Evolution In Changing Environments Research Articles

Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen

Copy number variation (CNV) can drive rapid evolution in changing environments. In microbial pathogens, such adaptation is a key factor underpinning epidemics and colonization of new niches. However, the genomic determinants of such adaptation remain poorly understood. Here, we systematically investigate CNVs in a large genome sequencing dataset spanning a worldwide collection of 1104 genomes from the major wheat pathogen Zymoseptoria tritici. We found overall strong purifying selection acting on most CNVs. Genomic defense mechanisms likely accelerated gene loss over episodes of continental colonization. Local adaptation along climatic gradients was likely facilitated by CNVs affecting secondary metabolite production and gene loss in general. One of the strongest loci for climatic adaptation is a highly conserved gene of the NAD-dependent Sirtuin family. The Sirtuin CNV locus localizes to an ~68-kb Starship mobile element unique to the species carrying genes highly expressed during plant infection. The element has likely lost the ability to transpose, demonstrating how the ongoing domestication of cargo-carrying selfish elements can contribute to selectable variation within populations. Our work highlights how standing variation in gene copy numbers at the global scale can be a major factor driving climatic and metabolic adaptation in microbial species.

Assessment of the spatiotemporal evolution and driving forces of meteorological drought in the North China Plain

AbstractWith the changing trend of global temperature increase, the occurrence of drought events can no longer be ignored. An investigation of the spatiotemporal evolution characteristics of meteorological droughts and their responses to climatic variables can elucidate the mechanisms of the water cycle evolution in changing environments. In the present study, the standardized precipitation evapotranspiration index was used to characterize meteorological drought in the North China Plain (NCP) from 1970 to 2020. The spatiotemporal patterns of meteorological drought were analysed, and the contributions of climatic factors on annual and seasonal time scale drought evolution were determined. The results revealed that meteorological drought showed a decreasing trend (−0.07/10a) in the NCP from 1970 to 2020 and the most severe meteorological drought occurred in winter, with 56.56% of the region experiencing an increased drought trend in this season. Significant trends were identified for mean temperature (Tmean), temperature difference, and wind speed in the drought trend evolution. Precipitation (P) and Tmean were the primary controlling factors of the drought evolution. The strongest effect on drought change were exerted by P in spring (contribution [Con]: 1.57%), summer (Con: 1.79%) and autumn (Con: 2.43%), and the negative contribution of Tmean in winter (Con: −3.64%) was greater than the positive contribution of P (Con: 2.69%). The contribution of climatic variables to drought were increased by regional altitude difference. The results reveal a novel explanatory mechanism of climate change's effects on drought.

Driven Disordered Systems Approach to Biological Evolution in Changing Environments

Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organism's environment, and evolution in changing environments is still poorly understood. We study a particular model of antibiotic resistance evolution in bacteria where the antibiotic concentration is an environmental parameter and the fitness landscapes incorporate tradeoffs between adaptation to low and high antibiotic concentration. With evolutionary dynamics that follow fitness gradients, the evolution of the system under slowly changing antibiotic concentration resembles the athermal dynamics of disordered physical systems under quasistatic external drives. Specifically, our model can be described as a system with interacting hysteretic elements, and it exhibits effects such as hysteresis loops and memory formation under antibiotic concentration cycling. Using methods familiar from studies in this field, we derive a number of analytical and numerical results. Our approach provides a general framework for studying motifs of evolutionary dynamics in biological systems in a changing environment.

Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex

Dinoflagellates of the Symbiodiniaceae family encompass diverse symbionts that are critical to corals and other species living in coral reefs. It is well known that sexual reproduction enhances adaptive evolution in changing environments. Although genes related to meiotic functions were reported in Symbiodiniaceae, cytological evidence of meiosis and fertilisation are however yet to be observed in these taxa. Using transcriptome and genome data from 21 Symbiodiniaceae isolates, we studied genes that encode proteins associated with distinct stages of meiosis and syngamy. We report the absence of genes that encode main components of the synaptonemal complex (SC), a protein structure that mediates homologous chromosomal pairing and class I crossovers. This result suggests an independent loss of canonical SCs in the alveolates, that also includes the SC-lacking ciliates. We hypothesise that this loss was due in part to permanently condensed chromosomes and repeat-rich sequences in Symbiodiniaceae (and other dinoflagellates) which favoured the SC-independent class II crossover pathway. Our results reveal novel insights into evolution of the meiotic molecular machinery in the ecologically important Symbiodiniaceae and in other eukaryotes.

