Publications
Preprints
Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs, by Nathaniel S Pope, Samuel Tallman, Benjamin Jeffery, Duncan Robertson, Yan Wong, Savita Karthikeyan, Peter L Ralph, Jerome Kelleher, 2026.
Provides a major update to the methods in tsdate.
Population-scale Ancestral Recombination Graphs with tskit 1.0, by Ben Jeffery, Yan Wong, Kevin Thornton, Georgia Tsambos, Gertjan Bisschop, Yun Deng, E Castedo Ellerman, Thomas B Forest, Halley Fritze, Daniel Goldstein, Gregor Gorjanc, Graham Gower, Simon Gravel, Jeremy Guez, Benjamin C Haller, Andrew D Kern, Lloyd Kirk, Ivan Krukov, Hanbin Lee, Brieuc Lehmann, Hossameldin Loay, Matthew M Osmond, Duncan S Palmer, Nathaniel S Pope, Aaron P Ragsdale, Duncan Robertson, Murillo F Rodrigues, Hugo van Kemenade, Clemens L Weiß, Anthony Wilder Wohns, Shing H Zhan, Brian C Zhang, Marianne Aspbury, Nikolas A Baya, Saurabh Belsare, Arjun Biddanda, Francisco Campuzano Jiménez, Ariella Gladstein, Bing Guo, Savita Karthikeyan, Warren W Kretzschmar, Inés Rebollo, Kumar Saunack, Ruhollah Shemirani, Alexis Simon, Chris Smith, Jeet Sukumaran, Jonathan Terhorst, Per Unneberg, Ao Zhang, Peter Ralph, Jerome Kelleher, 2026.
Provides the citation for the software package tskit.
A Statistical Framework to Infer the Mutation Model of Tandem Repeat Variants, by Luis Fernandez-Luna, Sebastián Iturbe, Carolina Adam, Nathaniel S Pope, Diego Ortega-Del Vecchyo, Rori Rohlfs, 2026.
A non-invasive method to genotype cephalopod sex by quantitative PCR, by Frederick A. Rubino, Gabrielle C. Coffing, Connor J. Gibbons, Scott T. Small, Thomas Desvignes, Jeffery Pessutti, Ann M. Petersen, Alexander Arkhipkin, Zhanna Shcherbich, John H. Postlethwait, Andrew D. Kern, Tessa G. Montague, 2025.
Neural Posterior Estimation for Population Genetics, by Jiseon Min, Yuxin Ning, Nathaniel S. Pope, Franz Baumdicker, Andrew D. Kern, 2025.
Genetic prediction with ARG-powered linear algebra, by Hanbin Lee, Nathaniel S Pope, Jerome Kelleher, Gregor Gorjanc, Peter L Ralph, 2025.
Describes the software package tslmm.
Coalescence and Translation: A Language Model for Population Genetics, by Kevin Korfmann, Nathaniel S. Pope, Melinda Meleghy, Aurelien Tellier, Andrew D Kern, 2025.
Bridging forward-in-time and coalescent simulations using pyslim, by Shyamalika Gopalan, Murillo F Rodrigues, Peter L Ralph, Benjamin C Haller, 2025.
Describes the software package pyslim.
Accurate Detection of Incomplete Lineage Sorting via Supervised Machine Learning, by Benjamin Rosenzweig, Andrew D. Kern, Matthew W. Hahn, 2023.
slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes, by Martin Petr, Benjamin C. Haller, Peter L. Ralph, and Fernando Racimo, 2022.
Publications
SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes, by Benjamin C Haller, Peter L Ralph, Philipp W Messer, in Molecular Biology and Evolution, 2026.
Quantitative genetics of microbiome-mediated traits, by Bob Week, Peter L Ralph, Hannah F Tavalire, William A Cresko, Brendan JM Bohannan, in Evolution, 2025.
Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae, by Clara T. Rehmann, Scott T. Small, Peter L. Ralph, and Andrew D. Kern, in Molecular Biology and Evolution, 2025.
Simulation-based spatially explicit close-kin mark-recapture, by Gilia Patterson, Claire K. Goodfellow, Nelson Ting, Andrew D. Kern, Peter L. Ralph, in Molecular Ecology Resources, 2025.
