Section: Evolutionary Biology
Topic: Evolution, Genetics/Genomics, Population biology

slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes

Petr, Martin1, 2  ; Haller, Benjamin C.3 ; Ralph, Peter L.4 ; Racimo, Fernando1, 2 
1 Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
2 Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
3 Department of Computational Biology, Cornell University, Ithaca, NY, USA
4 Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA

Corresponding author(s): Petr, Martin (mp@bodkan.net)

10.24072/pcjournal.354 - Peer Community Journal, Volume 3 (2023), article no. e121.

Get full text PDF Peer reviewed and recommended by PCI
article image

One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatio-temporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene-flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree-sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.

Published online:
DOI: 10.24072/pcjournal.354
Type: Software tool
Mots-clés : population genetics; simulation; spatio-temporal analysis; tree sequence; bioinformatics

Petr, Martin 1, 2; Haller, Benjamin C. 3; Ralph, Peter L. 4; Racimo, Fernando 1, 2

1 Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
2 Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
3 Department of Computational Biology, Cornell University, Ithaca, NY, USA
4 Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
@article{10_24072_pcjournal_354,
     author = {Petr, Martin and Haller, Benjamin C. and Ralph, Peter L. and Racimo, Fernando},
     title = {\protect\emph{slendr}: a framework for spatio-temporal population genomic simulations on geographic landscapes},
     journal = {Peer Community Journal},
     eid = {e121},
     publisher = {Peer Community In},
     volume = {3},
     year = {2023},
     doi = {10.24072/pcjournal.354},
     language = {en},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.354/}
}
TY  - JOUR
AU  - Petr, Martin
AU  - Haller, Benjamin C.
AU  - Ralph, Peter L.
AU  - Racimo, Fernando
TI  - slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes
JO  - Peer Community Journal
PY  - 2023
VL  - 3
PB  - Peer Community In
UR  - https://peercommunityjournal.org/articles/10.24072/pcjournal.354/
DO  - 10.24072/pcjournal.354
LA  - en
ID  - 10_24072_pcjournal_354
ER  - 
%0 Journal Article
%A Petr, Martin
%A Haller, Benjamin C.
%A Ralph, Peter L.
%A Racimo, Fernando
%T slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes
%J Peer Community Journal
%D 2023
%V 3
%I Peer Community In
%U https://peercommunityjournal.org/articles/10.24072/pcjournal.354/
%R 10.24072/pcjournal.354
%G en
%F 10_24072_pcjournal_354
Petr, Martin; Haller, Benjamin C.; Ralph, Peter L.; Racimo, Fernando. slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes. Peer Community Journal, Volume 3 (2023), article  no. e121. doi : 10.24072/pcjournal.354. https://peercommunityjournal.org/articles/10.24072/pcjournal.354/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.evolbiol.100630

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] Exposito-Alonso, M.; 500 Genomes Field Experiment Team; Burbano, H. A.; Bossdorf, O.; Nielsen, R.; Weigel, D. Natural Selection on the Arabidopsis Thaliana Genome in Present and Future Climates, Nature, Volume 573 (2019) no. 7772, pp. 126-129 | DOI

[2] Al-Asadi, H.; Petkova, D.; Stephens, M.; Novembre, J. Estimating Recent Migration and Population-Size Surfaces, PLOS Genetics, Volume 15 (2019) no. 1, p. e1007908 | DOI

[3] Allentoft, M. E.; Sikora, M.; Sjögren, K.-G.; Rasmussen, S.; Rasmussen, M.; Stenderup, J.; Damgaard, P. B.; Schroeder, H.; Ahlström, T.; Vinner, L.; Malaspinas, A.-S.; Margaryan, A.; Higham, T.; Chivall, D.; Lynnerup, N.; Harvig, L.; Baron, J.; Casa, P. D.; Dąbrowski, P.; Duffy, P. R.; Ebel, A. V.; Epimakhov, A.; Frei, K.; Furmanek, M.; Gralak, T.; Gromov, A.; Gronkiewicz, S.; Grupe, G.; Hajdu, T.; Jarysz, R.; Khartanovich, V.; Khokhlov, A.; Kiss, V.; Kolář, J.; Kriiska, A.; Lasak, I.; Longhi, C.; McGlynn, G.; Merkevicius, A.; Merkyte, I.; Metspalu, M.; Mkrtchyan, R.; Moiseyev, V.; Paja, L.; Pálfi, G.; Pokutta, D.; Pospieszny, Ł.; Price, T. D.; Saag, L.; Sablin, M.; Shishlina, N.; Smrčka, V.; Soenov, V. I.; Szeverényi, V.; Tóth, G.; Trifanova, S. V.; Varul, L.; Vicze, M.; Yepiskoposyan, L.; Zhitenev, V.; Orlando, L.; Sicheritz-Pontén, T.; Brunak, S.; Nielsen, R.; Kristiansen, K.; Willerslev, E. Population Genomics of Bronze Age Eurasia, Nature, Volume 522 (2015) no. 7555, pp. 167-172 | DOI

[4] Armbrecht, L. H.; Coolen, M. J.; Lejzerowicz, F.; George, S. C.; Negandhi, K.; Suzuki, Y.; Young, J.; Foster, N. R.; Armand, L. K.; Cooper, A.; Ostrowski, M.; Focardi, A.; Stat, M.; Moreau, J. W.; Weyrich, L. S. Ancient DNA from Marine Sediments: Precautions and Considerations for Seafloor Coring, Sample Handling and Data Generation, Earth-Science Reviews, Volume 196 (2019), p. 102887 | DOI

[5] Barton, N. H. Gene Flow Past a Cline, Heredity, Volume 43 (1979) no. 3, pp. 333-339 | DOI

[6] Barton, N. H.; Etheridge, A. M.; Véber, A. Modelling Evolution in a Spatial Continuum, Journal of Statistical Mechanics: Theory and Experiment, Volume 2013 (2013) no. 01, p. P01002 | DOI

[7] Barton, N. H.; Depaulis, F.; Etheridge, A. M. Neutral Evolution in Spatially Continuous Populations, Theoretical Population Biology, Volume 61 (2002) no. 1, pp. 31-48 | DOI

[8] Barton, N.; Etheridge, A.; Véber, A. A New Model for Evolution in a Spatial Continuum, Electronic Journal of Probability, Volume 15 (2010) no. none | DOI

[9] Baumdicker, F.; Bisschop, G.; Goldstein, D.; Gower, G.; Ragsdale, A. P.; Tsambos, G.; Zhu, S.; Eldon, B.; Ellerman, E. C.; Galloway, J. G.; Gladstein, A. L.; Gorjanc, G.; Guo, B.; Jeffery, B.; Kretzschumar, W. W.; Lohse, K.; Matschiner, M.; Nelson, D.; Pope, N. S.; Quinto-Cortés, C. D.; Rodrigues, M. F.; Saunack, K.; Sellinger, T.; Thornton, K.; Van Kemenade, H.; Wohns, A. W.; Wong, Y.; Gravel, S.; Kern, A. D.; Koskela, J.; Ralph, P. L.; Kelleher, J. Efficient Ancestry and Mutation Simulation with Msprime 1.0, Genetics, Volume 220 (2022) no. 3, p. iyab229 | DOI

[10] Beaumont, M. A.; Zhang, W.; Balding, D. J. Approximate Bayesian Computation in Population Genetics, Genetics, Volume 162 (2002) no. 4, pp. 2025-2035 | DOI

[11] Beaumont, M. A. Approximate Bayesian Computation in Evolution and Ecology, Annual Review of Ecology, Evolution, and Systematics, Volume 41 (2010) no. 1, pp. 379-406 | DOI

[12] Beerli, P.; Felsenstein, J. Maximum Likelihood Estimation of a Migration Matrix and Effective Population Sizes in n Subpopulations by Using a Coalescent Approach, Proceedings of the National Academy of Sciences, Volume 98 (2001) no. 8, pp. 4563-4568 | DOI