A model for the interplay between plastic tradeoffs and evolution in changing environments

Performance tradeoffs are ubiquitous in both ecological and evolutionary modeling, yet they are usually postulated and built into fitness and ecological landscapes. However, tradeoffs depend on genetic background and evolutionary history and can themselves evolve. We present a simple model capable of capturing the key feedback loop: evolutionary history shapes tradeoff strength, which, in turn, shapes evolutionary future. One consequence of this feedback is that genomes with identical fitness can have different evolutionary properties shaped by prior environmental exposure. Another is that, generically, the best adaptations to one environment may evolve in another. Our simple framework bridges the gap between the phenotypic Fisher's Geometric Model and the genotypic properties, such as modularity and evolvability, and can serve as a rich playground for investigating evolution in multiple or changing environments.

Hybridization increases population variation during adaptive radiation

Adaptive radiations are prominent components of the world's biodiversity. They comprise many species derived from one or a small number of ancestral species in a geologically short time that have diversified into a variety of ecological niches. Several authors have proposed that introgressive hybridization has been important in the generation of new morphologies and even new species, but how that happens throughout evolutionary history is not known. Interspecific gene exchange is expected to have greatest impact on variation if it occurs after species have diverged genetically and phenotypically but before genetic incompatibilities arise. We use a dated phylogeny to infer that populations of Darwin's finches in the Galápagos became more variable in morphological traits through time, consistent with the hybridization hypothesis, and then declined in variation after reaching a peak. Some species vary substantially more than others. Phylogenetic inferences of hybridization are supported by field observations of contemporary hybridization. Morphological effects of hybridization have been investigated on the small island of Daphne Major by documenting changes in hybridizing populations of Geospiza fortis and Geospiza scandens over a 30-y period. G. scandens showed more evidence of admixture than G. fortis Beaks of G. scandens became progressively blunter, and while variation in length increased, variation in depth decreased. These changes imply independent effects of introgression on 2, genetically correlated, beak dimensions. Our study shows how introgressive hybridization can alter ecologically important traits, increase morphological variation as a radiation proceeds, and enhance the potential for future evolution in changing environments.

Stranger in a strange land: an optimal-environments account of evolutionary mismatch

In evolutionary medicine, researchers characterize some outcomes as evolutionary mismatch. Mismatch problems arise as the result of organisms living in environments to which they are poorly adapted, typically as the result of some rapid environmental change. Depression, anxiety, obesity, myopia, insomnia, breast cancer, dental problems, and numerous other negative health outcomes have all been characterized as mismatch problems. The exact nature of evolutionary mismatch itself is unclear, however. This leads to a lack of clarity about the sorts of problems that evolutionary mismatch can actually explain. Resolving this challenge is important not only for the evolutionary health literature, but also because the notion of evolutionary mismatch involves central concepts in evolutionary biology: fitness, evolution in changing environments, and so forth. In this paper, I examine two characterizations of mismatch currently in the literature. I propose that we conceptualize mismatch as a relation between an optimal environment and an actual environment. Given an organism and its particular physiology, the optimal environment is the environment in which the organism’s fitness is maximized: in other words, the optimal environment is that in which the organism’s fitness is as high as it can possibly be. The actual environment is the environment in which the organism actually finds itself. To the extent that there is a discordance between the organism’s actual and optimal environments, there is an evolutionary mismatch. In the paper, I show that this account of mismatch gives us the right result when other accounts fail, and provides useful targets for investigation.

Using the resurrection approach to understand contemporary evolution in changing environments.

The resurrection approach of reviving ancestors from stored propagules and comparing them with descendants under common conditions has emerged as a powerful method of detecting and characterizing contemporary evolution. As climatic and other environmental conditions continue to change at a rapid pace, this approach is becoming particularly useful for predicting and monitoring evolutionary responses. We evaluate this approach, explain the advantages and limitations, suggest best practices for implementation, review studies in which this approach has been used, and explore how it can be incorporated into conservation and management efforts. We find that although the approach has thus far been used in a limited number of cases, these studies have provided strong evidence for rapid contemporary adaptive evolution in a variety of systems, particularly in response to anthropogenic environmental change, although it is far from clear that evolution will be able to rescue many populations from extinction given current rates of global changes. We also highlight one effort, known as Project Baseline, to create a collection of stored seeds that can take advantage of the resurrection approach to examine evolutionary responses to environmental change over the coming decades. We conclude that the resurrection approach is a useful tool that could be more widely employed to examine basic questions about evolution in natural populations and to assist in the conservation and management of these populations as they face continued environmental change.

