Perelman School of Medicine at the University of Pennsylvania

Mathieson Lab


Selected 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. 


Long runs of homozygosity are correlated with marriage preferences across global population samples. Sahoo SA, Zaidi AA, Anagol S, Mathieson I, bioRxiv Mar 2021 [preprint]

Estimating time-varying selection coefficients from time series data of allele frequencies. Mathieson I, bioRxiv Nov 2020 [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]

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*, eQTLGen Consortium, BIOS Consortium, Vaez A, van Zuydam B, Bitarello BD, Snieder H, den Hoed M, Ong K, Mills M**, Perry J**, Human Reproductive Behaviour Consortium, bioRxiv May 2020 [preprint]


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 Nov 2021 [paper]

Tracing the evolution of human gene regulation and its association with shifts in environmentColbran LL, Johnson MR,  Mathieson I, Capra JA, Genome Biology and Evolution Nov 2021 [paper]

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]


Demographic history impacts stratification in polygenic scores. Zaidi AAMathieson IeLife 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]


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]


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 EuropeMathieson I, Alpaslan Roodenberg S, Posth C, Szécsényi-Nagy A, Rohland N, Mallick S, et al. Nature March 2018 [paper]


Differences in the rare variant spectrum among human populationsMathieson I, Reich D PLoS Genetics Feb 2017 [paper][code]

Selected earlier papers

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 variantsMathieson 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 populationsMathieson I, McVean G Nature Genetics Feb 2012 [paper][PMC]