RangeShifter 2.0: an extended and enhanced platform for modelling spatial eco‐evolutionary dynamics and species' responses to environmental changes

AbstractReliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species’ distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses.We present RangeShiftR, an R package that provides flexible and fast simulations of spatial eco-evolutionary dynamics and species’ responses to environmental changes. It implements the individual-based simulation software RangeShifter for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package’s functionality, describe the underlying model structure with its main components and present a short example.RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with comprehensive documentation and elaborate tutorials to provide a low entry level. Thanks to the implementation of the core code in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible.The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification, and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.

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Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

Nature Communications ◽

10.1038/s41467-021-20958-2 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

H. De Kort ◽

J. G. Prunier ◽

S. Ducatez ◽

O. Honnay ◽

M. Baguette ◽

...

Keyword(s):

Genetic Diversity ◽

Life History ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Peripheral Populations ◽

Plant Dispersal ◽

Weak Support ◽

Animal Populations ◽

Plant Groups ◽

Conservation Genetic

AbstractUnderstanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

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Environmental changes dictate selection and nonspecific epistasis in an empirical phenotype-environment-fitness landscape

10.1101/2021.04.14.439889 ◽

2021 ◽

Author(s):

J.Z. Chen ◽

D.M. Fowler ◽

N. Tokuriki

Keyword(s):

Selection Pressure ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Fitness Landscape ◽

Resistance Level ◽

Phenotypic Changes ◽

Environmental Selection ◽

Selection Environment ◽

Data Points ◽

Environmental Dependence

SummaryThe fitness landscape, a function that maps genotypic and phenotypic changes to their effects on fitness, is an invaluable concept in evolutionary biochemistry. Though widely discussed, measurements of phenotype-fitness landscapes in proteins remain scarce. Here, we quantify all single mutational effects on fitness and phenotype (antibiotic resistance level) of VIM-2 β-lactamase (5600 variants) across a 64-fold range of ampicillin concentrations by deep mutational scanning. We then construct a phenotype-fitness landscape that takes variations in environmental selection pressure into account (a phenotype-environment-fitness landscape). We found that a simple, empirical landscape accurately models the ~39,000 mutational data points, which suggests the evolution of VIM-2 can be predicted based on the selection environment. Our landscape provides new quantitative knowledge on the evolution of the β-lactamases and proteins in general, particularly their evolutionary dynamics under sub-inhibitory antibiotic concentrations, as well as the mechanisms and environmental dependence of nonspecific epistasis.

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Fragmentation mediates thermal habitat choice in ciliate microcosms

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.2818 ◽

2020 ◽

Vol 287 (1919) ◽

pp. 20192818

Author(s):

Estelle Laurent ◽

Nicolas Schtickzelle ◽

Staffan Jacob

Keyword(s):

Habitat Fragmentation ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Tetrahymena Thermophila ◽

Habitat Choice ◽

Emigration And Immigration ◽

Dispersal Rate ◽

Thermal Habitat ◽

Twofold Increase ◽

Dynamics Of Populations

Habitat fragmentation is expected to reduce dispersal movements among patches as a result of increased inter-patch distances. Furthermore, since habitat fragmentation is expected to raise the costs of moving among patches in the landscape, it should hamper the ability or tendency of organisms to perform informed dispersal decisions. Here, we used microcosms of the ciliate Tetrahymena thermophila to test experimentally whether habitat fragmentation, manipulated through the length of corridors connecting patches differing in temperature, affects habitat choice. We showed that a twofold increase of inter-patch distance can as expected hamper the ability of organisms to choose their habitat at immigration. Interestingly, it also increased their habitat choice at emigration, suggesting that organisms become choosier in their decision to either stay or leave their patch when obtaining information about neighbouring patches gets harder. This study points out that habitat fragmentation might affect not only dispersal rate but also the level of non-randomness of dispersal, with emigration and immigration decisions differently affected. These consequences of fragmentation might considerably modify ecological and evolutionary dynamics of populations facing environmental changes.

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Remote Sensing Reveals Lasting Legacies of Land-Use by Small-Scale Foraging Communities in the Southwestern Indian Ocean

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.689399 ◽

2021 ◽

Vol 9 ◽

Author(s):

Dylan S. Davis ◽

Kristina Douglass

Keyword(s):

