A5003864505- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Plant and animal studies
- Species Distribution and Climate Change
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- Classical Antiquity Studies
- Animal Behavior and Reproduction
- Forest Management and Policy
- Ecology and Vegetation Dynamics Studies
- Forest ecology and management
- Wildlife Ecology and Conservation
- Ancient Near East History
- Gut microbiota and health
- Evolutionary Game Theory and Cooperation
- Mitochondrial Function and Pathology
- Microbial Community Ecology and Physiology
- Chromosomal and Genetic Variations
- Marine and fisheries research
- Organic Chemistry Synthesis Methods
- Plant Water Relations and Carbon Dynamics
- Genetic Associations and Epidemiology
McGill University
2011-2025
Cornell University
2016-2025
San Jose State University
2010-2015
Centre National de la Recherche Scientifique
2014
Centre d'Écologie Fonctionnelle et Évolutive
2014
With the desire to model population genetic processes under increasingly realistic scenarios, forward simulations have become a critical part of toolbox modern evolutionary biology. The SLiM simulation framework is one most powerful and widely used tools in this area. However, its foundation Wright–Fisher has been found pose an obstacle implementing many types models; it difficult adapt model, with assumptions, modeling ecologically scenarios such as explicit space, overlapping generations,...
Modern population genomic datasets hold immense promise for revealing the evolutionary processes operating in natural populations, but a crucial prerequisite this goal is ability to model realistic scenarios and predict their expected patterns data. To that end, we present SLiM 2: an simulation framework combines powerful, fast engine forward genetic simulations with capability of modeling wide variety complex scenarios. achieves flexibility through scriptability, which provides control over...
Abstract With the desire to model population genetic processes under increasingly realistic scenarios, forward simulations have become a critical part of toolbox modern evolutionary biology. The SLiM simulation framework is one most powerful and widely used tools in this area. However, its foundation Wright–Fisher has been found pose an obstacle implementing many types models; it difficult adapt model, with assumptions, modeling ecologically scenarios such as explicit space, overlapping...
Abstract There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites complex demography, population structure, and ecological interactions. Such can generally be implemented as individual‐based forward simulations, but the large computational overhead of these often makes simulation whole chromosome sequences in populations infeasible. This situation presents important obstacle field that requires conceptual...
AbstractThe SLiM software framework for genetically explicit forward simulation has been widely used in population genetics. However, it largely restricted to modeling only a single species, which limited its broader utility evolutionary biology. Indeed, our knowledge no general-purpose, flexible exists that provides support simulating multiple species while also providing other key features, such as genetics and continuous space. The lack of ability model higher biological levels...
Despite the potential for rapid evolution, stasis is commonly observed over geological timescales—the so-called "paradox of stasis." This paradox would be resolved if stabilizing selection were common, but infrequently detected in natural populations. We hypothesize a simple solution to this apparent disconnect: hard detect empirically once populations have adapted fitness peak. To test hypothesis, we developed an individual-based model population evolving under invariant function....
Abstract The potential of reef‐building corals to adapt increasing sea‐surface temperatures is often debated but has rarely been comprehensively modeled on a region‐wide scale. We used individual‐based simulations model adaptation warming in coral metapopulation comprising 680 reefs and representing the whole Central Indo‐West Pacific. Encouragingly, some reefs—most notably Vietnam, Japan, Taiwan, New Caledonia southern half Great Barrier Reef—exhibited high capacity for and, our model,...
Gradient Forest (GF) is a machine learning algorithm designed to analyze spatial patterns of biodiversity as function environmental gradients. An offset measure between the GF-predicted association adapted alleles and new environment (GF Offset) increasingly being used predict loss environmentally under rapid change, but remains mostly untested for this purpose. Here, we explore robustness GF Offset assumption violations, its relationship measures fitness, using SLiM simulations with...
Across many species where inversions have been implicated in local adaptation, genomes often evolve to contain multiple, large that arise early divergence. Why this occurs has yet be resolved. To address gap, we built forward-time simulations which flexible characteristics and can invade a metapopulation undergoing spatially divergent selection for highly polygenic trait. In our simulations, typically arose divergence, captured standing genetic variation upon mutation, then accumulated...
Populations must continuously respond to environmental change or risk extinction. These responses can be measured as phenotypic rates of change, which allow researchers predict their contemporary evolutionary responses. In 1999, a database in wild populations was compiled. Since then, have used (and expanded) this examine the function features study system (i.e., population set populations, given species, that experienced specific driver disturbance), traits, and methodological approaches....
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes...
