealed various cis-regulatory elements mediating stress tolerance with the predominance of MYB and STRE binding sites. The regulatory network showed AP2-EREBP TFs, miR164 and miR399 are prominent regulatory elements of K+ channels. The qRT-PCR analysis of K+ channels and regulatory miRNAs showed significant expressions in response to drought and waterlogging stresses. The present study expanded the knowledge on K+ channels in maize and will serve as a basis for an in-depth functional analysis.

Corrigendum: Response capability evaluation model of electric vehicle aggregator based on evolutionary game and response anticipation

Corrigendum: Response capability evaluation model of electric vehicle aggregator based on evolutionary game and response anticipation

Plasticity of shallow reef corals across a depth gradient

Global warming harms coral reefs. Mesophotic coral reef ecosystems (MCEs) have been suggested to serve as refugia for shallow reefs. Information on the adaptation potential of shallow corals at MCEs is a prerequisite for understanding the refuge potential of MCEs. In this study, we investigated the photoacclimation potential of four shallow coral species transplanted at different depths over 1 year. The results showed that the corals—Pocillopora damicornis, Porites cylindrica, and Turbinaria reniformis—survived and acclimated to a wide range of light regimes at the depths of 5, 20, and 40 m. However, Acropora tenuis survived only at 5 and 20 m depth and showed significant morphological alteration at 20 m depth. Our results indicate that shallow corals have substantial plasticity with respect to depth changes. Changes in photosynthetic performance and phenotypic plasticity within these coral species may act as a buffer for depth-related changes and as modulators of evolutionary responses.

Eco-evolutionary dynamics of experimental Pseudomonas aeruginosa populations under oxidative stress.

Within-host environments are likely to present a challenging and stressful environment for opportunistic pathogenic bacteria colonizing from the external environment. How populations of pathogenic bacteria respond to such environmental challenges and how this varies between strains is not well understood. Oxidative stress is one of the defences adopted by the human immune system to confront invading bacteria. In this study, we show that strains of the opportunistic pathogenic bacterium Pseudomonas aeruginosa vary in their eco-evolutionary responses to hydrogen peroxide stress. By quantifying their 24 h growth kinetics across hydrogen peroxide gradients we show that a transmissible epidemic strain isolated from a chronic airway infection of a cystic fibrosis patient, LESB58, is much more susceptible to hydrogen peroxide than either of the reference strains, PA14 or PAO1, with PAO1 showing the lowest susceptibility. Using a 12 day serial passaging experiment combined with a mathematical model, we then show that short-term susceptibility controls the longer-term survival of populations exposed to subinhibitory levels of hydrogen peroxide, but that phenotypic evolutionary responses can delay population extinction. Our model further suggests that hydrogen peroxide driven extinctions are more likely with higher rates of population turnover. Together, these findings suggest that hydrogen peroxide is likely to be an effective defence in host niches where there is high population turnover, which may explain the counter-intuitively high susceptibility of a strain isolated from chronic lung infection, where such ecological dynamics may be slower.

Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts.

Symbiotic microorganisms are crucial for the survival of corals and their resistance to coral bleaching in the face of climate change. However, the impact of microbe-microbe interactions on coral functioning is mostly unknown but could be essential factors for coral adaption to future climates. Here, we investigated interactions between cultured dinoflagellates of the Symbiodiniaceae family, essential photosymbionts of corals, and associated bacteria. By assessing the genomic potential of 49 bacteria, we found that they are likely beneficial for Symbiodiniaceae, through the production of B vitamins and antioxidants. Additionally, bacterial genes involved in host-symbiont interactions, such as secretion systems, accumulated mutations following long-term exposure to heat, suggesting symbiotic interactions may change under climate change. This highlights the importance of microbe-microbe interactions in coral functioning.

