An overview of the utility of population simulation software in molecular ecology

Genetic Simulation Resources: a website for the registration and discovery of genetic data simulators

(2013) B. Peng et al.   BIOINFORMATICS

Boosting forward-time population genetic simulators through genotype compression

(2013) Troy Ruths et al.   BMC BIOINFORMATICS

Rapid forward-in-time simulation at the chromosome and genome level

(2013) Andre J Aberer et al.   BMC BIOINFORMATICS

High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study

(2013) Sean M Hoban et al.   BMC BIOINFORMATICS

Achieving Conservation Science that Bridges the Knowledge-Action Boundary

(2013) CARLY N. COOK et al.   CONSERVATION BIOLOGY

SLiM: Simulating Evolution with Selection and Linkage

(2013) Philipp W. Messer   GENETICS

Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation

(2013) I. A. M. Marino et al.   MOLECULAR ECOLOGY

The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study

(2013) Sean M. Hoban et al.   MOLECULAR ECOLOGY

On the accumulation of deleterious mutations during range expansions

(2013) S. Peischl et al.   MOLECULAR ECOLOGY

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data

(2013) I. Paz-Vinas et al.   MOLECULAR ECOLOGY

Using genetic techniques to quantify reinvasion, survival andin situbreeding rates during control operations

(2013) A. J. Veale et al.   MOLECULAR ECOLOGY

A road map for molecular ecology

(2013) Rose L. Andrew et al.   MOLECULAR ECOLOGY

The Power to Detect Recent Fragmentation Events Using Genetic Differentiation Methods

(2013) Michael W. Lloyd et al.   PLoS One

Essential Biodiversity Variables

(2013) H. M. Pereira et al.   SCIENCE

Bringing genetic diversity to the forefront of conservation policy and management

(2013) Sean M. Hoban et al.   Conservation Genetics Resources

SimAdapt: an individual-based genetic model for simulating landscape management impacts on populations

(2013) François Rebaudo et al.   Methods in Ecology and Evolution

Population connectivity and genetic diversity of American marten (Martes americana) in the United States northern Rocky Mountains in a climate change context

(2012) Tzeidle N. Wasserman et al.   CONSERVATION GENETICS

A rare case of natural regeneration in butternut, a threatened forest tree, is parent and space limited

(2012) Sean M. Hoban et al.   CONSERVATION GENETICS

Sampling strategies for estimating brook trout effective population size

(2012) Andrew R. Whiteley et al.   CONSERVATION GENETICS

Long-distance gene flow and adaptation of forest trees to rapid climate change

(2012) Antoine Kremer et al.   ECOLOGY LETTERS

Understanding admixture patterns in supplemented populations: a case study combining molecular analyses and temporally explicit simulations in Atlantic salmon

(2012) Charles Perrier et al.   Evolutionary Applications

On the spatial scale of dispersal in coral reef fishes

(2012) O. Puebla et al.   MOLECULAR ECOLOGY

A simulation-based evaluation of methods for inferring linear barriers to gene flow

(2012) CHRISTOPHER BLAIR et al.   Molecular Ecology Resources

Rapid climate change and the rate of adaptation: insight from experimental quantitative genetics

(2012) Ruth G. Shaw et al.   NEW PHYTOLOGIST

Limited evolutionary rescue of locally adapted populations facing climate change

(2012) K. Schiffers et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Pre-Whaling Genetic Diversity and Population Ecology in Eastern Pacific Gray Whales: Insights from Ancient DNA and Stable Isotopes

(2012) S. Elizabeth Alter et al.   PLoS One

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

(2012) A. Keinan et al.   SCIENCE

Sample Planning Optimization Tool for conservation and population Genetics (SPOTG): a software for choosing the appropriate number of markers and samples

(2012) Sean Hoban et al.   Methods in Ecology and Evolution

Simulation of Molecular Data under Diverse Evolutionary Scenarios

(2012) Miguel Arenas   PLoS Computational Biology

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION-SELECTION BALANCE

(2011) Sam Yeaman et al.   EVOLUTION

Simulating the effects of climate change on population connectivity of American marten (Martes americana) in the northern Rocky Mountains, USA

(2011) T. N. Wasserman et al.   LANDSCAPE ECOLOGY

Estimating seed and pollen movement in a monoecious plant: a hierarchical Bayesian approach integrating genetic and ecological data

(2011) EMILY V. MORAN et al.   MOLECULAR ECOLOGY

Simulation modelling in landscape genetics: on the need to go further

(2011) NIKO BALKENHOL et al.   MOLECULAR ECOLOGY

Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern

(2011) ERIN L. LANDGUTH et al.   Molecular Ecology Resources

Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression

(2011) M. Currat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

(2011) Kirk E. Lohmueller et al.   PLoS Genetics

SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination

(2010) Nicolas Ray et al.   BIOINFORMATICS

How successful are plant species reintroductions?