On ARGs, pedigrees, and genetic relatedness matrices, by Brieuc Lehmann, Hanbin Lee, Luke Anderson-Trocmé, Jerome Kelleher, Gregor Gorjanc, Peter L Ralph, in Genetics, 2025.
Accessible, realistic genome simulation with selection using stdpopsim, by Graham Gower, Nathaniel S. Pope, Murillo F. Rodrigues, Silas Tittes, Linh N. Tran, Ornob Alam, Maria Izabel A. Cavassim, Peter D. Fields, Benjamin C. Haller, Xin Huang, Ben Jeffrey, Kevin Korfmann, Christopher C. Kyriazis, Jiseon Min, Inés Rebollo, Clara T. Rehmann, Scott T. Small, Chris C. R. Smith, Georgia Tsambos, Yan Wong, Yu Zhang, Christian D. Huber, Gregor Gorjanc, Aaron P. Ragsdale, Ilan Gronau, Ryan N. Gutenkunst, Jerome Kelleher, Kirk E. Lohmueller, Daniel R. Schrider, Peter L. Ralph, Andrew D. Kern, in Molecular Biology and Evolution, 2025.
A forest is more than its trees: haplotypes and ancestral recombination graphs, by Halley Fritze, Nathaniel Pope, Jerome Kelleher, Peter Ralph, in Genetics, 2025.
Describes methods implemented in tscompare.
Cephalopod Sex Determination and its Ancient Evolutionary Origin, by Gabrielle C. Coffing, Silas Tittes, Scott T. Small, Jeremea O. Songco-Casey, Denise M. Piscopo, Judit R. Pungor, Adam C. Miller, Cristopher M. Niell, Andrew D. Kern, in Current Biology, 2025.
Population genetics meets ecology: a guide to individual-based simulations in continuous landscapes, by Elizabeth T. Chevy, Jiseon Min, Victoria Caudill, Samuel E. Champer, Benjamin C. Haller, Clara T. Rehmann, Chris C. R. Smith, Silas Tittes, Philipp W. Messer, Andrew D. Kern, Sohini Ramachandran, and Peter L. Ralph, in Ecology and Evolution, 2025.
Likelihoods for a general class of ARGs under the SMC, by Gertjan Bisschop, Jerome Kelleher, Peter Ralph, in Genetics, 2025.
Estimation of spatial demographic maps from polymorphism data using a neural network, by Chris C. R. Smith, Gilia C. Patterson, Peter L. Ralph, Andrew D. Kern, in Mol Ecol Resour., 2024.
Shared evolutionary processes shape landscapes of genomic variation in the great apes, by Murillo F. Rodrigues, Andrew D. Kern, and Peter L. Ralph, in Genetics, 2024.
Evaluating evidence for co-geography in the Anopheles Plasmodium host-parasite system, by Clara T Rehmann, Peter L Ralph, and Andrew D Kern, in G3, 2024.
Large effects and the infinitesimal model, by Todd L. Parsons and Peter L. Ralph, in Theoretical Population Biology, 2024.
Looking forwards and backwards: dynamics and genealogies of locally regulated populations, by Alison M. Etheridge, Ian Letter, Thomas G. Kurtz, Peter L. Ralph, and Terence Tsui Ho Lung, in Electronic Journal of Probability, 2024.
Genetic architecture, spatial heterogeneity, and the coevolutionary arms race between newts and snakes, by Victoria Caudill and Peter L Ralph, in American Naturalist, 2024.
A Quantitative Genetic Model of Background Selection in Humans, by Vince Buffalo and Andrew D. Kern, in PLoS Genetics, 2024.
disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data, by Chris C. R. Smith and Andrew D. Kern, in BMC Bioinformatics, 2023.
Describes the software package disperseNN2.
Dispersal inference from population genetic variation using a convolutional neural network, by Chris C. R. Smith, Silas Tittes, Peter L. Ralph, Andrew D. Kern, in Genetics, 2023.
Describes the software package disperseNN.
Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito, by Scott T. Small, Carlo Costantini, N’Fale Sagnon, Moussa W. Guelbeogo, Scott J. Emrich, Andrew D. Kern, Michael C. Fontaine, Nora J. Besansky, in Proc. Natl. Acad. Sci. U.S.A., 2023.