Preconditions influencing the development of post-secondary training programs in universities for individuals with intellectual disabilities

ABSTRACT Background Research on post-secondary training for individuals with intellectual disabilities has generally focused on programs, with little consideration of the structures and mechanisms that give rise to them. This article adopts a critical realist perspective to comparatively analyse and theorise about the contextual structures contributing to the introduction of post-secondary training programs in universities for individuals with intellectual disabilities. Method Six stages in critical realist explanatory research were followed. They include (1) description, (2) analytical resolution, (3) abduction/theoretical redescription, (4) retroduction, (5) comparison between different theories and abstractions, and (6) concretisation and contextualisation. Results Historical, socio-political, and educational policy structures and mechanisms, indicated three program typologies: program as niche, as a generalisable prototype, and as an evolutionary response to evolving conditions. Conclusions By developing explanations about preconditions, the study draws out nuanced sub-types occurring within a single university-based program, theorises on trajectories for success, and lays the groundwork for future empirical and conceptual development.

Precipitation predictability drives evolution of drought strategies in the common poppy, Papaver rhoeas

Abstract Current climate change leads to an increase in the frequency and intensity of droughts and to a decreased precipitation predictability. The few studies investigating plant evolutionary responses to contrasting predictability regimes showed that intrinsic precipitation predictability shapes plant phenotypic variation, drives evolution of phenotypic plasticity and can vary in strength and direction of selection. This suggests that the selection pressure induced by decreased precipitation predictability may lead to plants coping better with severe drought events. To investigate whether past precipitation predictability influences plant responses to different drought conditions, we performed a common‐garden experiment applying control, short‐term and long‐term drought treatments on seedlings of Papaver rhoeas (Papaveraceae) whose progenitors experienced less versus more precipitation predictability treatments for three consecutive generations. In addition, to assess whether competition modulates plant responses, half of the plants were grown together with the widespread herbaceous plant Galium album (Rubiaceae). In the presence of long drought episodes, plants whose progenitors experienced less predictable precipitation survived longer than those whose progenitors experienced more predictable precipitation. Furthermore, plants whose progenitors experienced less predictable precipitation had lower biomass, which is likely to reduce water loss via transpiration, and, across all drought treatments, they showed lower root investment. However, no trait differences were detected under competition, indicating that interspecific competition may limit the expression of evolutionary responses to changes induced by precipitation predictability. Altogether our results indicate that lower precipitation predictability mainly promotes the evolution of drought‐escape and drought‐avoidance strategies. Overall, our experiment highlights that precipitation predictability is an important evolutionary driver of plant functional responses, potentially shifting evolutionary trajectories of plants under increasing intensity of drought events. Read the free Plain Language Summary for this article on the Journal blog.

Heritable variation in thermal profiles is associated with reproductive success in the world's largest bird.

Organisms inhabiting extreme thermal environments, such as desert birds, have evolved spectacular adaptations to thermoregulate during hot and cold conditions. However, our knowledge of selection for thermoregulation and the potential for evolutionary responses is limited, particularly for large organisms experiencing extreme temperature fluctuations. Here we use thermal imaging to quantify selection and genetic variation in thermoregulation in ostriches (Struthio camelus), the world's largest bird species that is experiencing increasingly volatile temperatures. We found that females who are better at regulating their head temperatures ("thermoregulatory capacity") had higher egg-laying rates under hotter conditions. Thermoregulatory capacity was both heritable and showed signatures of local adaptation: females originating from more unpredictable climates were better at regulating their head temperatures in response to temperature fluctuations. Together these results reveal that past and present evolutionary processes have shaped genetic variation in thermoregulatory capacity, which appears to protect critical organs, such as the brain, from extreme temperatures during reproduction.

Genetic adaptations of sea anemone to hydrothermal environment.

Hydrothermal vent habitats are characterized by high hydrostatic pressure, darkness, and the continuous release of toxic metal ions into the surrounding environment where sea anemones and other invertebrates thrive. Nevertheless, the understanding of metazoan metal ion tolerances and environmental adaptations remains limited. We assembled a chromosome-level genome for the vent sea anemone, Alvinactis idsseensis sp. nov. Comparative genomic analyses revealed gene family expansions and gene innovations in A. idsseensis sp. nov. as a response to high concentrations of metal ions. Impressively, the metal tolerance proteins MTPs is a unique evolutionary response to the high concentrations of Fe2+ and Mn2+ present in the environments of these anemones. We also found genes associated with high concentrations of polyunsaturated fatty acids that may respond to high hydrostatic pressure and found sensory and circadian rhythm-regulated genes that were essential for adaptations to darkness. Overall, our results provide insights into metazoan adaptation to metal ions, high pressure, and darkness in hydrothermal vents.