[13] Bergström, A.; Frantz, L.; Schmidt, R.; Ersmark, E.; Lebrasseur, O.; Girdland-Flink, L.; Lin, A. T.; Storå, J.; Sjögren, K.-G.; Anthony, D.; Antipina, E.; Amiri, S.; Bar-Oz, G.; Bazaliiskii, V. I.; Bulatović, J.; Brown, D.; Carmagnini, A.; Davy, T.; Fedorov, S.; Fiore, I.; Fulton, D.; Germonpré, M.; Haile, J.; Irving-Pease, E. K.; Jamieson, A.; Janssens, L.; Kirillova, I.; Horwitz, L. K.; Kuzmanovic-Cvetković, J.; Kuzmin, Y.; Losey, R. J.; Dizdar, D. L.; Mashkour, M.; Novak, M.; Onar, V.; Orton, D.; Pasarić, M.; Radivojević, M.; Rajković, D.; Roberts, B.; Ryan, H.; Sablin, M.; Shidlovskiy, F.; Stojanović, I.; Tagliacozzo, A.; Trantalidou, K.; Ullén, I.; Villaluenga, A.; Wapnish, P.; Dobney, K.; Götherström, A.; Linderholm, A.; Dalén, L.; Pinhasi, R.; Larson, G.; Skoglund, P. Origins and Genetic Legacy of Prehistoric Dogs, Science, Volume 370 (2020) no. 6516, pp. 557-564 | DOI

[14] Bradburd, G. S.; Coop, G. M.; Ralph, P. L. Inferring Continuous and Discrete Population Genetic Structure Across Space, Genetics, Volume 210 (2018) no. 1, pp. 33-52 | DOI

[15] Bradburd, G. S.; Ralph, P. L. Spatial Population Genetics: It's About Time, Annual Review of Ecology, Evolution, and Systematics, Volume 50 (2019) no. 1, pp. 427-449 | DOI

[16] Chambers, J. M. S, R, and Data Science, Proceedings of the ACM on Programming Languages, Volume 4 (2020) no. HOPL, pp. 1-17 | DOI

[17] Chang, W.; Cheng, J.; Allaire, J.; Sievert, C.; Schloerke, B.; Xie, Y.; Allen, J.; McPherson, J.; Dipert, A.; Borges, B. Shiny: Web Application Framework for R. R Package Version 1.8.0.9000, 2023

[18] Coop, G. Genetic Similarity versus Genetic Ancestry Groups as Sample Descriptors in Human Genetics, arXiv (2022) | DOI

[19] Crabtree, S. A.; White, D. A.; Bradshaw, C. J. A.; Saltré, F.; Williams, A. N.; Beaman, R. J.; Bird, M. I.; Ulm, S. Landscape Rules Predict Optimal Superhighways for the First Peopling of Sahul, Nature Human Behaviour, Volume 5 (2021) no. 10, pp. 1303-1313 | DOI

[20] Csilléry, K.; Blum, M. G.; Gaggiotti, O. E.; François, O. Approximate Bayesian Computation (ABC) in Practice, Trends in Ecology & Evolution, Volume 25 (2010) no. 7, pp. 410-418 | DOI

[21] Currat, M.; Arenas, M.; Quilodràn, C. S.; Excoffier, L.; Ray, N. SPLATCHE3: Simulation of Serial Genetic Data under Spatially Explicit Evolutionary Scenarios Including Long-Distance Dispersal, Bioinformatics, Volume 35 (2019) no. 21, pp. 4480-4483 | DOI

[22] Currat, M.; Ray, N.; Excoffier, L. Splatche: A Program to Simulate Genetic Diversity Taking into Account Environmental Heterogeneity, Molecular Ecology Notes, Volume 4 (2004) no. 1, pp. 139-142 | DOI

[23] Currat, M.; Excoffier, L. Strong Reproductive Isolation between Humans and Neanderthals Inferred from Observed Patterns of Introgression, Proceedings of the National Academy of Sciences, Volume 108 (2011) no. 37, pp. 15129-15134 | DOI

[24] Danecek, P.; Auton, A.; Abecasis, G.; Albers, C. A.; Banks, E.; DePristo, M. A.; Handsaker, R. E.; Lunter, G.; Marth, G. T.; Sherry, S. T.; McVean, G.; Durbin, R.; 1000 Genomes Project Analysis Group The Variant Call Format and VCFtools, Bioinformatics, Volume 27 (2011) no. 15, pp. 2156-2158 | DOI

[25] Delser, P. M.; Krapp, M.; Beyer, R.; Jones, E. R.; Miller, E. F.; Hovhannisyan, A.; Parker, M.; Siska, V.; Vizzari, M. T.; Pearmain, E. J.; Imaz-Rosshandler, I.; Leonardi, M.; Somma, G. L.; Hodgson, J.; Tysall, E.; Xue, Z.; Cassidy, L.; Bradley, D. G.; Eriksson, A.; Manica, A. Climate and Mountains Shaped Human Ancestral Genetic Lineages, bioRxiv (2021) | DOI

[26] Duchene, S.; Featherstone, L.; Haritopoulou-Sinanidou, M.; Rambaut, A.; Lemey, P.; Baele, G. Temporal Signal and the Phylodynamic Threshold of SARS-CoV-2, Virus evolution, Volume 6 (2020), p. 061 | DOI

[27] Duforet-Frebourg, N.; Blum, M. G. Nonstationary Patterns of Isolation-by-Distance: Inferring Measures of Local Genetic Differentiation with Bayesian Kriging, Evolution, Volume 68 (2014) no. 4, pp. 1110-1123 | DOI

[28] Eddelbuettel, D. Parallel Computing with R: A Brief Review, WIREs Computational Statistics, Volume 13 (2021) no. 2, p. e1515 | DOI

[29] Ewing, G.; Hermisson, J. MSMS: A Coalescent Simulation Program Including Recombination, Demographic Structure and Selection at a Single Locus, Bioinformatics, Volume 26 (2010) no. 16, pp. 2064-2065 | DOI

[30] Felsenstein, J. A Pain in the Torus: Some Difficulties with Models of Isolation by Distance, The American Naturalist, Volume 109 (1975) no. 967, pp. 359-368 | DOI

[31] Feuerborn, T. R.; Carmagnini, A.; Losey, R. J.; Nomokonova, T.; Askeyev, A.; Askeyev, I.; Askeyev, O.; Antipina, E. E.; Appelt, M.; Bachura, O. P.; Beglane, F.; Bradley, D. G.; Daly, K. G.; Gopalakrishnan, S.; Murphy Gregersen, K.; Guo, C.; Gusev, A. V.; Jones, C.; Kosintsev, P. A.; Kuzmin, Y. V.; Mattiangeli, V.; Perri, A. R.; Plekhanov, A. V.; Ramos-Madrigal, J.; Schmidt, A. L.; Shaymuratova, D.; Smith, O.; Yavorskaya, L. V.; Zhang, G.; Willerslev, E.; Meldgaard, M.; Gilbert, M. T. P.; Larson, G.; Dalén, L.; Hansen, A. J.; Sinding, M.-H. S.; Frantz, L. Modern Siberian Dog Ancestry Was Shaped by Several Thousand Years of Eurasian-wide Trade and Human Dispersal, Proceedings of the National Academy of Sciences, Volume 118 (2021) no. 39, p. e2100338118 | DOI

[32] Fisher, R. A. The Wave of Advance of Advantageous Genes, Annals of Eugenics, Volume 7 (1937) no. 4, pp. 355-369 | DOI

[33] Fitzpatrick, M. C.; Keller, S. R. Ecological Genomics Meets Community-level Modelling of Biodiversity: Mapping the Genomic Landscape of Current and Future Environmental Adaptation, Ecology Letters, Volume 18 (2015) no. 1, pp. 1-16 | DOI