Remote Sensing ◽

Land Use ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Spatial Scales ◽

Small Scale ◽

Environment Interaction ◽

Human Environment ◽

Landscape Modification ◽

Geochemical Properties

Archaeologists interested in the evolution of anthropogenic landscapes have productively adopted Niche Construction Theory (NCT), in order to assess long-term legacies of human-environment interactions. Applications of NCT have especially been used to elucidate co-evolutionary dynamics in agricultural and pastoral systems. Meanwhile, foraging and/or highly mobile small-scale communities, often thought of as less intensive in terms of land-use than agropastoral economies, have received less theoretical and analytical attention from a landscape perspective. Here we address this lacuna by contributing a novel remote sensing approach for investigating legacies of human-environment interaction on landscapes that have a long history of co-evolution with highly mobile foraging communities. Our study is centered on coastal southwest Madagascar, a region inhabited by foraging and fishing communities for close to two millennia. Despite significant environmental changes in southwest Madagascar’s environment following human settlement, including a wave of faunal extinctions, little is known about the scale, pace and nature of anthropogenic landscape modification. Archaeological deposits in this area generally bear ephemeral traces of past human activity and do not exhibit readily visible signatures of intensive land-use and landscape modification (e.g., agricultural modifications, monumental architecture, etc.). In this paper we use high-resolution satellite imagery and vegetative indices to reveal a legacy of human-landscape co-evolution by comparing the characteristics – vegetative productivity and geochemical properties – of archaeological sites to those of locations with no documented archaeological materials. Then, we use a random forest (RF) algorithm and spatial statistics to quantify the extent of archaeological activity and use this analysis to contextualize modern-day human-environment dynamics. Our results demonstrate that coastal foraging communities in southwest Madagascar over the past 1,000 years have extensively altered the landscape. Our study thus expands the temporal and spatial scales at which we can evaluate human-environment dynamics on Madagascar, providing new opportunities to study early periods of the island’s human history when mobile foraging communities were the dominant drivers of landscape change.

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Evolutionary Dynamics in the RNA Bacteriophage Qβ Depends on the Pattern of Change in Selective Pressures

Pathogens ◽

10.3390/pathogens8020080 ◽

2019 ◽

Vol 8 (2) ◽

pp. 80 ◽

Cited By ~ 3

Author(s):

Pilar Somovilla ◽

Susanna Manrubia ◽

Ester Lázaro

Keyword(s):

Genetic Diversity ◽

Temperature Change ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Evolutionary Process ◽

Rate Of Change ◽

High Genetic Diversity ◽

Adaptive Mutations ◽

Beneficial Effects ◽

Selective Pressures

The rate of change in selective pressures is one of the main factors that determines the likelihood that populations can adapt to stress conditions. Generally, the reduction in the population size that accompanies abrupt environmental changes makes it difficult to generate and select adaptive mutations. However, in systems with high genetic diversity, as happens in RNA viruses, mutations with beneficial effects under new conditions can already be present in the population, facilitating adaptation. In this work, we have propagated an RNA bacteriophage (Qβ) at temperatures higher than the optimum, following different patterns of change. We have determined the fitness values and the consensus sequences of all lineages throughout the evolutionary process in order to establish correspondences between fitness variations and adaptive pathways. Our results show that populations subjected to a sudden temperature change gain fitness and fix mutations faster than those subjected to gradual changes, differing also in the particular selected mutations. The life-history of populations prior to the environmental change has great importance in the dynamics of adaptation. The conclusion is that in the bacteriophage Qβ, the standing genetic diversity together with the rate of temperature change determine both the rapidity of adaptation and the followed evolutionary pathways.

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Molecular and cellular bases of adaptation to a changing environment in microorganisms

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.1458 ◽

2016 ◽

Vol 283 (1841) ◽

pp. 20161458 ◽

Cited By ~ 42

Author(s):

Clara Bleuven ◽

Christian R. Landry

Keyword(s):

Molecular Mechanisms ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Variable Environment ◽

Adaptive Changes ◽

Molecular Change ◽

Emerging Trends ◽

Recent Emergence ◽

The Face ◽

Molecular Relationships

Environmental heterogeneity constitutes an evolutionary challenge for organisms. While evolutionary dynamics under variable conditions has been explored for decades, we still know relatively little about the cellular and molecular mechanisms involved. It is of paramount importance to examine these molecular bases because they may play an important role in shaping the course of evolution. In this review, we examine the diversity of adaptive mechanisms in the face of environmental changes. We exploit the recent literature on microbial systems because those have benefited the most from the recent emergence of genetic engineering and experimental evolution followed by genome sequencing. We identify four emerging trends: (i) an adaptive molecular change in a pathway often results in fitness trade-off in alternative environments but the effects are dependent on a mutation's genetic background; (ii) adaptive changes often modify transcriptional and signalling pathways; (iii) several adaptive changes may occur within the same molecular pathway but be associated with pleiotropy of different signs across environments; (iv) because of their large associated costs, macromolecular changes such as gene amplification and aneuploidy may be a rapid mechanism of adaptation in the short-term only. The course of adaptation in a variable environment, therefore, depends on the complexity of the environment but also on the molecular relationships among the genes involved and between the genes and the phenotypes under selection.

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The Ecology of Bacterial Genes and the Survival of the New

International Journal of Evolutionary Biology ◽

10.1155/2012/394026 ◽

2012 ◽

Vol 2012 ◽

pp. 1-14 ◽

Cited By ~ 17

Author(s):

M. Pilar Francino

Keyword(s):

Evolutionary Dynamics ◽

Environmental Changes ◽

Gene Families ◽

Relative Importance ◽

Gene Duplications ◽

Bacterial Genomes ◽

Selective Pressures ◽

Different Types ◽

Bacterial Genes ◽

Gains And Losses

Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.

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