Genomics for monitoring and understanding species responses to global climate change.

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

Rapid Evolutionary Adaptation to Diet Composition in the Black Soldier Fly (Hermetia illucens).

Genetic adaptation of Hermetia illucens (BSF) to suboptimal single sourced waste streams can open new perspectives for insect production. Here, four BSF lines were maintained on a single sourced, low-quality wheat bran diet (WB) or on a high-quality chicken feed diet (CF) for 13 generations. We continuously evaluated presumed evolutionary responses in several performance traits to rearing on the two diets. Subsequently, we tested responses to interchanged diets, i.e., of larvae that had been reared on low-quality feed and tested on high-quality feed and vice versa to evaluate costs associated with adaptation to different diets. BSF were found to experience rapid adaptation to the diet composition. While performances on the WB diet were always inferior to the CF diet, the adaptive responses were stronger to the former diet. This stronger response was likely due to stronger selection pressure experienced by BSF fed on the low-quality single sourced diet. The interchanged diet experiment found no costs associated with diet adaptation, but revealed cross generational gain associated with the parental CF diet treatment. Our results revealed that BSF can rapidly respond adaptively to diet, although the mechanisms are yet to be determined. This has potential to be utilized in commercial insect breeding to produce lines tailored to specific diets.

Marine heatwaves impact mortality of triploid Pacific oysters.

Studies of heatwave impacts on marine organisms are needed to understand biological tolerance to heat stress. Such studies should include integrative analyses across different levels of biological organization, which often reveal that predictions are non‐linear (e.g., gene–protein–physiology–organism). Further insights into potential evolutionary responses of organisms to rapid environmental change can be gained from formal genetic studies of multigenerational pedigreed families.

Sexual conflict, heterochrony and tissue specificity as evolutionary problems of adaptive plasticity in development.

Differential gene expression represents a fundamental cause and manifestation of phenotypic plasticity. Adaptive phenotypic plasticity in gene expression as a trait evolves when alleles that mediate gene regulation serve to increase organismal fitness by improving the alignment of variation in gene expression with variation in circumstances. Among the diverse circumstances that a gene encounters are distinct cell types, developmental stages and sexes, as well as an organism's extrinsic ecological environments. Consequently, adaptive phenotypic plasticity provides a common framework to consider diverse evolutionary problems by considering the shared implications of alleles that produce context-dependent gene expression. From this perspective, adaptive plasticity represents an evolutionary resolution to conflicts of interest that arise from any negatively pleiotropic effects of expression of a gene across ontogeny, among tissues, between the sexes, or across extrinsic environments. This view highlights shared properties within the general relation of fitness, trait expression and context that may nonetheless differ substantively in the grain of selection within and among generations to influence the likelihood of adaptive plasticity as an evolutionary response. Research programmes that historically have focused on these separate issues may use the insights from one another by recognizing their shared dependence on context-dependent gene regulatory evolution.

Effects of experimental warming at the microhabitat scale on oak leaf traits and insect herbivory across a contrasting environmental gradient

Forest microclimatic variation can result in substantial temperature differences at local scales with concomitant impacts on plant defences and herbivory. Such microclimatic effects, however, may differ across abiotically contrasting sites depending on background environmental differences. To test these cross‐scale effects shaping species ecological and evolutionary responses, we experimentally tested the effects of aboveground microhabitat warming on insect leaf herbivory and leaf defences (toughness, phenolic compounds) for saplings of sessile oak Quercus petraea across two abiotically contrasting sites spanning 9° latitude. We found higher levels of herbivory at the low‐latitude site, but leaf traits showed mixed patterns across sites. Toughness and condensed tannins were higher at the high‐latitude site, whereas hydrolysable tannins and hydroxycinnamic acids were higher at the low‐latitude site. At the microhabitat scale, experimental warming increased herbivory, but did not affect any of the measured leaf traits. Condensed tannins were negatively correlated with herbivory, suggesting that they drive variation in leaf damage at both scales. Moreover, the effects of microhabitat warming on herbivory and leaf traits were consistent across sites, i.e. effects at the microhabitat scale play out similarly despite variation in factors acting at broader scales. These findings together suggest that herbivory responds to both microhabitat (warming) and broad‐scale environmental factors, whereas leaf traits appear to respond more to environmental factors operating at broad scales (e.g. macroclimatic factors) than to warming at the microhabitat scale. In turn, leaf secondary chemistry (tannins) appears to drive both broad‐scale and microhabitat‐scale variation in herbivory. Further studies are needed using reciprocal transplants with more populations across a greater number of sites to tease apart plant plasticity from genetic differences contributing to leaf trait and associated herbivory responses across scales and, in doing so, better understand the potential for dynamics such as local adaptation and range expansion or contraction under shifting climatic regimes.

