Publications
Papers from the lab, and some of Iain's older papers (complete list). Please contact Iain if you have any trouble accessing any of these.
Preprints
Predicting functional consequences of recent natural selection in Britain. Poyraz L, Colbran LL, Mathieson I. bioRxiv Oct 2023 [preprint]
Insufficient evidence for natural selection associated with the Black Death. Barton AR*, Santander CG*, Skoglund P, Moltke I, Reich D, Mathieson I. bioRxiv Mar 2023 [preprint]
Interpreting Generative Adversarial Networks to Infer Natural Selection from Genetic Data. Riley R, Mathieson I, Mathieson S. bioRxiv Mar 2023 [preprint]
Ancient Admixture into Africa from the ancestors of non-Africans. Cole CB, Zhu SJ, Mathieson I, Prüfer K, Lunter G, bioRxiv June 2020 [preprint]
2023
Human genetics: An extreme fitness landscape. Mathieson I, Current Biology, Oct 2023 [commentary]
Socio-cultural practices affect sexual dimorphism in stature in Early Neolithic Europe. Cox SL, Nicklisch N, Franken M, Wahl J, Meller H, Haak W, Alt KW, Rosenstock E, Mathieson I, Nature Human Behavior, In Press [preprint]
Regularized sequence-context mutational trees capture variation in mutation rates across the human genome. Adams CJ, Conery M, Auerbach BJ, Jensen ST, Mathieson I Voight B, PLOS Genetics July 2023 [paper]
The genetic and phenotypic correlates of mtDNA copy number in a multi-ancestry cohort. Zaidi AA, Verma A, Morse C, Penn Medicine BioBank, Ritchie MD, Mathieson I, HGG Advances July 2023 [paper]
A gene-level test for directional selection on gene expression. Colbran LL, Ramos-Almodovar FC, Mathieson I, Genetics Apr 2023 [paper]
Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers. Davy T, Ju D, Mathieson I*, Skoglund P*, Current Biology Mar 2023 [paper]
Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus. Mathieson I*, Day F*, Barban N*, Tropf F,* Brazel D*, et al. , Nature Human Behavior Mar 2023 [paper][preprint]
Gene burden analysis identifies genes associated with increased risk and severity of adult-onset hearing loss in a diverse hospital-based cohort. Hui D, Mehrabi S, Quimby AE, Chen T, Chen S, Park J, Li B, Regeneron Genetics Center, Penn Medicine Biobank, Ruckenstein MJ, Rader DJ, Ritchie MD, Brant JA, Epstein DJ*, Mathieson I*, PLoS Genetics Jan 2023 [paper]
2022
Direct detection of natural selection in Bronze Age Britain. Mathieson I, Terhorst J, Genome Research Dec 2022 [paper]
Long runs of homozygosity are correlated with marriage preferences across global population samples. Sahoo SA, Zaidi AA, Anagol S, Mathieson I, Human Biology May 2022 [preprint]
The challenge of detecting recent natural selection in human populations. Mills MC, Mathieson I, PNAS, Apr 2022 [commentary]
Predicting skeletal stature using ancient DNA. Cox SL, Moots H, Stock JT, Shbat A, Bitarello BD, Haak W, Rosenstock E, Ruff CB, Mathieson I, American Journal of Biology Anthropology Jan 2022 [paper]
2021
Tracing the evolution of human gene regulation and its association with shifts in environment. Colbran LL, Johnson MR, Mathieson I, Capra JA, Genome Biology and Evolution Nov 2021 [paper]
The omnigenic model and polygenic prediction of complex traits. Mathieson I, American Journal of Human Genetics, Sep 2021 [perspective]
Automatic Inference of Demographic Parameters Using Generative Adversarial Networks. Wang Z, Wang J, Kourakos M, Hoang N, Lee HH, Mathieson I, Mathieson S, Molecular Ecology Resources Mar 2021 [paper]
The evolution of skin pigmentation associated variation in West Eurasia. Ju D, Mathieson I, PNAS Jan 2021. [paper]
2020
Demographic history impacts stratification in polygenic scores. Zaidi AA, Mathieson I, eLife Dec 2020. [paper]
Polygenic scores for height in admixed populations. Bitarello BD, Mathieson I, G3 Nov 2020. [paper]
Human adaptation over the past 40,000 years. Mathieson I, Current Opinions in Genetics and Development; June 2020. [review]
What is Ancestry? Mathieson I, Scally A. PLOS Genetics; Mar 2020. [opinion]
Limited evidence for selection at the FADS locus in Native American populations. Mathieson I
Molecular Biology and Evolution; Mar 2020. [paper]
Tracking human population structure through time from whole genome sequences. Wang K , Mathieson I, O’Connell J, Schiffels S. PLOS Genetics; Mar 2020. [paper]
An ancient baboon genome demonstrates long-term population continuity in southern Africa. Mathieson I*, Abascal F*, Vinner L, Skoglund P, Pomilla C, Mitchell P, Arthur C, Gurdasani D, Willerslev E, Sandhu M, Dewar G. Genome Biology and Evolution; Feb 2020. [paper]
2019
Genetic contributions to variation in human stature in prehistoric Europe. Cox SL, Ruff CB, Maier RM, Mathieson I.
PNAS; Oct 2019; [paper]
Signals of polygenic adaptation on height have been overestimated due to uncorrected population structure in genome-wide association studies. M Sohail*, R M Maier*, A Ganna, A Bloemendal, A R Martin, M C Turchin, C W K Chiang, J N Hirschhorn, M Daly, N Patterson, B Neale**, I Mathieson**, D Reich**, S R Sunyaev**. eLife; Mar 2019. [paper]
2018
FADS1 and the timing of human adaptation to agriculture. S Mathieson, I Mathieson. Molecular Biology and Evolution December 2018 [paper]
Ancient Genomics of Modern Humans: The First Decade. Skoglund P, Mathieson I. Annual Review of Genomics and Human Genetics August 2018 [review]
The Genomic History Of Southeastern Europe. Mathieson I, Alpaslan Roodenberg S, Posth C, Szécsényi-Nagy A, Rohland N, Mallick S, et al. Nature March 2018 [paper]
Some earlier papers
Differences in the rare variant spectrum among human populations. Mathieson I, Reich D PLoS Genetics Feb 2017 [paper][code]
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Mallick S, Li H*, Lipson M*, Mathieson I*, Gymreck M, Racimo F, et al. Nature Jun 2016 [paper][data]
Genome-wide patterns of selection in 230 ancient Eurasians. Mathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N, Alpaslan Roodenberg S, et al. Nature Dec 2015 [paper][preprint][data][bams][code]
Demography and the age of rare variants. Mathieson I, McVean G PLoS Genetics Aug 2014 [paper][code]
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Rimmer A*, Phan H*, Mathieson I, Iqbal Z, Twigg SRF, WGS500 Consortium, Wilkie AOM, McVean G, Lunter G Nature Genetics Jul 2014 [paper][software]
Strong male bias drives germline mutation in chimpanzees. Venn O, Turner I, Mathieson I, de Groot N, Bontrop R, McVean G Science Jun 2014 [paper]
Estimating selection coefficients in spatially structured populations from time series data of allele frequencies. Mathieson I, McVean G Genetics Jan 2013 [paper][code]
Meta-analysis indicates that common variants at the DISC1 locus are not associated with schizophrenia Mathieson I, Munafò M, Flint J Molecular Psychiatry Apr 2012 [paper]
Differential confounding of rare and common variants in spatially structured populations. Mathieson I, McVean G Nature Genetics Feb 2012 [paper][PMC]