[34] Fordham, D. A.; Haythorne, S.; Brown, S. C.; Buettel, J. C.; Brook, B. W. Poems: R Package for Simulating Species' Range Dynamics Using Pattern-oriented Validation, Methods in Ecology and Evolution, Volume 12 (2021) no. 12, pp. 2364-2371 | DOI

[35] Frachetti, M. D.; Smith, C. E.; Traub, C. M.; Williams, T. Nomadic Ecology Shaped the Highland Geography of Asia's Silk Roads, Nature, Volume 543 (2017) no. 7644, pp. 193-198 | DOI

[36] Fu, Q.; Posth, C.; Hajdinjak, M.; Petr, M.; Mallick, S.; Fernandes, D.; Furtwängler, A.; Haak, W.; Meyer, M.; Mittnik, A.; Nickel, B.; Peltzer, A.; Rohland, N.; Slon, V.; Talamo, S.; Lazaridis, I.; Lipson, M.; Mathieson, I.; Schiffels, S.; Skoglund, P.; Derevianko, A. P.; Drozdov, N.; Slavinsky, V.; Tsybankov, A.; Cremonesi, R. G.; Mallegni, F.; Gély, B.; Vacca, E.; Morales, M. R. G.; Straus, L. G.; Neugebauer-Maresch, C.; Teschler-Nicola, M.; Constantin, S.; Moldovan, O. T.; Benazzi, S.; Peresani, M.; Coppola, D.; Lari, M.; Ricci, S.; Ronchitelli, A.; Valentin, F.; Thevenet, C.; Wehrberger, K.; Grigorescu, D.; Rougier, H.; Crevecoeur, I.; Flas, D.; Semal, P.; Mannino, M. A.; Cupillard, C.; Bocherens, H.; Conard, N. J.; Harvati, K.; Moiseyev, V.; Drucker, D. G.; Svoboda, J.; Richards, M. P.; Caramelli, D.; Pinhasi, R.; Kelso, J.; Patterson, N.; Krause, J.; Pääbo, S.; Reich, D. The Genetic History of Ice Age Europe, Nature, Volume 534 (2016) no. 7606, pp. 200-205 | DOI

[37] Gerbault, P.; Allaby, R. G.; Boivin, N.; Rudzinski, A.; Grimaldi, I. M.; Pires, J. C.; Climer Vigueira, C.; Dobney, K.; Gremillion, K. J.; Barton, L.; Arroyo-Kalin, M.; Purugganan, M. D.; Rubio De Casas, R.; Bollongino, R.; Burger, J.; Fuller, D. Q.; Bradley, D. G.; Balding, D. J.; Richerson, P. J.; Gilbert, M. T. P.; Larson, G.; Thomas, M. G. Storytelling and Story Testing in Domestication, Proceedings of the National Academy of Sciences, Volume 111 (2014) no. 17, pp. 6159-6164 | DOI