Rapid evolution of novel biotic interactions in the UK Brown Argus butterfly uses genomic variation from across its geographical range.

Understanding the rate and extent to which populations can adapt to novel environments at their ecological margins is fundamental to predicting the persistence of biological communities during ongoing and rapid global change. Recent range expansion in response to climate change in the UK butterfly Aricia agestis is associated with the evolution of novel interactions with a larval food plant, and the loss of its ability to use an ancestral host species. Using ddRAD analysis of 61,210 variable SNPs from 261 females from throughout the UK range of this species, we identify genomic regions at multiple chromosomes that are associated with evolutionary responses, and their association with demographic history and ecological variation. Gene flow appears widespread throughout the range, despite the apparently fragmented nature of the habitats used by this species. Patterns of haplotype variation between selected and neutral genomic regions suggest that evolution associated with climate adaptation is polygenic, resulting from the independent spread of alleles throughout the established range of this species, rather than the colonization of pre-adapted genotypes from coastal populations. These data suggest that rapid responses to climate change do not depend on the availability of pre-adapted genotypes. Instead, the evolution of novel forms of biotic interaction in A. agestis has occurred during range expansion, through the assembly of novel genotypes from alleles from multiple localities.

Patterns of reproduction and autozygosity distinguish the breeding from nonbreeding gray wolves of Yellowstone National Park.

For species of management concern, accurate estimates of inbreeding and associated consequences on reproduction are crucial for predicting their future viability. However, few studies have partitioned this aspect of genetic viability with respect to reproduction in a group-living social mammal. We investigated the contributions of foundation stock lineages, putative fitness consequences of inbreeding, and genetic diversity of the breeding versus nonreproductive segment of the Yellowstone National Park gray wolf population. Our dataset spans 25 years and seven generations since reintroduction, encompassing 152 nuclear families and 329 litters. We found more than 87% of the pedigree foundation genomes persisted and report influxes of allelic diversity from two translocated wolves from a divergent source in Montana. As expected for group-living species, mean kinship significantly increased over time but with minimal loss of observed heterozygosity. Strikingly, the reproductive portion of the population carried a significantly lower genome-wide inbreeding coefficients, autozygosity, and more rapid decay for linkage disequilibrium relative to the nonbreeding population. Breeding wolves had significantly longer lifespans and lower inbreeding coefficients than nonbreeding wolves. Our model revealed that the number of litters was negatively significantly associated with heterozygosity (R = -0.11). Our findings highlight genetic contributions to fitness, and the importance of the reproductively active individuals in a population to counteract loss of genetic variation in a wild, free-ranging social carnivore. It is crucial for managers to mitigate factors that significantly reduce effective population size and genetic connectivity, which supports the dispersion of genetic variation that aids in rapid evolutionary responses to environmental challenges.

Anthropogenic Change and the Process of Speciation.

Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and "despeciation" dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.

Evolutionary response of cold‐adapted chasmophytic plants to Quaternary climatic oscillations in the Mountains of Central Asia (a world hotspot of biodiversity)