Environmental effects on the structure of the G-matrix.

Genetic correlations between traits determine the multivariate response to selection in the short term, and thereby play a causal role in evolutionary change. Although individual studies have documented environmentally induced changes in genetic correlations, the nature and extent of environmental effects on multivariate genetic architecture across species and environments remain largely uncharacterized. We reviewed the literature for estimates of the genetic variance-covariance (G) matrix in multiple environments, and compared differences in G between environments to the divergence in G between conspecific populations (measured in a common garden). We found that the predicted evolutionary trajectory differed as strongly between environments as it did between populations. Between-environment differences in the underlying structure of G (total genetic variance and the relative magnitude and orientation of genetic correlations) were equal to or greater than between-population differences. Neither environmental novelty, nor the difference in mean phenotype predicted these differences in G. Our results suggest that environmental effects on multivariate genetic architecture may be comparable to the divergence that accumulates over dozens or hundreds of generations between populations. We outline avenues of future research to address the limitations of existing data and characterize the extent to which lability in genetic correlations shapes evolution in changing environments.

Evolution in changing environments: modifiers of mutation, recombination, and migration.

The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection and the signatures of environmental changes in the patterns of this variation have been important areas of focus in population genetics. On one hand, periods of constant selection pull the genetic makeup of populations toward local fitness optima. On the other, to cope with changes in the selection regime, populations may evolve mechanisms that create a diversity of genotypes. By tuning the rates at which variability is produced--such as the rates of recombination, mutation, or migration--populations may increase their long-term adaptability. Here we use theoretical models to gain insight into how the rates of these three evolutionary forces are shaped by fluctuating selection. We compare and contrast the evolution of recombination, mutation, and migration under similar patterns of environmental change and show that these three sources of phenotypic variation are surprisingly similar in their response to changing selection. We show that the shape, size, variance, and asymmetry of environmental fluctuation have different but predictable effects on evolutionary dynamics.

The implications of nongenetic inheritance for evolution in changing environments.

Nongenetic inheritance is a potentially important but poorly understood factor in population responses to rapid environmental change. Accumulating evidence indicates that nongenetic inheritance influences a diverse array of traits in all organisms and can allow for the transmission of environmentally induced phenotypic changes (‘acquired traits’), as well as spontaneously arising and highly mutable variants. We review models of adaptation to changing environments under the assumption of a broadened model of inheritance that incorporates nongenetic mechanisms of transmission, and survey relevant empirical examples. Theory suggests that nongenetic inheritance can increase the rate of both phenotypic and genetic change and, in some cases, alter the direction of change. Empirical evidence shows that a diversity of phenotypes – spanning a continuum from adaptive to pathological – can be transmitted nongenetically. The presence of nongenetic inheritance therefore complicates our understanding of evolutionary responses to environmental change. We outline a research program encompassing experimental studies that test for transgenerational effects of a range of environmental factors, followed by theoretical and empirical studies on the population-level consequences of such effects.

Feeding behavior of two ommastrephid squids Ommastrephes bartramii and Sthenoteuthis oualaniensis off Hawaii