[38] Gravel, S.; Henn, B. M.; Gutenkunst, R. N.; Indap, A. R.; Marth, G. T.; Clark, A. G.; Yu, F.; Gibbs, R. A.; The 1000 Genomes Project; Bustamante, C. D.; Altshuler, D. L.; Durbin, R. M.; Abecasis, G. R.; Bentley, D. R.; Chakravarti, A.; Clark, A. G.; Collins, F. S.; De La Vega, F. M.; Donnelly, P.; Egholm, M.; Flicek, P.; Gabriel, S. B.; Gibbs, R. A.; Knoppers, B. M.; Lander, E. S.; Lehrach, H.; Mardis, E. R.; McVean, G. A.; Nickerson, D. A.; Peltonen, L.; Schafer, A. J.; Sherry, S. T.; Wang, J.; Wilson, R. K.; Gibbs, R. A.; Deiros, D.; Metzker, M.; Muzny, D.; Reid, J.; Wheeler, D.; Wang, J.; Li, J.; Jian, M.; Li, G.; Li, R.; Liang, H.; Tian, G.; Wang, B.; Wang, J.; Wang, W.; Yang, H.; Zhang, X.; Zheng, H.; Lander, E. S.; Altshuler, D. L.; Ambrogio, L.; Bloom, T.; Cibulskis, K.; Fennell, T. J.; Gabriel, S. B.; Jaffe, D. B.; Shefler, E.; Sougnez, C. L.; Bentley, D. R.; Gormley, N.; Humphray, S.; Kingsbury, Z.; Koko-Gonzales, P.; Stone, J.; McKernan, K. J.; Costa, G. L.; Ichikawa, J. K.; Lee, C. C.; Sudbrak, R.; Lehrach, H.; Borodina, T. A.; Dahl, A.; Davydov, A. N.; Marquardt, P.; Mertes, F.; Nietfeld, W.; Rosenstiel, P.; Schreiber, S.; Soldatov, A. V.; Timmermann, B.; Tolzmann, M.; Egholm, M.; Affourtit, J.; Ashworth, D.; Attiya, S.; Bachorski, M.; Buglione, E.; Burke, A.; Caprio, A.; Celone, C.; Clark, S.; Conners, D.; Desany, B.; Gu, L.; Guccione, L.; Kao, K.; Kebbel, A.; Knowlton, J.; Labrecque, M.; McDade, L.; Mealmaker, C.; Minderman, M.; Nawrocki, A.; Niazi, F.; Pareja, K.; Ramenani, R.; Riches, D.; Song, W.; Turcotte, C.; Wang, S.; Mardis, E. R.; Wilson, R. K.; Dooling, D.; Fulton, L.; Fulton, R.; Weinstock, G.; Durbin, R. M.; Burton, J.; Carter, D. M.; Churcher, C.; Coffey, A.; Cox, A.; Palotie, A.; Quail, M.; Skelly, T.; Stalker, J.; Swerdlow, H. P.; Turner, D.; De Witte, A.; Giles, S.; Gibbs, R. A.; Wheeler, D.; Bainbridge, M.; Challis, D.; Sabo, A.; Yu, F.; Yu, J.; Wang, J.; Fang, X.; Guo, X.; Li, R.; Li, Y.; Luo, R.; Tai, S.; Wu, H.; Zheng, H.; Zheng, X.; Zhou, Y.; Li, G.; Wang, J.; Yang, H.; Marth, G. T.; Garrison, E. P.; Huang, W.; Indap, A.; Kural, D.; Lee, W.-P.; Leong, W. F.; Quinlan, A. R.; Stewart, C.; Stromberg, M. P.; Ward, A. N.; Wu, J.; Lee, C.; Mills, R. E.; Shi, X.; Daly, M. J.; DePristo, M. A.; Altshuler, D. L.; Ball, A. D.; Banks, E.; Bloom, T.; Browning, B. L.; Cibulskis, K.; Fennell, T. J.; Garimella, K. V.; Grossman, S. R.; Handsaker, R. E.; Hanna, M.; Hartl, C.; Jaffe, D. B.; Kernytsky, A. M.; Korn, J. M.; Li, H.; Maguire, J. R.; McCarroll, S. A.; McKenna, A.; Nemesh, J. C.; Philippakis, A. A.; Poplin, R. E.; Price, A.; Rivas, M. A.; Sabeti, P. C.; Schaffner, S. F.; Shefler, E.; Shlyakhter, I. A.; Cooper, D. N.; Ball, E. V.; Mort, M.; Phillips, A. D.; Stenson, P. D.; Sebat, J.; Makarov, V.; Ye, K.; Yoon, S. C.; Bustamante, C. D.; Clark, A. G.; Boyko, A.; Degenhardt, J.; Gravel, S.; Gutenkunst, R. N.; Kaganovich, M.; Keinan, A.; Lacroute, P.; Ma, X.; Reynolds, A.; Clarke, L.; Flicek, P.; Cunningham, F.; Herrero, J.; Keenen, S.; Kulesha, E.; Leinonen, R.; McLaren, W. M.; Radhakrishnan, R.; Smith, R. E.; Zalunin, V.; Zheng-Bradley, X.; Korbel, J. O.; Stütz, A. M.; Humphray, S.; Bauer, M.; Cheetham, R. K.; Cox, T.; Eberle, M.; James, T.; Kahn, S.; Murray, L.; Chakravarti, A.; Ye, K.; De La Vega, F. M.; Fu, Y.; Hyland, F. C. L.; Manning, J. M.; McLaughlin, S. F.; Peckham, H. E.; Sakarya, O.; Sun, Y. A.; Tsung, E. F.; Batzer, M. A.; Konkel, M. K.; Walker, J. A.; Sudbrak, R.; Albrecht, M. W.; Amstislavskiy, V. S.; Herwig, R.; Parkhomchuk, D. V.; Sherry, S. T.; Agarwala, R.; Khouri, H. M.; Morgulis, A. O.; Paschall, J. E.; Phan, L. D.; Rotmistrovsky, K. E.; Sanders, R. D.; Shumway, M. F.; Xiao, C.; McVean, G. A.; Auton, A.; Iqbal, Z.; Lunter, G.; Marchini, J. L.; Moutsianas, L.; Myers, S.; Tumian, A.; Desany, B.; Knight, J.; Winer, R.; Craig, D. W.; Beckstrom-Sternberg, S. M.; Christoforides, A.; Kurdoglu, A. A.; Pearson, J. V.; Sinari, S. A.; Tembe, W. D.; Haussler, D.; Hinrichs, A. S.; Katzman, S. J.; Kern, A.; Kuhn, R. M.; Przeworski, M.; Hernandez, R. D.; Howie, B.; Kelley, J. L.; Melton, S. C.; Abecasis, G. R.; Li, Y.; Anderson, P.; Blackwell, T.; Chen, W.; Cookson, W. O.; Ding, J.; Kang, H. M.; Lathrop, M.; Liang, L.; Moffatt, M. F.; Scheet, P.; Sidore, C.; Snyder, M.; Zhan, X.; Zöllner, S.; Awadalla, P.; Casals, F.; Idaghdour, Y.; Keebler, J.; Stone, E. A.; Zilversmit, M.; Jorde, L.; Xing, J.; Eichler, E. E.; Aksay, G.; Alkan, C.; Hajirasouliha, I.; Hormozdiari, F.; Kidd, J. M.; Sahinalp, S. C.; Sudmant, P. H.; Mardis, E. R.; Chen, K.; Chinwalla, A.; Ding, L.; Koboldt, D. C.; McLellan, M. D.; Dooling, D.; Weinstock, G.; Wallis, J. W.; Wendl, M. C.; Zhang, Q.; Durbin, R. M.; Albers, C. A.; Ayub, Q.; Balasubramaniam, S.; Barrett, J. C.; Carter, D. M.; Chen, Y.; Conrad, D. F.; Danecek, P.; Dermitzakis, E. T.; Hu, M.; Huang, N.; Hurles, M. E.; Jin, H.; Jostins, L.; Keane, T. M.; Le, S. Q.; Lindsay, S.; Long, Q.; MacArthur, D. G.; Montgomery, S. B.; Parts, L.; Stalker, J.; Tyler-Smith, C.; Walter, K.; Zhang, Y.; Gerstein, M. B.; Snyder, M.; Abyzov, A.; Balasubramanian, S.; Bjornson, R.; Du, J.; Grubert, F.; Habegger, L.; Haraksingh, R.; Jee, J.; Khurana, E.; Lam, H. Y. K.; Leng, J.; Mu, X. J.; Urban, A. E.; Zhang, Z.; Li, Y.; Luo, R.; Marth, G. T.; Garrison, E. P.; Kural, D.; Quinlan, A. R.; Stewart, C.; Stromberg, M. P.; Ward, A. N.; Wu, J.; Lee, C.; Mills, R. E.; Shi, X.; McCarroll, S. A.; Banks, E.; DePristo, M. A.; Handsaker, R. E.; Hartl, C.; Korn, J. M.; Li, H.; Nemesh, J. C.; Sebat, J.; Makarov, V.; Ye, K.; Yoon, S. C.; Degenhardt, J.; Kaganovich, M.; Clarke, L.; Smith, R. E.; Zheng-Bradley, X.; Korbel, J. O.; Humphray, S.; Cheetham, R. K.; Eberle, M.; Kahn, S.; Murray, L.; Ye, K.; De La Vega, F. M.; Fu, Y.; Peckham, H. E.; Sun, Y. A.; Batzer, M. A.; Konkel, M. K.; Walker, J. A.; Xiao, C.; Iqbal, Z.; Desany, B.; Blackwell, T.; Snyder, M.; Xing, J.; Eichler, E. E.; Aksay, G.; Alkan, C.; Hajirasouliha, I.; Hormozdiari, F.; Kidd, J. M.; Chen, K.; Chinwalla, A.; Ding, L.; McLellan, M. D.; Wallis, J. W.; Hurles, M. E.; Conrad, D. F.; Walter, K.; Zhang, Y.; Gerstein, M. B.; Snyder, M.; Abyzov, A.; Du, J.; Grubert, F.; Haraksingh, R.; Jee, J.; Khurana, E.; Lam, H. Y. K.; Leng, J.; Mu, X. J.; Urban, A. E.; Zhang, Z.; Gibbs, R. A.; Bainbridge, M.; Challis, D.; Coafra, C.; Dinh, H.; Kovar, C.; Lee, S.; Muzny, D.; Nazareth, L.; Reid, J.; Sabo, A.; Yu, F.; Yu, J.; Marth, G. T.; Garrison, E. P.; Indap, A.; Leong, W. F.; Quinlan, A. R.; Stewart, C.; Ward, A. N.; Wu, J.; Cibulskis, K.; Fennell, T. J.; Gabriel, S. B.; Garimella, K. V.; Hartl, C.; Shefler, E.; Sougnez, C. L.; Wilkinson, J.; Clark, A. G.; Gravel, S.; Grubert, F.; Clarke, L.; Flicek, P.; Smith, R. E.; Zheng-Bradley, X.; Sherry, S. T.; Khouri, H. M.; Paschall, J. E.; Shumway, M. F.; Xiao, C.; McVean, G. A.; Katzman, S. J.; Abecasis, G. R.; Blackwell, T.; Mardis, E. R.; Dooling, D.; Fulton, L.; Fulton, R.; Koboldt, D. C.; Durbin, R. M.; Balasubramaniam, S.; Coffey, A.; Keane, T. M.; MacArthur, D. G.; Palotie, A.; Scott, C.; Stalker, J.; Tyler-Smith, C.; Gerstein, M. B.; Balasubramanian, S.; Chakravarti, A.; Knoppers, B. M.; Abecasis, G. R.; Bustamante, C. D.; Gharani, N.; Gibbs, R. A.; Jorde, L.; Kaye, J. S.; Kent, A.; Li, T.; McGuire, A. L.; McVean, G. A.; Ossorio, P. N.; Rotimi, C. N.; Su, Y.; Toji, L. H.; TylerSmith, C.; Brooks, L. D.; Felsenfeld, A. L.; McEwen, J. E.; Abdallah, A.; Juenger, C. R.; Clemm, N. C.; Collins, F. S.; Duncanson, A.; Green, E. D.; Guyer, M. S.; Peterson, J. L.; Schafer, A. J.; Abecasis, G. R.; Altshuler, D. L.; Auton, A.; Brooks, L. D.; Durbin, R. M.; Gibbs, R. A.; Hurles, M. E.; McVean, G. A. Demographic History and Rare Allele Sharing among Human Populations, Proceedings of the National Academy of Sciences, Volume 108 (2011) no. 29, pp. 11983-11988 | DOI

