scholarly journals RangeShiftR: an R package for individual‐based simulation of spatial eco‐evolutionary dynamics and species' responses to environmental changes

Ecography ◽  
2021 ◽  
Author(s):  
Anne‐Kathleen Malchow ◽  
Greta Bocedi ◽  
Stephen C. F. Palmer ◽  
Justin M. J. Travis ◽  
Damaris Zurell
Keyword(s):  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
R Package ◽  
Species Responses ◽  
Individual Based Simulation

scholarly journals RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and species’ responses to environmental change

2020 ◽  
Author(s):  
Anne-Kathleen Malchow ◽  
Greta Bocedi ◽  
Stephen C. F. Palmer ◽  
Justin M. J. Travis ◽  
Damaris Zurell
Keyword(s):  
Evolutionary Dynamics ◽  
Planning Process ◽  
Environmental Changes ◽  
R Package ◽  
Simulation Software ◽  
Model Specification ◽  
Model Complexity ◽  
List Type ◽  
Species Responses ◽  
Individual Based Simulation

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.

RangeShifter: a platform for modelling spatial eco-evolutionary dynamics and species' responses to environmental changes

2014 ◽  
Vol 5 (4) ◽  
pp. 388-396 ◽  
Author(s):  
Greta Bocedi ◽  
Stephen C.F. Palmer ◽  
Guy Pe'er ◽  
Risto K. Heikkinen ◽  
Yiannis G. Matsinos ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Species Responses

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

Ecography ◽  
2021 ◽  
Author(s):  
Greta Bocedi ◽  
Stephen C. F. Palmer ◽  
Anne‐Kathleen Malchow ◽  
Damaris Zurell ◽  
Kevin Watts ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Species Responses

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

2021 ◽  
Vol 12 (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.

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

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.

scholarly journals Fragmentation mediates thermal habitat choice in ciliate microcosms

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.

scholarly journals There and Back to the Present: An Evolutionary Tale on Biological Diversity

2021 ◽  
Author(s):  
Leandro Duarte ◽  
Gabriel Nakamura ◽  
Vanderlei Debastiani ◽  
Renan Maestri ◽  
Maria Joao Veloso da Costa Ramos Pereira ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Environmental Gradients ◽  
Dispersal Limitation ◽  
R Package ◽  
Analytical Framework ◽  
Niche Evolution ◽  
Ecological Patterns ◽  
Local Species ◽  
Individual Based Simulation ◽  
Approximate Bayesian

Ecologists often agree on the importance of macroevolution for niche-mediated distribution of biological diversity along environmental gradients. Yet, macroevolutionary diversification and dispersal in time and space generate uneven geographic distribution of phylogenetic pools, which affects the imprint let by macroevolution on local species pools. In this article we introduce an individual-based simulation approach coupled to Approximate Bayesian Computation (ABC) that allows to parameterize the adaptation rate of species niche positions along the evolution of a monophyletic lineage, and the intensity of dispersal limitation, associated with the distribution of biological diversity between assemblages potentially connected by dispersal (metacommunity). The analytical tool was implemented in an R package called mcfly. We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate adaptation rate and dispersal limitation parameters. Further, we evaluated the role played by niche evolution and dispersal limitation on species diversity distribution of Phyllostomidae bats across the Neotropics. The framework proposed here shed light on the links between niche evolution, dispersal limitation and the distribution of biological diversity, and thereby improved our understanding of evolutionary imprints on ecological patterns. Perhaps more importantly, it offers new possibilities for solving the eco-evolutionary puzzle.

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

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.

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

Pathogens ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 80 ◽  
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.

scholarly journals BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

2014 ◽  
Vol 5 (7) ◽  
pp. 701-707 ◽  
Author(s):  
Daniel L. Rabosky ◽  
Michael Grundler ◽  
Carlos Anderson ◽  
Pascal Title ◽  
Jeff J. Shi ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Dynamics ◽  
R Package
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