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 318:229-235 (2006) - doi:10.3354/meps318229 Feeding behavior of two ommastrephid squids Ommastrephes bartramii and Sthenoteuthis oualaniensis off Hawaii Matthew Parry* Pacific Islands Regional Office, National Oceanic and Atmospheric Administration, 1601 Kapiolani Boulevard, Suite 1110 Honolulu, Hawaii 96814-0047, USA *Email: matthew.parry@noaa.gov ABSTRACT: The feeding behaviors of squids Ommastrephes bartramii (n = 315) and Sthenoteuthis oualaniensis (n = 280), collected during yearly 2 wk cruises from 1996 to 2001, were compared. Fish and squid prey dominated the stomach contents and were identified from otoliths and beaks, respectively. A total of 2561 otoliths and 424 beaks were recovered; 84% of O. bartramii stomachs contained otoliths while 54% contained cephalopod beaks. For S. oualaniensis, 75% of stomachs contained otoliths while 34% contained cephalopod beaks. Myctophidae were the most prevalent fish prey item for both species in frequency and abundance; however, O. bartramii fed on a wider range of prey items than S. oualaniensis at the family and species level. The myctophid Symbolophorus evermanni was a substantial prey item for both species. Both predators fed substantially on the squid families Onychoteuthidae and Enoploteuthidae, but O. bartramii fed on a wider range of squid prey items than S. oualaniensis. Levins’ (1968; ‘Evolution in changing environments’, Princeton University Press) standardized measure of niche breadth was greater for O. bartramii than for S. oualaniensis when calculated using either otoliths (0.56 vs. 0.086) or beaks (0.22 vs. 0.097). MacArthur & Levins’ (1967; Am Nat 101:377–385) measure of niche overlap of S. oualaniensis on O. bartramii was greater than that of O. bartramii on S. oualaniensis, for both fish otoliths (1.16 vs. 0.22) and squid beaks (0.93 vs. 0.46). These results suggested that O. bartramii is a more generalized predator than S. oualaniensis. Competition for food resources appears low between O. bartramii and S. oualaniensis where they overlap in the North Pacific. KEY WORDS: Ommastrephidae · Squid · Feeding behavior · Hawaii · Ommastrephes bartramii · Sthenoteuthis oualaniensis · Myctophidae · Trophic ecology · Otoliths · Beaks Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 318. Online publication date: August 03, 2006 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2006 Inter-Research.

Environmental stress, adaptation and evolution: an overview

Extreme environments and adaptation.- The evolution of plants in metal-contaminated environments.- Responses of aquatic organisms to pollutant stress: Theoretical and practical implications.- Conifers from the cold.- Genetic variation and environmental stress.- Phenotypic plasticity and fluctuating asymmetry as responses to environmental stress in the butterflyBicyclus anynana.- Environmental stress and the expression of genetic variation.- Worldwide latitudinal clines for the alcohol dehydrogenase polymorphism in Drosophila melanogaster: What is the unit of selection?.- Stress and metabolic regulation inDrosophila.- Acclimation and response to thermal stress.- Phenotypic and evolutionary adaptation of a model bacterial system to stressful thermal environments.- Ecological and evolutionary physiology of heat shock proteins and the stress response inDrosophila: Complementary insights from genetic engineering and natural variation.- High-temperature stress and the evolution of thermal resistance inDrosophila.- Stress, selection and extinction.- Genetic and environmental stress, and the persistence of populations.- Adaptation and extinction in changing environments.- Environmental stress and evolution: A theoretical study.- Stress, developmental stability and sexual selection.- Evolution and stress.- Genetic variability and adaptation to stress.- Stress-resistance genotypes, metabolic efficiency and interpreting evolutionary change.- The Plus ca change model: Explaining stasis and evolution in response to abiotic stress over geological timescales.

Community Assembly, Niche Conservatism, and Adaptive Evolution in Changing Environments

The widespread correspondence between phenotypic variation and environmental conditions, the “fit” of organisms to their environment, reflects the adaptive value of plant functional traits. Several processes contribute to these patterns: plasticity, ecological sorting, and adaptive evolution. This article addresses the importance of ecological sorting processes (community assembly, migration, habitat tracking, etc.) as primary causes of functional trait distributions at the local and landscape level. In relatively saturated communities, plants will establish and regenerate in environments to which they are well adapted, so their distributions, and the distributions of associated functional traits, will reflect the distribution of optimal or near‐optimal environmental conditions in space and time. The predicted evolutionary corollary of this process is that traits related to habitat occupancy, e.g., environmental tolerances, will be under stabilizing selection. This process contributes to the widely observed pattern of phylogenetic niche conservatism, i.e., ecological and phenotypic similarities of closely related species. Evidence for niche conservatism in plants is reviewed. Based on Jackson and Overpeck’s concept of the realized environment, I propose three scenarios in which a species’ distributional responses to environmental conditions will lead to a “mismatch” between its environmental tolerances and the environments it occupies, thus creating opportunities for adaptive evolution: (1) the colonization of “environmental islands” (habitats that are discontinuous in niche space) that require large adaptive shifts in tolerance of one or more environmental factors; (2) the persistence of “trailing‐edge” populations in species tracking changing climate, if barriers to dispersal of competitors prevent competitive exclusion in the deteriorating conditions; and (3) responses to changes in the realized environment in multidimensional niche space, in which species are predicted to track environmental factors for which they exhibit narrow tolerances and exhibit adaptive evolutionary response along axes where they exhibit greater niche breadth. These three scenarios provide a conceptual framework that emphasizes the role of ecological sorting processes and stabilizing selection as the context for understanding opportunities for adaptive evolution in heterogeneous and changing environments.