(2010) Sandrine Godefroid et al.   BIOLOGICAL CONSERVATION

Applications of landscape genetics in conservation biology: concepts and challenges

(2010) Gernot Segelbacher et al.   CONSERVATION GENETICS

Habitat continuity and geographic distance predict population genetic differentiation in giant kelp

(2010) Filipe Alberto et al.   ECOLOGY

Early detection of population declines: high power of genetic monitoring using effective population size estimators

(2010) Tiago Antao et al.   Evolutionary Applications

Increased mortality can promote evolutionary adaptation of forest trees to climate change

(2010) Anna Kuparinen et al.   FOREST ECOLOGY AND MANAGEMENT

Modelling exploration of the future of European beech (Fagus sylvatica L.) under climate change—Range, abundance, genetic diversity and adaptive response

(2010) Koen Kramer et al.   FOREST ECOLOGY AND MANAGEMENT

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

(2010) L. Chikhi et al.   GENETICS

Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

(2010) T. I. Gossmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genetics reveals origin and number of founders in a biological invasion

(2010) GENTILE FRANCESCO FICETOLA et al.   MOLECULAR ECOLOGY

ABC as a flexible framework to estimate demography over space and time: some cons, many pros

(2010) G. BERTORELLE et al.   MOLECULAR ECOLOGY

High genetic diversity in the remnant island population of hihi and the genetic consequences of re-introduction

(2010) PATRICIA BREKKE et al.   MOLECULAR ECOLOGY

Genetic structure of a recent climate change-driven range extension

(2010) SAM C. BANKS et al.   MOLECULAR ECOLOGY

On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs

(2010) ANNA W. SANTURE et al.   MOLECULAR ECOLOGY

Use of resistance surfaces for landscape genetic studies: considerations for parameterization and analysis

(2010) STEPHEN F. SPEAR et al.   MOLECULAR ECOLOGY

Utility of computer simulations in landscape genetics

(2010) BRYAN K. EPPERSON et al.   MOLECULAR ECOLOGY

Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene

(2010) PAULA F. CAMPOS et al.   MOLECULAR ECOLOGY

Quantifying the lag time to detect barriers in landscape genetics

(2010) E. L. LANDGUTH et al.   MOLECULAR ECOLOGY

Combining genetic, historical and geographical data to reconstruct the dynamics of bioinvasions: application to the cane toad Bufo marinus

(2010) ARNAUD ESTOUP et al.   Molecular Ecology Resources

Ecosystem Services for 2020

(2010) C. Perrings et al.   SCIENCE

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

Introducing a ‘stochastic movement simulator’ for estimating habitat connectivity

(2010) Stephen C. F. Palmer et al.   Methods in Ecology and Evolution

Projecting genetic diversity and population viability for the fragmented orang-utan population in the Kinabatangan floodplain, Sabah, Malaysia

(2010) MW Bruford et al.   Endangered Species Research

Founder effect and bottleneck signatures in an introduced, insular population of elk

(2009) Kris J. Hundertmark et al.   CONSERVATION GENETICS

MHC diversity in bottlenecked populations: a simulation model

(2009) Maciej Jan Ejsmond et al.   CONSERVATION GENETICS

Simulation of Genes and Genomes Forward in Time

(2009) Antonio Carvajal-Rodriguez   CURRENT GENOMICS

PREDICTING ADAPTATION UNDER MIGRATION LOAD: THE ROLE OF GENETIC SKEW

(2009) Sam Yeaman et al.   EVOLUTION

TESTING PHYLOGEOGRAPHIC HYPOTHESES IN A EURO-SIBERIAN COLD-ADAPTED LEAF BEETLE WITH COALESCENT SIMULATIONS

(2009) Patrick Mardulyn et al.   EVOLUTION

pedagog: software for simulating eco-evolutionary population dynamics

(2009) JASON A. COOMBS et al.   Molecular Ecology Resources

cdpop: A spatially explicit cost distance population genetics program

(2009) ERIN L. LANDGUTH et al.   Molecular Ecology Resources

Stability Predicts Genetic Diversity in the Brazilian Atlantic Forest Hotspot

(2009) A. C. Carnaval et al.   SCIENCE

Skeeter Buster: A Stochastic, Spatially Explicit Modeling Tool for Studying Aedes aegypti Population Replacement and Population Suppression Strategies

(2009) Krisztian Magori et al.   PLoS Neglected Tropical Diseases

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS

quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation

(2008) S. Neuenschwander et al.   BIOINFORMATICS

Sensitivity Analyses of Spatial Population Viability Analysis Models for Species at Risk and Habitat Conservation Planning

(2008) ILONA R. NAUJOKAITIS-LEWIS et al.   CONSERVATION BIOLOGY

IBDSim: a computer program to simulate genotypic data under isolation by distance

(2008) RAPHAËL LEBLOIS et al.   Molecular Ecology Resources