[39] Green, R. E.; Krause, J.; Briggs, A. W.; Maricic, T.; Stenzel, U.; Kircher, M.; Patterson, N.; Li, H.; Zhai, W.; Fritz, M. H.-Y.; Hansen, N. F.; Durand, E. Y.; Malaspinas, A.-S.; Jensen, J. D.; Marques-Bonet, T.; Alkan, C.; Prüfer, K.; Meyer, M.; Burbano, H. A.; Good, J. M.; Schultz, R.; Aximu-Petri, A.; Butthof, A.; Höber, B.; Höffner, B.; Siegemund, M.; Weihmann, A.; Nusbaum, C.; Lander, E. S.; Russ, C.; Novod, N.; Affourtit, J.; Egholm, M.; Verna, C.; Rudan, P.; Brajkovic, D.; Kucan, Ž.; Gušic, I.; Doronichev, V. B.; Golovanova, L. V.; Lalueza-Fox, C.; De La Rasilla, M.; Fortea, J.; Rosas, A.; Schmitz, R. W.; Johnson, P. L. F.; Eichler, E. E.; Falush, D.; Birney, E.; Mullikin, J. C.; Slatkin, M.; Nielsen, R.; Kelso, J.; Lachmann, M.; Reich, D.; Pääbo, S. A Draft Sequence of the Neandertal Genome, Science, Volume 328 (2010) no. 5979, pp. 710-722 | DOI

[40] Guillot, G.; Leblois, R.; Coulon, A.; Frantz, A. C. Statistical Methods in Spatial Genetics, Molecular Ecology, Volume 18 (2009) no. 23, pp. 4734-4756 | DOI

[41] Haak, W.; Lazaridis, I.; Patterson, N.; Rohland, N.; Mallick, S.; Llamas, B.; Brandt, G.; Nordenfelt, S.; Harney, E.; Stewardson, K.; Fu, Q.; Mittnik, A.; Bánffy, E.; Economou, C.; Francken, M.; Friederich, S.; Pena, R. G.; Hallgren, F.; Khartanovich, V.; Khokhlov, A.; Kunst, M.; Kuznetsov, P.; Meller, H.; Mochalov, O.; Moiseyev, V.; Nicklisch, N.; Pichler, S. L.; Risch, R.; Rojo Guerra, M. A.; Roth, C.; Szécsényi-Nagy, A.; Wahl, J.; Meyer, M.; Krause, J.; Brown, D.; Anthony, D.; Cooper, A.; Alt, K. W.; Reich, D. Massive Migration from the Steppe Was a Source for Indo-European Languages in Europe, Nature, Volume 522 (2015) no. 7555, pp. 207-211 | DOI

[42] Haller, B. C.; Messer, P. W. SLiM 2: Flexible, Interactive Forward Genetic Simulations, Molecular Biology and Evolution, Volume 34 (2017) no. 1, pp. 230-240 | DOI

[43] Haller, B. C.; Messer, P. W. SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model, Molecular Biology and Evolution, Volume 36 (2019) no. 3, pp. 632-637 | DOI

[44] Haller, B. C.; Messer, P. W. SLiM 4: Multispecies Eco-Evolutionary Modeling, The American Naturalist, Volume 201 (2023) no. 5, p. E127-E139 | DOI

[45] Haller, B. C.; Galloway, J.; Kelleher, J.; Messer, P. W.; Ralph, P. L. Tree-sequence Recording in SLiM Opens New Horizons for Forward-time Simulation of Whole Genomes, Molecular Ecology Resources, Volume 19 (2019) no. 2, pp. 552-566 | DOI

[46] Hanks, E. M.; Hooten, M. B. Circuit Theory and Model-Based Inference for Landscape Connectivity, Journal of the American Statistical Association, Volume 108 (2013) no. 501, pp. 22-33 | DOI

[47] Hudson, R. R. Generating Samples under a Wright–Fisher Neutral Model of Genetic Variation, Bioinformatics, Volume 18 (2002) no. 2, pp. 337-338 | DOI

[48] Kamm, J.; Terhorst, J.; Durbin, R.; Song, Y. S. Efficiently Inferring the Demographic History of Many Populations With Allele Count Data, Journal of the American Statistical Association, Volume 115 (2020) no. 531, pp. 1472-1487 | DOI

[49] Kelleher, J.; Etheridge, A.; Barton, N. Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size, Theoretical Population Biology, Volume 95 (2014), pp. 13-23 | DOI

[50] Kelleher, J.; Etheridge, A. M.; McVean, G. Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes, PLOS Computational Biology, Volume 12 (2016) no. 5, p. e1004842 | DOI

[51] Kelleher, J.; Thornton, K. R.; Ashander, J.; Ralph, P. L. Efficient Pedigree Recording for Fast Population Genetics Simulation, PLOS Computational Biology, Volume 14 (2018) no. 11, p. e1006581 | DOI

[52] Kelleher, J.; Wong, Y.; Wohns, A. W.; Fadil, C.; Albers, P. K.; McVean, G. Inferring Whole-Genome Histories in Large Population Datasets, Nature Genetics, Volume 51 (2019) no. 9, pp. 1330-1338 | DOI

[53] Khan, A. T.; Gogarten, S. M.; McHugh, C. P.; Stilp, A. M.; Sofer, T.; Bowers, M. L.; Wong, Q.; Cupples, L. A.; Hidalgo, B.; Johnson, A. D.; McDonald, M.-L. N.; McGarvey, S. T.; Taylor, M. R.; Fullerton, S. M.; Conomos, M. P.; Nelson, S. C. Recommendations on the Use and Reporting of Race, Ethnicity, and Ancestry in Genetic Research: Experiences from the NHLBI TOPMed Program, Cell Genomics, Volume 2 (2022) no. 8, p. 100155 | DOI

[54] Lazaridis, I.; Patterson, N.; Mittnik, A.; Renaud, G.; Mallick, S.; Kirsanow, K.; Sudmant, P. H.; Schraiber, J. G.; Castellano, S.; Lipson, M.; Berger, B.; Economou, C.; Bollongino, R.; Fu, Q.; Bos, K. I.; Nordenfelt, S.; Li, H.; De Filippo, C.; Prüfer, K.; Sawyer, S.; Posth, C.; Haak, W.; Hallgren, F.; Fornander, E.; Rohland, N.; Delsate, D.; Francken, M.; Guinet, J.-M.; Wahl, J.; Ayodo, G.; Babiker, H. A.; Bailliet, G.; Balanovska, E.; Balanovsky, O.; Barrantes, R.; Bedoya, G.; Ben-Ami, H.; Bene, J.; Berrada, F.; Bravi, C. M.; Brisighelli, F.; Busby, G. B. J.; Cali, F.; Churnosov, M.; Cole, D. E. C.; Corach, D.; Damba, L.; Van Driem, G.; Dryomov, S.; Dugoujon, J.-M.; Fedorova, S. A.; Gallego Romero, I.; Gubina, M.; Hammer, M.; Henn, B. M.; Hervig, T.; Hodoglugil, U.; Jha, A. R.; Karachanak-Yankova, S.; Khusainova, R.; Khusnutdinova, E.; Kittles, R.; Kivisild, T.; Klitz, W.; Kučinskas, V.; Kushniarevich, A.; Laredj, L.; Litvinov, S.; Loukidis, T.; Mahley, R. W.; Melegh, B.; Metspalu, E.; Molina, J.; Mountain, J.; Näkkäläjärvi, K.; Nesheva, D.; Nyambo, T.; Osipova, L.; Parik, J.; Platonov, F.; Posukh, O.; Romano, V.; Rothhammer, F.; Rudan, I.; Ruizbakiev, R.; Sahakyan, H.; Sajantila, A.; Salas, A.; Starikovskaya, E. B.; Tarekegn, A.; Toncheva, D.; Turdikulova, S.; Uktveryte, I.; Utevska, O.; Vasquez, R.; Villena, M.; Voevoda, M.; Winkler, C. A.; Yepiskoposyan, L.; Zalloua, P.; Zemunik, T.; Cooper, A.; Capelli, C.; Thomas, M. G.; Ruiz-Linares, A.; Tishkoff, S. A.; Singh, L.; Thangaraj, K.; Villems, R.; Comas, D.; Sukernik, R.; Metspalu, M.; Meyer, M.; Eichler, E. E.; Burger, J.; Slatkin, M.; Pääbo, S.; Kelso, J.; Reich, D.; Krause, J. Ancient Human Genomes Suggest Three Ancestral Populations for Present-Day Europeans, Nature, Volume 513 (2014) no. 7518, pp. 409-413 | DOI