Evolution in changing environments: the "synthetic" work of Clausen, Keck, and Hiesey.

The studies of Clausen, Keck, and Hiesey (CKH) have been widely cited as exemplars of ecotypic differentiation in textbooks and in the primary literature. However, the scope of their findings and achievements is significantly greater than this. In this paper we analyze the research program of CKH, highlighting their major findings during the years when the modern synthesis of evolution was taking shape. That synthesis, curiously, drew little from their examples, although their studies at the Carnegie Institution represent conceptual and methodological work that is still relevant. The works of CKH not only embodied the principles of the nascent synthesis, but often provided needed supporting data. Their classic work, especially on Achillea and Potentilla, produced abundant evidence on population differentiation of many quantitative traits and plant phenotypes, as well as demonstrating the now commonly reported distinction between environmental and genetic determination of traits. Their ecological genetic investigations of quantitative traits in plants were in sharp contrast to contemporaneous animal studies on adaptation that focused on discrete polymorphisms--with correspondingly little influence of the environment on phenotypic expression. Of utmost importance was the demonstration by CKH of adaptive differentiation by natural selection and their approaches to understanding the genetic structure of populations.

Organic Selection: Proximate Environmental Effects on the Evolution of Morphology and Behaviour

Organic selection (the Baldwin Effect) by which an environmentally elicitedphenotypic adaptation comes under genotypic control following selectionwas proposed independently in 1896 by the psychologists James Baldwinand Conwy Lloyd Morgan and by the paleontologist Henry Fairfield Osborn.Modified forms of organic selection were proposed as autonomization bySchmalhausen in 1938, as genetic assimilation by Waddington in 1942, andas an explanation for evolution in changing environments or for speciationby Matsuda and West-Eberhard in the 1980s. Organic selection as amechanism mediating proximate environmental effects on the evolution ofmorphology and behaviour is the topic of this essay. Discussion includesthe context in which organic selection was proposed, Lamarckian or neo-Lamarckian implications of organic selection, Waddington’s experimentalstudies demonstrating the existence and efficacy of genetic assimilation,stabilizing selection and norms of reaction favoured by Schmalhausen, andMatsuda’s search for a mechanism of organic selection in endocrine changesand in heterochrony.

Variation and Change in Behavioral Ecology

This paper argues for the importance of time in the behavioral ecology of changing environments; that is, how behavior changes in response to the time scale of environmental change. I distinguish between change, which occurs over time, and variation, which is measured instantaneously. Variation and change can be equated; this amounts to viewing a dynamical process as static. For example, a predator-prey oscillation involves changes, over time, in numbers of predators and prey. An atemporal measure of such changes might be the range of variation in population sizes, corresponding to the amplitude of the oscillation. Consideration of time scale tends to be submerged when variation is confounded with change. There are two reasons why time-dependent behavior merits further attention. First, it has important ecological consequences. Second, in the theory of evolution in changing environments, questions of the time scales of phenotypic and environmental change are crucial. But such questions have received less attention in behavioral ecology. A further emphasis on temporal factors is needed to link empirical, behavioral studies of changing environments with theoretical, evolutionary ones. After providing some definitions, to clarify what is meant here by time-dependent behavioral responses, variation, and change, I use some examples of the behavior of seed-eating ants to illustrate the ecological importance of time-dependent behavioral change. The following section reviews how current work on behavior in changing environments treats questions of variation and change, arguing that this work emphasizes instantaneous variation rather than temporal change. Finally, I consider how models of phenotypic response to changing environments, derived from other fields of evolutionary ecology, have explicitly considered temporal factors, and how these models might be extended to behavioral ecology.