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References from slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes. Local targets link to admitted publications; unresolved targets remain external evidence.
Natural Selection on the Arabidopsis Thaliana Genome in Present and Future Climates
10.1038/s41586-019-1520-9 · 2019 · External reference
Estimating Recent Migration and Population-Size Surfaces
10.1371/journal.pgen.1007908 · 2019 · External reference
Population Genomics of Bronze Age Eurasia
10.1038/nature14507 · 2015 · External reference
Ancient DNA from Marine Sediments: Precautions and Considerations for Seafloor Coring, Sample Handling and Data Generation
10.1016/j.earscirev.2019.102887 · 2019 · External reference
Gene Flow Past a Cline
10.1038/hdy.1979.86 · 1979 · External reference
Modelling Evolution in a Spatial Continuum
10.1088/1742-5468/2013/01/p01002 · 2013 · External reference
Neutral Evolution in Spatially Continuous Populations
10.1006/tpbi.2001.1557 · 2002 · External reference
A New Model for Evolution in a Spatial Continuum
10.1214/ejp.v15-741 · 2010 · External reference
Efficient Ancestry and Mutation Simulation with Msprime 1.0
10.1093/genetics/iyab229 · 2022 · External reference
Approximate Bayesian Computation in Population Genetics
10.1093/genetics/162.4.2025 · 2002 · External reference
Approximate Bayesian Computation in Evolution and Ecology
10.1146/annurev-ecolsys-102209-144621 · 2010 · External reference
Maximum Likelihood Estimation of a Migration Matrix and Effective Population Sizes in n Subpopulations by Using a Coalescent Approach
10.1073/pnas.081068098 · 2001 · External reference
Origins and Genetic Legacy of Prehistoric Dogs
10.1126/science.aba9572 · 2020 · External reference
Inferring Continuous and Discrete Population Genetic Structure Across Space
10.1534/genetics.118.301333 · 2018 · External reference
Spatial Population Genetics: It's About Time
10.1146/annurev-ecolsys-110316-022659 · 2019 · External reference
S, R, and Data Science
10.1145/3386334 · 2020 · External reference
Shiny: Web Application Framework for R. R Package Version 1.8.0.9000
2023 · External reference
Genetic Similarity versus Genetic Ancestry Groups as Sample Descriptors in Human Genetics
10.48550/arxiv.2207.11595 · 2022 · External reference
Landscape Rules Predict Optimal Superhighways for the First Peopling of Sahul
10.1038/s41562-021-01106-8 · 2021 · External reference
Approximate Bayesian Computation (ABC) in Practice
10.1016/j.tree.2010.04.001 · 2010 · External reference
SPLATCHE3: Simulation of Serial Genetic Data under Spatially Explicit Evolutionary Scenarios Including Long-Distance Dispersal
10.1093/bioinformatics/btz311 · 2019 · External reference
Splatche: A Program to Simulate Genetic Diversity Taking into Account Environmental Heterogeneity
10.1046/j.1471-8286.2003.00582.x · 2004 · External reference
Strong Reproductive Isolation between Humans and Neanderthals Inferred from Observed Patterns of Introgression
10.1073/pnas.1107450108 · 2011 · External reference
The Variant Call Format and VCFtools
10.1093/bioinformatics/btr330 · 2011 · External reference
Climate and Mountains Shaped Human Ancestral Genetic Lineages
10.1101/2021.07.13.452067 · 2021 · External reference
Temporal Signal and the Phylodynamic Threshold of SARS-CoV-2
10.1093/ve/veaa061 · 2020 · External reference
Nonstationary Patterns of Isolation-by-Distance: Inferring Measures of Local Genetic Differentiation with Bayesian Kriging
10.1111/evo.12342 · 2014 · External reference
Parallel Computing with R: A Brief Review
10.1002/wics.1515 · 2021 · External reference
MSMS: A Coalescent Simulation Program Including Recombination, Demographic Structure and Selection at a Single Locus
10.1093/bioinformatics/btq322 · 2010 · External reference
A Pain in the Torus: Some Difficulties with Models of Isolation by Distance
10.1086/283003 · 1975 · External reference
Modern Siberian Dog Ancestry Was Shaped by Several Thousand Years of Eurasian-wide Trade and Human Dispersal