[55] Levene, H. Genetic Equilibrium When More Than One Ecological Niche Is Available, The American Naturalist, Volume 87 (1953) no. 836, pp. 331-333 | DOI

[56] Librado, P.; Khan, N.; Fages, A.; Kusliy, M. A.; Suchan, T.; Tonasso-Calvière, L.; Schiavinato, S.; Alioglu, D.; Fromentier, A.; Perdereau, A.; Aury, J.-M.; Gaunitz, C.; Chauvey, L.; Seguin-Orlando, A.; Der Sarkissian, C.; Southon, J.; Shapiro, B.; Tishkin, A. A.; Kovalev, A. A.; Alquraishi, S.; Alfarhan, A. H.; Al-Rasheid, K. A. S.; Seregély, T.; Klassen, L.; Iversen, R.; Bignon-Lau, O.; Bodu, P.; Olive, M.; Castel, J.-C.; Boudadi-Maligne, M.; Alvarez, N.; Germonpré, M.; Moskal-del Hoyo, M.; Wilczyński, J.; Pospuła, S.; Lasota-Kuś, A.; Tunia, K.; Nowak, M.; Rannamäe, E.; Saarma, U.; Boeskorov, G.; Lōugas, L.; Kyselý, R.; Peške, L.; Bălășescu, A.; Dumitrașcu, V.; Dobrescu, R.; Gerber, D.; Kiss, V.; Szécsényi-Nagy, A.; Mende, B. G.; Gallina, Z.; Somogyi, K.; Kulcsár, G.; Gál, E.; Bendrey, R.; Allentoft, M. E.; Sirbu, G.; Dergachev, V.; Shephard, H.; Tomadini, N.; Grouard, S.; Kasparov, A.; Basilyan, A. E.; Anisimov, M. A.; Nikolskiy, P. A.; Pavlova, E. Y.; Pitulko, V.; Brem, G.; Wallner, B.; Schwall, C.; Keller, M.; Kitagawa, K.; Bessudnov, A. N.; Bessudnov, A.; Taylor, W.; Magail, J.; Gantulga, J.-O.; Bayarsaikhan, J.; Erdenebaatar, D.; Tabaldiev, K.; Mijiddorj, E.; Boldgiv, B.; Tsagaan, T.; Pruvost, M.; Olsen, S.; Makarewicz, C. A.; Valenzuela Lamas, S.; Albizuri Canadell, S.; Nieto Espinet, A.; Iborra, M. P.; Lira Garrido, J.; Rodríguez González, E.; Celestino, S.; Olària, C.; Arsuaga, J. L.; Kotova, N.; Pryor, A.; Crabtree, P.; Zhumatayev, R.; Toleubaev, A.; Morgunova, N. L.; Kuznetsova, T.; Lordkipanize, D.; Marzullo, M.; Prato, O.; Bagnasco Gianni, G.; Tecchiati, U.; Clavel, B.; Lepetz, S.; Davoudi, H.; Mashkour, M.; Berezina, N. Y.; Stockhammer, P. W.; Krause, J.; Haak, W.; Morales-Muñiz, A.; Benecke, N.; Hofreiter, M.; Ludwig, A.; Graphodatsky, A. S.; Peters, J.; Kiryushin, K. Y.; Iderkhangai, T.-O.; Bokovenko, N. A.; Vasiliev, S. K.; Seregin, N. N.; Chugunov, K. V.; Plasteeva, N. A.; Baryshnikov, G. F.; Petrova, E.; Sablin, M.; Ananyevskaya, E.; Logvin, A.; Shevnina, I.; Logvin, V.; Kalieva, S.; Loman, V.; Kukushkin, I.; Merz, I.; Merz, V.; Sakenov, S.; Varfolomeyev, V.; Usmanova, E.; Zaibert, V.; Arbuckle, B.; Belinskiy, A. B.; Kalmykov, A.; Reinhold, S.; Hansen, S.; Yudin, A. I.; Vybornov, A. A.; Epimakhov, A.; Berezina, N. S.; Roslyakova, N.; Kosintsev, P. A.; Kuznetsov, P. F.; Anthony, D.; Kroonen, G. J.; Kristiansen, K.; Wincker, P.; Outram, A.; Orlando, L. The Origins and Spread of Domestic Horses from the Western Eurasian Steppes, Nature, Volume 598 (2021) no. 7882, pp. 634-640 | DOI

[57] Liu, H.; Prugnolle, F.; Manica, A.; Balloux, F. A Geographically Explicit Genetic Model of Worldwide Human-Settlement History, The American Journal of Human Genetics, Volume 79 (2006) no. 2, pp. 230-237 | DOI

[58] Loog, L.; Mirazón Lahr, M.; Kovacevic, M.; Manica, A.; Eriksson, A.; Thomas, M. G. Estimating Mobility Using Sparse Data: Application to Human Genetic Variation, Proceedings of the National Academy of Sciences, Volume 114 (2017) no. 46, pp. 12213-12218 | DOI

[59] Loog, L. Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories, Philosophical Transactions of the Royal Society B: Biological Sciences, Volume 376 (2020) no. 1816 | DOI

[60] Lovelace, R.; Nowosad, J.; Muenchow, J. Geocomputation with R, Chapman and Hall/CRC, 2019 | DOI

[61] Lynggaard, C.; Bertelsen, M. F.; Jensen, C. V.; Johnson, M. S.; Frøslev, T. G.; Olsen, M. T.; Bohmann, K. Airborne Environmental DNA for Terrestrial Vertebrate Community Monitoring, Current Biology, Volume 32 (2022) no. 3, p. 701 | DOI

[62] Malécot, G. Un traitement stochastique des problèmes linéaires en génétique de population, Ann. Univ. Lyon. Sci. Sec., Volume 14 (1951), pp. 79-117

[63] Mallick, S.; Li, H.; Lipson, M.; Mathieson, I.; Gymrek, M.; Racimo, F.; Zhao, M.; Chennagiri, N.; Nordenfelt, S.; Tandon, A.; Skoglund, P.; Lazaridis, I.; Sankararaman, S.; Fu, Q.; Rohland, N.; Renaud, G.; Erlich, Y.; Willems, T.; Gallo, C.; Spence, J. P.; Song, Y. S.; Poletti, G.; Balloux, F.; Van Driem, G.; De Knijff, P.; Romero, I. G.; Jha, A. R.; Behar, D. M.; Bravi, C. M.; Capelli, C.; Hervig, T.; Moreno-Estrada, A.; Posukh, O. L.; Balanovska, E.; Balanovsky, O.; Karachanak-Yankova, S.; Sahakyan, H.; Toncheva, D.; Yepiskoposyan, L.; Tyler-Smith, C.; Xue, Y.; Abdullah, M. S.; Ruiz-Linares, A.; Beall, C. M.; Di Rienzo, A.; Jeong, C.; Starikovskaya, E. B.; Metspalu, E.; Parik, J.; Villems, R.; Henn, B. M.; Hodoglugil, U.; Mahley, R.; Sajantila, A.; Stamatoyannopoulos, G.; Wee, J. T. S.; Khusainova, R.; Khusnutdinova, E.; Litvinov, S.; Ayodo, G.; Comas, D.; Hammer, M. F.; Kivisild, T.; Klitz, W.; Winkler, C. A.; Labuda, D.; Bamshad, M.; Jorde, L. B.; Tishkoff, S. A.; Watkins, W. S.; Metspalu, M.; Dryomov, S.; Sukernik, R.; Singh, L.; Thangaraj, K.; Pääbo, S.; Kelso, J.; Patterson, N.; Reich, D. The Simons Genome Diversity Project: 300 Genomes from 142 Diverse Populations, Nature, Volume 538 (2016) no. 7624, pp. 201-206 | DOI