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations, by M. Elise Lauterbur, Maria Izabel A. Cavassim, Ariella L. Gladstein, Graham Gower, Nathaniel S. Pope, Georgia Tsambos, Jeffrey Adrion, Saurabh Belsare, Arjun Biddanda, Victoria Caudill, Jean Cury, Ignacio Echevarria, Benjamin C. Haller, Ahmed R. Hasan, Xin Huang, Leonardo Nicola Martin Iasi, Ekaterina Noskova, Jana Obšteter, Vitor Antonio Corrêa Pavinato, Alice Pearson, David Peede, Manolo F. Perez, Murillo F. Rodrigues, Chris C.R. Smith, Jeffrey P. Spence, Anastasia Teterina, Silas Tittes, Per Unneberg, Juan Manuel Vazquez, Ryan K. Waples, Anthony Wilder Wohns, Yan Wong, Franz Baumdicker, Reed A. Cartwright, Gregor Gorjanc, Ryan N. Gutenkunst, Jerome Kelleher, Andrew D. Kern, Aaron P. Ragsdale, Peter L. Ralph, Daniel R. Schrider, Ilan Gronau, in eLife, 2023.
Cell types and molecular architecture of the octopus visual system, by Jeremea O. Songco-Casey, Gabrielle C. Coffing, Denise M. Piscopo, Judit R. Pungor, Andrew D. Kern, Adam C. Miller, and Cristopher M. Niell, in Current Biology, 2022.
System drift and speciation, by Josh S Schiffman and Peter L. Ralph, in Evolution, 2022.
Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency, by Frederick A. Matsen, Peter L. Ralph, in Journal of Computational Biology, 2022.
Efficient ancestry and mutation simulation with msprime 1.0, by Franz Baumdicker, Gertjan Bisschop, Daniel Goldstein, Graham Gower, Aaron P Ragsdale, Georgia Tsambos, Sha Zhu, Bjarki Eldon, E Castedo Ellerman, Jared G Galloway, Ariella L Gladstein, Gregor Gorjanc, Bing Guo, Ben Jeffery, Warren W Kretzschumar, Konrad Lohse, Michael Matschiner, Dominic Nelson, Nathaniel S Pope, Consuelo D Quinto-Cortés, Murillo F Rodrigues, Kumar Saunack, Thibaut Sellinger, Kevin Thornton, Hugo van Kemenade, Anthony W Wohns, Yan Wong, Simon Gravel, Andrew D Kern, Jere Koskela, Peter L Ralph, Jerome Kelleher, in Genetics, 2022.
Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning, by Alexander T. Xue, Daniel R. Schrider, Andrew D. Kern, and the Ag1000G Consortium, in Mol. Biol. Evol., 2021.
Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks, by Katja R Kasimatis, Abin Abraham, Peter L Ralph, Andrew D Kern, John A Capra, Patrick C Phillips, in Genetics, 2021.
Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin’s paradox, by Vince Buffalo, in eLife, 2021.
Visualizing population structure with variational autoencoders, by C J Battey, Gabrielle C Coffing, Andrew D Kern, in G3 Genes|Genomes|Genetics, 2021.
A Few Stickleback Suffice for the Transport of Alleles to New Lakes, by Jared Galloway, William A Cresko, Peter Ralph, in G3 Genes|Genomes|Genetics, 2020.
Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data, by CJ Battey, Peter L. Ralph, and Andrew D. Kern, in Genetics, 2020.
Predicting geographic location from genetic variation with deep neural networks, by CJ Battey, Peter L. Ralph, and Andrew D. Kern, in eLife, 2020.
Describes the software package ‘locator’.
Predicting the Landscape of Recombination Using Deep Learning, by Jeffrey R Adrion, Jared G Galloway, Andrew D Kern, in Molecular Biology and Evolution, 2020.
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers, by Sean Stankowski, Madeline A. Chase, Allison M. Fuiten, Murillo F. Rodrigues, Peter L. Ralph, and Matthew A Streisfeld, in PLoS Biology, 2019.
An empirical approach to demographic inference with genomic data, by Peter L. Ralph, in Theoretical Population Biology, 2019.
Are populations like a circuit? Comparing isolation by resistance to a new coalescent-based method, by Erik Lundgren and Peter L. Ralph, in Molecular Ecology Resources, 2019.