Abstract As biodiversity loss outpaces recovery, conservationists are increasingly turning to novel tools for preventing extinction, including cloning and in vitro gametogenesis of biobanked cells. However, restoration populations can be hindered by low genetic diversity deleterious load. The persistence the northern white rhino ( Ceratotherium simum cottoni ) now depends on cryopreserved cells 12 individuals. These banked genomes have higher than southern rhinos C. s. ), a sister subspecies...
The McDonald-Kreitman (MK) test is a widely used method for quantifying the role of positive selection in molecular evolution. One key shortcoming this lies its sensitivity to presence slightly deleterious mutations, which can severely bias estimates. An asymptotic version MK was recently introduced that addresses problem by evaluating polymorphism levels different mutation frequencies separately, and then extrapolating function fitted data. Here, we present asymptoticMK, web-based...
Additive Manufacturing (AM) is currently a frequently discussed topic in the industry, with promising benefits for development and manufacturing of high-value products. This paper aims to investigate structure application purposes additive manufacturing, especially Laser-based Powder Bed Fusion (LPBF), showing additional values created by technology. Therefore concept "Enablers Objectives" linked use AM developed. Based on this concept, 128 cases from industry applications are investigated....
Simulation of genomic data is a key tool in population genetics, yet, to date, there no forward-in-time simulator bacterial populations that both computationally efficient and adaptable wide range scenarios.Here we demonstrate how simulate with SLiM, built for eukaryotes.SLiM has gained many users recent years, due its speed power, extensive documentation showcasing various scenarios it can simulate.This paper focuses on simple demographic scenario, explore unique aspects modeling bacteria...
One of the goals population genetics is to understand how evolutionary forces shape patterns genetic variation over time. However, because populations evolve across both time and space, most processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution resources. This dimension often neglected, partly due lack tools specifically designed for building evaluating complex spatio-temporal models. To address...
Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations incorporating realistic selection along heterogeneous genomes in complex demographic histories are challenging, limiting our ability to benchmark statistical methods aimed at detecting and explore theoretical predictions. stdpopsim community-maintained simulation library already provides an extensive catalog species-specific population models. Here we present major...
A new 1,5-dipyridyl verdazyl, synthesized from the corresponding dipyridyl hydrazone, coordinates nickel(II) to form a structurally characterized, pseudooctahedral complex analogous Ni(terpy)22+. The unusually short Ni–verdazyl distance results in strong ferromagnetic exchange (JNi–rad = +300, Jrad–rad +160 cm−1) between all three paramagnetic species along with metal–ligand charge transfer band electronic spectrum.
The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population modeling. However, as complex piece of software with many features that allow simulating diverse assortment evolutionary models, its initial learning curve can difficult. Here we provide step-by-step demonstration how build simple model in 3, help new users get started. We will begin panmictic neutral model, up the evolution polygenic quantitative trait under selection an environmental...
ABSTRACT Individual‐based simulation has become an increasingly crucial tool for many fields of population biology. However, continuous geography is important to applications, and implementing realistic stable simulations in space presents a variety difficulties, from modeling choices computational efficiency. This paper aims be practical guide spatial simulation, helping researchers implement individual‐based avoid common pitfalls. To do this, we delve into mechanisms mating, reproduction,...
Gene drives offer revolutionary potential for the management of problematic plant populations, such as invasive weeds and herbicide-resistant species, by rapidly spreading desired genetic alterations. Two recent studies have provided first experimental demonstrations engineered CRISPR gene drive systems in plants (CAIN ClvR). However, successful application field will critically depend on an accurate understanding plant-specific life-history traits, especially seed dormancy, a ubiquitous yet...
Divergent adaptation to different environments can promote speciation, and it is thus important consider spatial structure in models of speciation. Earlier theoretical work, however, has been limited particularly simple types (linear environmental gradients spatially discrete metapopulations), leaving unaddressed the effects more realistic patterns landscape heterogeneity, such as nonlinear continuous patchiness. To elucidate consequences complex landscapes, we adapt an established explicit...
Temporal variation in phenotypic selection is often attributed to environmental change causing movements of the adaptive surface relating traits fitness, but this connection rarely established empirically. Fluctuating can be measured by variance and autocorrelation directional gradients through time. However, dynamics these depend not only on changes altering fitness surface, also evolution distribution. Therefore, it unclear what extent variability inform us about underlying drivers their...
Scientific research is often conceptually divided into empirical and theoretical approaches, researchers specialize as empiricists or theorists. Both approaches are essential to scientific progress, but interactions between the two groups have at times seemed problematic. I present results from a recent survey of 614 scientists (predominantly ecologists evolutionary biologists) regarding work. Some overall themes emerged these results. One theme widespread mutual lack trust, understanding,...