10.1073/pnas.2100338118 · 2021 · External reference
The Wave of Advance of Advantageous Genes
10.1111/j.1469-1809.1937.tb02153.x · 1937 · External reference
Ecological Genomics Meets Community-level Modelling of Biodiversity: Mapping the Genomic Landscape of Current and Future Environmental Adaptation
10.1111/ele.12376 · 2015 · External reference
Poems: R Package for Simulating Species' Range Dynamics Using Pattern-oriented Validation
10.1111/2041-210x.13720 · 2021 · External reference
Nomadic Ecology Shaped the Highland Geography of Asia's Silk Roads
10.1038/nature21696 · 2017 · External reference
The Genetic History of Ice Age Europe
10.1038/nature17993 · 2016 · External reference
Storytelling and Story Testing in Domestication
10.1073/pnas.1400425111 · 2014 · External reference
Demographic History and Rare Allele Sharing among Human Populations
10.1073/pnas.1019276108 · 2011 · External reference
A Draft Sequence of the Neandertal Genome
10.1126/science.1188021 · 2010 · External reference
Statistical Methods in Spatial Genetics
10.1111/j.1365-294x.2009.04410.x · 2009 · External reference
Massive Migration from the Steppe Was a Source for Indo-European Languages in Europe
10.1038/nature14317 · 2015 · External reference
SLiM 2: Flexible, Interactive Forward Genetic Simulations
10.1093/molbev/msw211 · 2017 · External reference
SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model
10.1093/molbev/msy228 · 2019 · External reference
SLiM 4: Multispecies Eco-Evolutionary Modeling
10.1086/723601 · 2023 · External reference
Tree-sequence Recording in SLiM Opens New Horizons for Forward-time Simulation of Whole Genomes
10.1111/1755-0998.12968 · 2019 · External reference
Circuit Theory and Model-Based Inference for Landscape Connectivity
10.1080/01621459.2012.724647 · 2013 · External reference
Generating Samples under a Wright–Fisher Neutral Model of Genetic Variation
10.1093/bioinformatics/18.2.337 · 2002 · External reference
Efficiently Inferring the Demographic History of Many Populations With Allele Count Data
10.1080/01621459.2019.1635482 · 2020 · External reference
Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size
10.1016/j.tpb.2014.05.001 · 2014 · External reference
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
10.1371/journal.pcbi.1004842 · 2016 · External reference
Efficient Pedigree Recording for Fast Population Genetics Simulation
10.1371/journal.pcbi.1006581 · 2018 · External reference
Inferring Whole-Genome Histories in Large Population Datasets
10.1038/s41588-019-0483-y · 2019 · External reference
Recommendations on the Use and Reporting of Race, Ethnicity, and Ancestry in Genetic Research: Experiences from the NHLBI TOPMed Program
10.1016/j.xgen.2022.100155 · 2022 · External reference
Ancient Human Genomes Suggest Three Ancestral Populations for Present-Day Europeans
10.1038/nature13673 · 2014 · External reference
Genetic Equilibrium When More Than One Ecological Niche Is Available
10.1086/281792 · 1953 · External reference
The Origins and Spread of Domestic Horses from the Western Eurasian Steppes
10.1038/s41586-021-04018-9 · 2021 · External reference
A Geographically Explicit Genetic Model of Worldwide Human-Settlement History
10.1086/505436 · 2006 · External reference
Estimating Mobility Using Sparse Data: Application to Human Genetic Variation
10.1073/pnas.1703642114 · 2017 · External reference
Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories
10.1098/rstb.2019.0719 · 2020 · External reference
10.1201/9780203730058
10.1201/9780203730058 · 2019 · External reference
Airborne Environmental DNA for Terrestrial Vertebrate Community Monitoring
10.1016/j.cub.2021.12.014 · 2022 · External reference
Un traitement stochastique des problèmes linéaires en génétique de population
1951 · External reference
The Simons Genome Diversity Project: 300 Genomes from 142 Diverse Populations
10.1038/nature18964 · 2016 · External reference
Fast and Flexible Estimation of Effective Migration Surfaces
10.7554/elife.61927 · 2021 · External reference
What Is Ancestry?