AbstractAimPast climatic oscillations are the main driving force of evolutionary changes in alpine species. Species' response to paleoclimatic oscillations is crucial in forecasting their future response in face of climate warming. The aim of this research is to explore the effect of climatic fluctuations on the evolutionary history, demography, and distribution of high‐mountain bellflowers (Campanula lehmannianacomplex), the flagship and taxonomically problematic members of chasmophytic vegetation within an underexplored biodiversity hotspot, the Mountains of Central Asia.LocationCentral Asia (Tian Shan, Alai and Zeravshan‐Hissar Mountains).MethodsWe used molecular data (ITS, cpDNA, DArTseq‐based SNPs) of 262 individuals (70 for the phylogeny reconstruction, and 247 from 31 localities for population studies). We analysed the data using phylogenetic and molecular clock reconstructions, coalescent simulations, and ecological niche modelling.ResultsTertiary isolation between the Tian‐Shanian and Pamir‐Alaian populations led to the differentiation of the two main lineages (~5–6 Mya) corresponding toC. eugeniaeandC. lehmanniana, whereas further Quaternary isolation into subregions led to intraspecific genetic differentiation, which starts almost simultaneously for both species (~2.7–1.5 Mya). The relatively small genetic admixture among populations indicates rare historic events of connectivity. In response to Holocene warming, the analysed species experienced a substantial decline in effective population size. Currently, the distribution of both taxa is highly influenced by precipitation in the coldest and driest quarters.Main ConclusionsOur results highlight a general principle that glacial–interglacial cycles and contemporary island‐like habitats distribution, shape the genomic variation of high‐mountain species. The similar declining demographic trend of examined taxa may suggest the overall response to ongoing climate warming. The results underline also the urgent need for conservation action in alpine regions to preserve their biodiversity.

Evolutionary history and climate co‐determine the geographical variation in pollination modes of angiosperms in China

AbstractAimPollination is an essential stage of angiosperm reproduction, and the mode of pollination plays a major role in driving evolutionary and ecological responses of plants to environmental changes. However, the effects of climate, evolutionary history and floral traits (i.e. plant sexual systems) on pollination mode variation remain unclear. Here, we explored the biogeographic patterns in pollination mode frequency and tested the hypothesis that insect pollination prevails in warm humid regions with old floras due to high pollinator dependence, whereas wind pollination is more frequent in arid regions with younger floras and is more strongly associated with dioecy.LocationChina.Time periodSince the Last Glacial Maximum.Major taxa studiedAngiosperms.MethodsUsing data on pollination modes and geographic ranges of 29,719 angiosperm species in China, we mapped the biogeographic pattern of pollination mode frequency. Phylogenetic logistic regressions and generalized linear mixed models were employed to evaluate the relative importance of climate, evolutionary history (represented by phylogenetic conservatism and grid‐level mean genus age) and sexual systems on variations in pollination modes across species and space.ResultsEvolutionary history was the strongest correlate of pollination mode variation across species and space. The proportion of insect‐pollinated species was higher in humid regions with old floras, but lower in arid regions with young floras. Evolutionary history and temperature dominated variations in pollination mode frequency in humid areas, while precipitation dominated in arid areas. Climate influenced geographic pattern in pollination mode frequency both directly and indirectly via its effects on species richness and plant sexual systems.Main ConclusionsOur results showed that geographic pattern in angiosperm pollination mode frequency is dominated by evolutionary history followed by climate, which extended previous findings of climate‐driven mechanisms. Our findings demonstrate the importance to incorporate evolutionary history in understanding the mechanisms underlying the functional biogeography of plant traits.

Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses.

Dalbergia cultrata Pierre Graham ex Benth (D. cultrata) is a precious rosewood tree species that grows in the tropical and subtropical regions of Asia. In this study, we used PacBio long-reading sequencing technology and Hi-C assistance to sequence and assemble the reference genome of D. cultrata. We generated 171.47 Gb PacBio long reads and 72.43 Gb Hi-C data and yielded an assembly of 10 pseudochromosomes with a total size of 690.99 Mb and Scaffold N50 of 65.76 Mb. The analysis of specific genes revealed that the triterpenoids represented by lupeol may play an important role in D. cultrata's potential medicinal value. Using the new reference genome, we analyzed the resequencing of 19 Dalbergia accessions and found that D. cultrata and D. cochinchinensis have the latest genetic relationship. Transcriptome sequencing of D. cultrata leaves grown under cold stress revealed that MYB transcription factor and E3 ubiquitin ligase may be playing an important role in the cold response of D. cultrata. Genome resources and identified genetic variation, especially those genes related to the biosynthesis of phytochemicals and cold stress response, will be helpful for the introduction, domestication, utilization, and further breeding of Dalbergia species.