[64] Marcus, J.; Ha, W.; Barber, R. F.; Novembre, J. Fast and Flexible Estimation of Effective Migration Surfaces, eLife, Volume 10 (2021), p. e61927 | DOI

[65] Mathieson, I.; Scally, A. What Is Ancestry?, PLOS Genetics, Volume 16 (2020) no. 3, p. e1008624 | DOI

[66] McRae, B. H. Isolation by Resistance, Evolution, Volume 60 (2006) no. 8, pp. 1551-1561 | DOI

[67] Meyer, M.; Palkopoulou, E.; Baleka, S.; Stiller, M.; Penkman, K. E. H.; Alt, K. W.; Ishida, Y.; Mania, D.; Mallick, S.; Meijer, T.; Meller, H.; Nagel, S.; Nickel, B.; Ostritz, S.; Rohland, N.; Schauer, K.; Schüler, T.; Roca, A. L.; Reich, D.; Shapiro, B.; Hofreiter, M. Palaeogenomes of Eurasian Straight-Tusked Elephants Challenge the Current View of Elephant Evolution, eLife, Volume 6 (2017), p. e25413 | DOI

[68] Muktupavela, R. A.; Petr, M.; Ségurel, L.; Korneliussen, T.; Novembre, J.; Racimo, F. Modeling the Spatiotemporal Spread of Beneficial Alleles Using Ancient Genomes, eLife, Volume 11 (2022), p. e73767 | DOI

[69] Nagylaki, T. The Relation between Distant Individuals in Geographically Structured Populations, Mathematical Biosciences, Volume 28 (1976) no. 1-2, pp. 73-80 | DOI

[70] Osmond, M.; Coop, G. Estimating Dispersal Rates and Locating Genetic Ancestors with Genome-Wide Genealogies, bioRxiv (2021) | DOI

[71] Palkopoulou, E.; Lipson, M.; Mallick, S.; Nielsen, S.; Rohland, N.; Baleka, S.; Karpinski, E.; Ivancevic, A. M.; To, T.-H.; Kortschak, R. D.; Raison, J. M.; Qu, Z.; Chin, T.-J.; Alt, K. W.; Claesson, S.; Dalén, L.; MacPhee, R. D. E.; Meller, H.; Roca, A. L.; Ryder, O. A.; Heiman, D.; Young, S.; Breen, M.; Williams, C.; Aken, B. L.; Ruffier, M.; Karlsson, E.; Johnson, J.; Di Palma, F.; Alfoldi, J.; Adelson, D. L.; Mailund, T.; Munch, K.; Lindblad-Toh, K.; Hofreiter, M.; Poinar, H.; Reich, D. A Comprehensive Genomic History of Extinct and Living Elephants, Proceedings of the National Academy of Sciences, Volume 115 (2018) no. 11 | DOI

[72] Paradis, E. Analysis of Phylogenetics and Evolution with R, Springer New York, New York, NY, 2012 | DOI

[73] Paradis, E.; Schliep, K. Ape 5.0: An Environment for Modern Phylogenetics and Evolutionary Analyses in R, Bioinformatics, Volume 35 (2019) no. 3, pp. 526-528 | DOI

[74] Parducci, L.; Bennett, K. D.; Ficetola, G. F.; Alsos, I. G.; Suyama, Y.; Wood, J. R.; Pedersen, M. W. Ancient Plant DNA in Lake Sediments, New Phytologist, Volume 214 (2017) no. 3, pp. 924-942 | DOI

[75] Patterson, N.; Moorjani, P.; Luo, Y.; Mallick, S.; Rohland, N.; Zhan, Y.; Genschoreck, T.; Webster, T.; Reich, D. Ancient Admixture in Human History, Genetics, Volume 192 (2012) no. 3, pp. 1065-1093 | DOI

[76] Pebesma, E. Simple Features for R: Standardized Support for Spatial Vector Data, The R Journal, Volume 10 (2018) no. 1, p. 439 | DOI

[77] Peter, B.; Slatkin, M. Detecting Range Expansions from Genetic Data, Evolution; international journal of organic evolution, Volume 67 (2013), pp. 3274-3289 | DOI

[78] Petkova, D.; Novembre, J.; Stephens, M. Visualizing Spatial Population Structure with Estimated Effective Migration Surfaces, Nature Genetics, Volume 48 (2016) no. 1, pp. 94-100 | DOI

[79] Petr, M. slendr GitHub repository (Peer Community Journal archive), Zenodo, 2023 | DOI

[80] Pickrell, J. K.; Pritchard, J. K. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data, PLoS Genetics, Volume 8 (2012) no. 11, p. e1002967 | DOI

[81] Pickrell, J. K.; Reich, D. Toward a New History and Geography of Human Genes Informed by Ancient DNA, Trends in Genetics, Volume 30 (2014) no. 9, pp. 377-389 | DOI

[82] Purcell, S.; Neale, B.; Todd-Brown, K.; Thomas, L.; Ferreira, M. A.; Bender, D.; Maller, J.; Sklar, P.; De Bakker, P. I.; Daly, M. J.; Sham, P. C. PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses, The American Journal of Human Genetics, Volume 81 (2007) no. 3, pp. 559-575 | DOI

[83] Racimo, F.; Woodbridge, J.; Fyfe, R. M.; Sikora, M.; Sjögren, K.-G.; Kristiansen, K.; Vander Linden, M. The Spatiotemporal Spread of Human Migrations during the European Holocene, Proceedings of the National Academy of Sciences, Volume 117 (2020) no. 16, pp. 8989-9000 | DOI

[84] Ralph, P.; Thornton, K.; Kelleher, J. Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes, Genetics, Volume 215 (2020) no. 3, pp. 779-797 | DOI

[85] Ralph, P.; Coop, G. The Geography of Recent Genetic Ancestry across Europe, PLoS Biology, Volume 11 (2013) no. 5, p. e1001555 | DOI

[86] Rasmussen, M.; Li, Y.; Lindgreen, S.; Pedersen, J. S.; Albrechtsen, A.; Moltke, I.; Metspalu, M.; Metspalu, E.; Kivisild, T.; Gupta, R.; Bertalan, M.; Nielsen, K.; Gilbert, M. T. P.; Wang, Y.; Raghavan, M.; Campos, P. F.; Kamp, H. M.; Wilson, A. S.; Gledhill, A.; Tridico, S.; Bunce, M.; Lorenzen, E. D.; Binladen, J.; Guo, X.; Zhao, J.; Zhang, X.; Zhang, H.; Li, Z.; Chen, M.; Orlando, L.; Kristiansen, K.; Bak, M.; Tommerup, N.; Bendixen, C.; Pierre, T. L.; Grønnow, B.; Meldgaard, M.; Andreasen, C.; Fedorova, S. A.; Osipova, L. P.; Higham, T. F. G.; Ramsey, C. B.; Hansen, T. V. O.; Nielsen, F. C.; Crawford, M. H.; Brunak, S.; Sicheritz-Pontén, T.; Villems, R.; Nielsen, R.; Krogh, A.; Wang, J.; Willerslev, E. Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo, Nature, Volume 463 (2010) no. 7282, pp. 757-762 | DOI

[87] Rasmussen, S.; Allentoft, M. E.; Nielsen, K.; Orlando, L.; Sikora, M.; Sjögren, K.-G.; Pedersen, A. G.; Schubert, M.; Van Dam, A.; Kapel, C. M. O.; Nielsen, H. B.; Brunak, S.; Avetisyan, P.; Epimakhov, A.; Khalyapin, M. V.; Gnuni, A.; Kriiska, A.; Lasak, I.; Metspalu, M.; Moiseyev, V.; Gromov, A.; Pokutta, D.; Saag, L.; Varul, L.; Yepiskoposyan, L.; Sicheritz-Pontén, T.; Foley, R. A.; Lahr, M. M.; Nielsen, R.; Kristiansen, K.; Willerslev, E. Early Divergent Strains of Yersinia Pestis in Eurasia 5,000 Years Ago, Cell, Volume 163 (2015) no. 3, pp. 571-582 | DOI