Local PCA shows how the effect of population structure differs along the genome, by Han Li and Peter Ralph, in Genetics, 2019.
Describes the R package lostruct.
Limits to Genomic Divergence Under Sexually Antagonistic Selection, by Katja R. Kasimatis, Peter L. Ralph and Patrick C. Phillips, in G3, 2019.
Spatial Population Genetics: It’s About Time, by Gideon Bradburd and Peter L. Ralph, in Annual Review of Ecology, Evolution, and Systematics, 2019.
Selected older publications
Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia, by Daniel R. Schrider, Julien Ayroles, Daniel R. Matute, Andrew D. Kern, in PLoS Genet, 2018.
Supervised Machine Learning for Population Genetics: A New Paradigm, by Daniel R. Schrider, Andrew D. Kern, in Trends in Genetics, 2018.
diploS/HIC: An Updated Approach to Classifying Selective Sweeps, by Andrew D Kern, Daniel R Schrider, in G3 Genes|Genomes|Genetics, 2018.
Efficient pedigree recording for fast population genetics simulation, by Jerome Kelleher, Kevin Thornton, Jaime Ashander, and Peter Ralph, in PLoS Computational Biology, 2018.
The tools described here are part of tskit.
Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes, by Benjamin C Haller, Jared Galloway, Jerome Kelleher, Philipp W Messer, and Peter L Ralph., in Molecular Ecology Resources, 2018.
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome, by Daniel R. Schrider, Andrew D. Kern, in Molecular Biology and Evolution, 2017.
Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models, by Andrew D Kern, Jody Hey, in Genetics, 2017.
S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning, by Daniel R. Schrider, Andrew D. Kern, in PLoS Genetics, 2016.
Effects of Linked Selective Sweeps on Demographic Inference and Model Selection, by Daniel R Schrider, Alexander G Shanku, Andrew D Kern, in Genetics, 2016.
Discoal: flexible coalescent simulations with selection, by Andrew D. Kern, Daniel R. Schrider, in Bioinformatics, 2016.
Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps, by Daniel R Schrider, Fábio K Mendes, Matthew W Hahn, Andrew D Kern, in Genetics, 2015.
The role of standing variation in geographic convergent adaptation, by Peter Ralph and Graham Coop, in American Naturalist, 2015.
Convergent evolution during local adaptation to patchy landscapes, by Peter Ralph and Graham Coop, in PLoS Genetics, 2015.
Parallel Geographic Variation in Drosophila melanogaster, by Josie A Reinhardt, Bryan Kolaczkowski, Corbin D Jones, David J Begun, Andrew D Kern, in Genetics, 2014.
The geography of recent genetic ancestry across Europe, by Peter Ralph and Graham Coop,, in PLoS Biology, 2013.
Our summary plus discussion at haldane’s sieve; also discussed at the Loom and nature news)
Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster, by Bryan Kolaczkowski, Andrew D Kern, Alisha K Holloway, David J Begun, in Genetics, 2011.
Parallel adaptation: One or many waves of advance of an advantageous allele?, by Peter Ralph and Graham Coop, in Genetics, 2010.
Reviewed by Daniel Wilson, John Hawks, Luke Jostins, and various at Faculty of 1000.
A Population Genetic Hidden Markov Model for Detecting Genomic Regions Under Selection, by A. D. Kern, D. Haussler, in Molecular Biology and Evolution, 2010.
Human Genome Ultraconserved Elements Are Ultraselected, by S. Katzman, A. D. Kern, G. Bejerano, G. Fewell, L. Fulton, R. K. Wilson, S. R. Salama, D. Haussler, in Science, 2007.
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans, by David J Begun, Alisha K Holloway, Kristian Stevens, LaDeana W Hillier, Yu-Ping Poh, Matthew W Hahn, Phillip M Nista, Corbin D Jones, Andrew D Kern, Colin N Dewey, Lior Pachter, Eugene Myers, Charles H Langley, in PLoS Biol, 2007.
Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein-Interaction Networks, by Matthew W. Hahn, Andrew D. Kern, in Molecular Biology and Evolution, 2004.
Genomic effects of nucleotide substitution in Drosophila simulans, by A. D. Kern, C. D. Jones, D. J. Begun, in Genetics, 2002.