Simulation Modeling in Landscape Genetics

[1]  S. Cushman,et al.  sGD: software for estimating spatially explicit indices of genetic diversity , 2011, Molecular ecology resources.

[2]  Birgit Müller,et al.  A standard protocol for describing individual-based and agent-based models , 2006 .

[3]  Oscar Gaggiotti,et al.  Identifying the Environmental Factors That Determine the Genetic Structure of Populations , 2006, Genetics.

[4]  Erin L. Landguth,et al.  Sample design effects in landscape genetics , 2012, Conservation Genetics.

[5]  S. Cushman,et al.  Simulating the effects of climate change on population connectivity of American marten (Martes americana) in the northern Rocky Mountains, USA , 2011, Landscape Ecology.

[6]  Niko Balkenhol,et al.  Relative sensitivity of neutral versus adaptive genetic data for assessing population differentiation , 2012, Conservation Genetics.

[7]  Marie-Josée Fortin,et al.  Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern , 2012 .

[8]  Damaris Zurell,et al.  Integrating movement ecology with biodiversity research - exploring new avenues to address spatiotemporal biodiversity dynamics , 2013, Movement Ecology.

[9]  N Perrin,et al.  Inferring landscape effects on dispersal from genetic distances: how far can we go? , 2011, Molecular ecology.

[10]  M. Fortin,et al.  Comparison of Bayesian Clustering and Edge Detection Methods for Inferring Boundaries in Landscape Genetics , 2011, International journal of molecular sciences.

[11]  Peter L. Ralph,et al.  DISENTANGLING THE EFFECTS OF GEOGRAPHIC AND ECOLOGICAL ISOLATION ON GENETIC DIFFERENTIATION , 2013, Evolution; international journal of organic evolution.

[12]  Samuel A. Cushman,et al.  Landscape genetics and limiting factors , 2012, Conservation Genetics.

[13]  T. Ohta,et al.  On some principles governing molecular evolution. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Nicolas Ray,et al.  SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination , 2010, Bioinform..

[15]  G. Luikart,et al.  Combining demographic and genetic factors to assess population vulnerability in stream species. , 2014, Ecological applications : a publication of the Ecological Society of America.

[16]  S. Cushman,et al.  Inferring landscape effects on gene flow: a new model selection framework , 2010, Molecular ecology.

[17]  Stéphane Dupas,et al.  SimAdapt: an individual‐based genetic model for simulating landscape management impacts on populations , 2013 .

[18]  F. Pompanon,et al.  Optimizing the trade‐off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual‐based sampling scheme , 2013, Molecular ecology.

[19]  James S. Clark,et al.  Pelagic movements of pacific leatherback turtles (dermochelys coriacea) highlight the role of prey and ocean currents , 2013, Movement Ecology.

[20]  Uta Berger,et al.  Pattern-Oriented Modeling of Agent-Based Complex Systems: Lessons from Ecology , 2005, Science.

[21]  David O. Wallin,et al.  Spatial scaling and multi-model inference in landscape genetics: Martes americana in northern Idaho , 2010, Landscape Ecology.

[22]  Samuel A. Cushman,et al.  Scale dependent inference in landscape genetics , 2010, Landscape Ecology.

[23]  Marie-Josée Fortin,et al.  The influence of landscape characteristics and home-range size on the quantification of landscape-genetics relationships , 2012, Landscape Ecology.

[24]  Nicolas Ray,et al.  A first step towards inferring levels of long‐distance dispersal during past expansions , 2010, Molecular ecology resources.

[25]  Population connectivity and genetic diversity of American marten (Martes americana) in the United States northern Rocky Mountains in a climate change context , 2013, Conservation Genetics.

[26]  G. Luikart,et al.  Relationships between migration rates and landscape resistance assessed using individual‐based simulations , 2010, Molecular ecology resources.

[27]  Melanie Murphy,et al.  A simulation‐based evaluation of methods for inferring linear barriers to gene flow , 2012, Molecular ecology resources.

[28]  CDFISH: an individual-based, spatially-explicit, landscape genetics simulator for aquatic species in complex riverscapes , 2012, Conservation Genetics Resources.

[29]  J. Nason,et al.  Landscape modelling of gene flow: improved power using conditional genetic distance derived from the topology of population networks , 2010, Molecular ecology.

[30]  Raymond J. Dezzani,et al.  Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data , 2009 .

[31]  Samuel A. Cushman,et al.  Specialty Grand Challenge Article Grand Challenges in Evolutionary and Population Genetics: the Importance of Integrating Epigenetics, Genomics, Modeling, and Experimentation , 2022 .

[32]  J Andrew Royle,et al.  Current approaches using genetic distances produce poor estimates of landscape resistance to interindividual dispersal , 2013, Molecular ecology.

[33]  R. V. Adams,et al.  INTEGRATING LANDSCAPE GENOMICS AND SPATIALLY EXPLICIT APPROACHES TO DETECT LOCI UNDER SELECTION IN CLINAL POPULATIONS , 2013, Evolution; international journal of organic evolution.

[34]  J. Gareth Polhill,et al.  The ODD protocol: A review and first update , 2010, Ecological Modelling.

[35]  S. Cushman,et al.  Simulating Pattern-Process Relationships to Validate Landscape Genetic Models , 2012 .

[36]  S. Cushman,et al.  Re-Evaluating Causal Modeling with Mantel Tests in Landscape Genetics , 2013 .

[37]  Oscar E. Gaggiotti,et al.  Computer simulations: tools for population and evolutionary genetics , 2012, Nature Reviews Genetics.

[38]  Gilles Guillot,et al.  Dismantling the Mantel tests , 2011, 1112.0651.

[39]  Edward J. Rykiel,et al.  Testing ecological models: the meaning of validation , 1996 .

[40]  F. Balloux.  EASYPOP (version 1.7): a computer program for population genetics simulations. , 2001, The Journal of heredity.

[41]  S. Cushman,et al.  Spurious correlations and inference in landscape genetics , 2010, Molecular ecology.

[42]  S. Cushman,et al.  Landscape effects on gene flow for a climate‐sensitive montane species, the American pika , 2014, Molecular ecology.

[43]  A. Estoup,et al.  Spatial genetic structure of a small rodent in a heterogeneous landscape , 2008, Molecular ecology.

[44]  G. Luikart,et al.  Quantifying the lag time to detect barriers in landscape genetics , 2010, Molecular ecology.

[45]  S. Neuenschwander.  AQUASPLATCHE: a program to simulate genetic diversity in populations living in linear habitats , 2006 .

[46]  Jérôme Goudet,et al.  quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation , 2008, Bioinform..

[47]  S. Cushman,et al.  cdpop: A spatially explicit cost distance population genetics program , 2010, Molecular ecology resources.