[88] Ringbauer, H.; Kolesnikov, A.; Field, D. L.; Barton, N. H. Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns, Genetics, Volume 208 (2018) no. 3, pp. 1231-1245 | DOI

[89] Rousset, F. Genetic Differentiation and Estimation of Gene Flow from F-statistics under Isolation by Distance, Genetics, Volume 145 (1997) no. 4, pp. 1219-1228 | DOI

[90] Safner, T.; Miller, M. P.; McRae, B. H.; Fortin, M.-J.; Manel, S. Comparison of Bayesian Clustering and Edge Detection Methods for Inferring Boundaries in Landscape Genetics, International Journal of Molecular Sciences, Volume 12 (2011) no. 2, pp. 865-889 | DOI

[91] Sandve, G. K.; Nekrutenko, A.; Taylor, J.; Hovig, E. Ten Simple Rules for Reproducible Computational Research, PLoS Computational Biology, Volume 9 (2013) no. 10, p. e1003285 | DOI

[92] Slatkin, M.; Racimo, F. Ancient DNA and Human History, Proceedings of the National Academy of Sciences, Volume 113 (2016) no. 23, pp. 6380-6387 | DOI

[93] Slatkin, M. Gene Flow and Selection in a Cline, Genetics, Volume 75 (1973) no. 4, pp. 733-756 | DOI

[94] Slatkin, M.; Excoffier, L. Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift, Genetics, Volume 191 (2012) no. 1, pp. 171-181 | DOI

[95] Speidel, L.; Forest, M.; Shi, S.; Myers, S. R. A Method for Genome-Wide Genealogy Estimation for Thousands of Samples, Nature Genetics, Volume 51 (2019) no. 9, pp. 1321-1329 | DOI

[96] Staab, P. R.; Zhu, S.; Metzler, D.; Lunter, G. Scrm: Efficiently Simulating Long Sequences Using the Approximated Coalescent with Recombination, Bioinformatics, Volume 31 (2015) no. 10, pp. 1680-1682 | DOI

[97] Stat, M.; Huggett, M. J.; Bernasconi, R.; DiBattista, J. D.; Berry, T. E.; Newman, S. J.; Harvey, E. S.; Bunce, M. Ecosystem Biomonitoring with eDNA: Metabarcoding across the Tree of Life in a Tropical Marine Environment, Scientific Reports, Volume 7 (2017) no. 1, p. 12240 | DOI

[98] Taberlet, P.; Coissac, E.; Pompanon, F.; Brochmann, C.; Willerslev, E. Towards Next-generation Biodiversity Assessment Using DNA Metabarcoding, Molecular Ecology, Volume 21 (2012) no. 8, pp. 2045-2050 | DOI

[99] R.Core Team R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, 2021 (https://www.R-project.org)

[100] Terasaki Hart, D. E.; Bishop, A. P.; Wang, I. J. Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations, Molecular Biology and Evolution, Volume 38 (2021) no. 10, pp. 4634-4646 | DOI

[101] The 1000 Genomes Project Consortium A Map of Human Genome Variation from Population-Scale Sequencing, Nature, Volume 467 (2010) no. 7319, pp. 1061-1073 | DOI

[102] Theodoridis, S.; Fordham, D. A.; Brown, S. C.; Li, S.; Rahbek, C.; Nogues-Bravo, D. Evolutionary History and Past Climate Change Shape the Distribution of Genetic Diversity in Terrestrial Mammals, Nature Communications, Volume 11 (2020) no. 1, p. 2557 | DOI

[103] Trucchi, E. A New Powerful Tool to Easily Encode the Geo-Spatial Dimension in Population Genetics Simulations, Peer Community in Evolutionary Biology (2023), p. 100630 | DOI

[104] Vernot, B.; Zavala, E. I.; Gómez-Olivencia, A.; Jacobs, Z.; Slon, V.; Mafessoni, F.; Romagné, F.; Pearson, A.; Petr, M.; Sala, N.; Pablos, A.; Aranburu, A.; De Castro, J. M. B.; Carbonell, E.; Li, B.; Krajcarz, M. T.; Krivoshapkin, A. I.; Kolobova, K. A.; Kozlikin, M. B.; Shunkov, M. V.; Derevianko, A. P.; Viola, B.; Grote, S.; Essel, E.; Herráez, D. L.; Nagel, S.; Nickel, B.; Richter, J.; Schmidt, A.; Peter, B.; Kelso, J.; Roberts, R. G.; Arsuaga, J.-L.; Meyer, M. Unearthing Neanderthal Population History Using Nuclear and Mitochondrial DNA from Cave Sediments, Science, Volume 372 (2021) no. 6542, p. eabf1667 | DOI

[105] Wang, Y.; Pedersen, M. W.; Alsos, I. G.; De Sanctis, B.; Racimo, F.; Prohaska, A.; Coissac, E.; Owens, H. L.; Merkel, M. K. F.; Fernandez-Guerra, A.; Rouillard, A.; Lammers, Y.; Alberti, A.; Denoeud, F.; Money, D.; Ruter, A. H.; McColl, H.; Larsen, N. K.; Cherezova, A. A.; Edwards, M. E.; Fedorov, G. B.; Haile, J.; Orlando, L.; Vinner, L.; Korneliussen, T. S.; Beilman, D. W.; Bjørk, A. A.; Cao, J.; Dockter, C.; Esdale, J.; Gusarova, G.; Kjeldsen, K. K.; Mangerud, J.; Rasic, J. T.; Skadhauge, B.; Svendsen, J. I.; Tikhonov, A.; Wincker, P.; Xing, Y.; Zhang, Y.; Froese, D. G.; Rahbek, C.; Bravo, D. N.; Holden, P. B.; Edwards, N. R.; Durbin, R.; Meltzer, D. J.; Kjær, K. H.; Möller, P.; Willerslev, E. Late Quaternary Dynamics of Arctic Biota from Ancient Environmental Genomics, Nature, Volume 600 (2021) no. 7887, pp. 86-92 | DOI

[106] Wickham, H.; Grolemund, G. R for Data Science, O'Reilly Media, Inc., 2016 (https://r4ds.had.co.nz/)

[107] Wickham, H.; Averick, M.; Bryan, J.; Chang, W.; McGowan, L.; François, R.; Grolemund, G.; Hayes, A.; Henry, L.; Hester, J.; Kuhn, M.; Pedersen, T.; Miller, E.; Bache, S.; Müller, K.; Ooms, J.; Robinson, D.; Seidel, D.; Spinu, V.; Takahashi, K.; Vaughan, D.; Wilke, C.; Woo, K.; Yutani, H. Welcome to the Tidyverse, Journal of Open Source Software, Volume 4 (2019) no. 43, p. 1686 | DOI

[108] Willerslev, E.; Hansen, A. J.; Binladen, J.; Brand, T. B.; Gilbert, M. T. P.; Shapiro, B.; Bunce, M.; Wiuf, C.; Gilichinsky, D. A.; Cooper, A. Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments, Science, Volume 300 (2003) no. 5620, pp. 791-795 | DOI

[109] Wohns, A. W.; Wong, Y.; Jeffery, B.; Akbari, A.; Mallick, S.; Pinhasi, R.; Patterson, N.; Reich, D.; Kelleher, J.; McVean, G. A Unified Genealogy of Modern and Ancient Genomes, Science, Volume 375 (2022) no. 6583, p. eabi8264 | DOI

[110] Wright, S. Isolation by Distance, Genetics, Volume 28 (1943) no. 2, pp. 114-138 | DOI

[111] Yu, G.; Smith, D. K.; Zhu, H.; Guan, Y.; Lam, T. T.-Y. Ggtree : An R Package for Visualization and Annotation of Phylogenetic Trees with Their Covariates and Other Associated Data, Methods in Ecology and Evolution, Volume 8 (2017) no. 1, pp. 28-36 | DOI

Cited by Sources:

block.super