10.1371/journal.pgen.1008624 · 2020 · External reference
Isolation by Resistance
10.1111/j.0014-3820.2006.tb00500.x · 2006 · External reference
Palaeogenomes of Eurasian Straight-Tusked Elephants Challenge the Current View of Elephant Evolution
10.7554/elife.25413 · 2017 · External reference
Modeling the Spatiotemporal Spread of Beneficial Alleles Using Ancient Genomes
10.7554/elife.73767 · 2022 · External reference
The Relation between Distant Individuals in Geographically Structured Populations
10.1016/0025-5564(76)90096-1 · 1976 · External reference
Estimating Dispersal Rates and Locating Genetic Ancestors with Genome-Wide Genealogies
10.1101/2021.07.13.452277 · 2021 · External reference
A Comprehensive Genomic History of Extinct and Living Elephants
10.1073/pnas.1720554115 · 2018 · External reference
10.1007/978-1-4614-1743-9
10.1007/978-1-4614-1743-9 · 2012 · External reference
Ape 5.0: An Environment for Modern Phylogenetics and Evolutionary Analyses in R
10.1093/bioinformatics/bty633 · 2019 · External reference
Ancient Plant DNA in Lake Sediments
10.1111/nph.14470 · 2017 · External reference
Ancient Admixture in Human History
10.1534/genetics.112.145037 · 2012 · External reference
Simple Features for R: Standardized Support for Spatial Vector Data
10.32614/rj-2018-009 · 2018 · External reference
Detecting Range Expansions from Genetic Data
10.1111/evo.12202 · 2013 · External reference
Visualizing Spatial Population Structure with Estimated Effective Migration Surfaces
10.1038/ng.3464 · 2016 · External reference
slendr GitHub repository (Peer Community Journal archive)
10.5281/zenodo.10384289 · 2023 · External reference
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
10.1371/journal.pgen.1002967 · 2012 · External reference
Toward a New History and Geography of Human Genes Informed by Ancient DNA
10.1016/j.tig.2014.07.007 · 2014 · External reference
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
10.1086/519795 · 2007 · External reference
The Spatiotemporal Spread of Human Migrations during the European Holocene
10.1073/pnas.1920051117 · 2020 · External reference
Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes
10.1534/genetics.120.303253 · 2020 · External reference
The Geography of Recent Genetic Ancestry across Europe
10.1371/journal.pbio.1001555 · 2013 · External reference
Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo
10.1038/nature08835 · 2010 · External reference
Early Divergent Strains of Yersinia Pestis in Eurasia 5,000 Years Ago
10.1016/j.cell.2015.10.009 · 2015 · External reference
Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns
10.1534/genetics.117.300638 · 2018 · External reference
Genetic Differentiation and Estimation of Gene Flow from F-statistics under Isolation by Distance
10.1093/genetics/145.4.1219 · 1997 · External reference
Comparison of Bayesian Clustering and Edge Detection Methods for Inferring Boundaries in Landscape Genetics
10.3390/ijms12020865 · 2011 · External reference
Ten Simple Rules for Reproducible Computational Research
10.1371/journal.pcbi.1003285 · 2013 · External reference
Ancient DNA and Human History
10.1073/pnas.1524306113 · 2016 · External reference
Gene Flow and Selection in a Cline
10.1093/genetics/75.4.733 · 1973 · External reference
Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift
10.1534/genetics.112.139022 · 2012 · External reference
A Method for Genome-Wide Genealogy Estimation for Thousands of Samples
10.1038/s41588-019-0484-x · 2019 · External reference
Scrm: Efficiently Simulating Long Sequences Using the Approximated Coalescent with Recombination
10.1093/bioinformatics/btu861 · 2015 · External reference
Ecosystem Biomonitoring with eDNA: Metabarcoding across the Tree of Life in a Tropical Marine Environment
10.1038/s41598-017-12501-5 · 2017 · External reference
Towards Next-generation Biodiversity Assessment Using DNA Metabarcoding
10.1111/j.1365-294x.2012.05470.x · 2012 · External reference
R: A Language and Environment for Statistical Computing
2021 · External reference
Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations
10.1093/molbev/msab175 · 2021 · External reference
A Map of Human Genome Variation from Population-Scale Sequencing
10.1038/nature09534 · 2010 · External reference
Evolutionary History and Past Climate Change Shape the Distribution of Genetic Diversity in Terrestrial Mammals
10.1038/s41467-020-16449-5 · 2020 · External reference
A New Powerful Tool to Easily Encode the Geo-Spatial Dimension in Population Genetics Simulations
10.24072/pci.evolbiol.100630 · 2023 · External reference
Unearthing Neanderthal Population History Using Nuclear and Mitochondrial DNA from Cave Sediments
10.1126/science.abf1667 · 2021 · External reference
Late Quaternary Dynamics of Arctic Biota from Ancient Environmental Genomics
10.1038/s41586-021-04016-x · 2021 · External reference
Unresolved reference
2016 · External reference
Welcome to the Tidyverse
10.21105/joss.01686 · 2019 · External reference
Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments
10.1126/science.1084114 · 2003 · External reference
A Unified Genealogy of Modern and Ancient Genomes
10.1126/science.abi8264 · 2022 · External reference
Isolation by Distance
10.1093/genetics/28.2.114 · 1943 · External reference
Ggtree : An R Package for Visualization and Annotation of Phylogenetic Trees with Their Covariates and Other Associated Data
10.1111/2041-210x.12628 · 2017 · External reference