Evo_papers

Papers on human evolutionary genomics

These papers represent some important resources for the study of human evolutionary genomics. This is not an exhaustive list and I will likley add to it over time!

Reviews

1. Gregory TR. Understanding natural selection: essential concepts and common misconceptions. Evolution: Education and outreach. 2009 Jun;2(2):156-75.
2. Fu W, Akey JM. Selection and adaptation in the human genome. Annual review of genomics and human genetics. 2013 Aug 31;14:467-89.
3. Visscher PM, Brown MA, McCarthy MI, Yang J. Five years of GWAS discovery. The American Journal of Human Genetics. 2012 Jan 13;90(1):7-24.
4. Alföldi J, Lindblad-Toh K. Comparative genomics as a tool to understand evolution and disease. Genome research. 2013 Jul 1;23(7):1063-8.
5. Vitti JJ, Grossman SR, Sabeti PC. Detecting natural selection in genomic data. Annual review of genetics. 2013.
6. Marciniak S, Perry GH. Harnessing ancient genomes to study the history of human adaptation. Nature Reviews Genetics. 2017 Nov;18(11):659-74.
7. Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. The influence of evolutionary history on human health and disease. Nature Reviews Genetics. 2021 May;22(5):269-83.
8. Timpson NJ, Greenwood CM, Soranzo N, Lawson DJ, Richards JB. Genetic architecture: the shape of the genetic contribution to human traits and disease. Nature Reviews Genetics. 2018 Feb;19(2):110-24.
9. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH. Finding the missing heritability of complex diseases. Nature. 2009 Oct;461(7265):747-53.

Foundational Papers

1. Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O’connor TD, Santpere G, Cagan A. Great ape genetic diversity and population history. Nature. 2013 Jul;499(7459):471-5.
2. Telenti A, Pierce LC, Biggs WH, Di Iulio J, Wong EH, Fabani MM, Kirkness EF, Moustafa A, Shah N, Xie C, Brewerton SC. Deep sequencing of 10,000 human genomes. Proceedings of the National Academy of Sciences. 2016 Oct 18;113(42):11901-6.
3. Boyle EA, Li YI, Pritchard JK. An expanded view of complex traits: from polygenic to omnigenic. Cell. 2017 Jun 15;169(7):1177-86.

Methods Papers

1. Akey JM. Constructing genomic maps of positive selection in humans: where do we go from here?. Genome research. 2009 May 1;19(5):711-22.
2. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS computational biology. 2010 Dec 2;6(12):e1001025.
3. Rasmussen MD, Hubisz MJ, Gronau I, Siepel A. Genome-wide inference of ancestral recombination graphs. PLoS genetics. 2014 May 15;10(5):e1004342.
4. Booker TR, Jackson BC, Keightley PD. Detecting positive selection in the genome. BMC biology. 2017 Dec;15(1):1-0.
5. Huang YF, Gulko B, Siepel A. Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nature genetics. 2017 Apr;49(4):618-24.
6. Siewert KM, Voight BF. Detecting long-term balancing selection using allele frequency correlation. Molecular biology and evolution. 2017 Nov 1;34(11):2996-3005.
7. Guo J, Yang J, Visscher PM. Leveraging GWAS for complex traits to detect signatures of natural selection in humans. Current opinion in genetics & development. 2018 Dec 1;53:9-14.
8. Zeng J, De Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue A, Sidorenko J, McRae AF, Powell JE. Signatures of negative selection in the genetic architecture of human complex traits. Nature genetics. 2018 May;50(5):746-53.
9. Li J, Hong X, Mesiano S, Muglia LJ, Wang X, Snyder M, Stevenson DK, Shaw GM. Natural selection has differentiated the progesterone receptor among human populations. The American Journal of Human Genetics. 2018 Jul 5;103(1):45-57.
10. LaBella AL, Abraham A, Pichkar Y, Fong SL, Zhang G, Muglia LJ, Abbot P, Rokas A, Capra JA. Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nature communications. 2020 Jul 24;11(1):1-2.
11. Mika K, Marinić M, Singh M, Muter J, Brosens JJ, Lynch VJ. Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes. Elife. 2021 Oct 8;10:e69584.
12. Zeng J, Xue A, Jiang L, Lloyd-Jones LR, Wu Y, Wang H, Zheng Z, Yengo L, Kemper KE, Goddard ME, Wray NR. Widespread signatures of natural selection across human complex traits and functional genomic categories. Nature communications. 2021 Feb 19;12(1):1-2.
13. Song W, Shi Y, Wang W, Pan W, Qian W, Yu S, Zhao M, Lin GN. A selection pressure landscape for 870 human polygenic traits. Nature Human Behaviour. 2021 Dec;5(12):1731-43. Note This paper made some conclusions that were controversial in the field - if you read this let's chat about it!
14. Abraham A, LaBella AL, Capra JA, Rokas A. Mosaic patterns of selection in genomic regions associated with diverse human traits. bioRxiv. 2022 Jan 1.

Methods and Databases links

• VCF Tools - VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project http://vcftools.sourceforge.net/
• SNPsnap -identification and annotation of matched SNPs - https://data.broadinstitute.org/mpg/snpsnap/index.html
• UCSC Genome Browswer - a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data - https://genome.ucsc.edu/
• 1000 Genomes Selection Browswer - A database of signatures of natural selection in the human genome - https://hsb.upf.edu/
• rehh Vignette - whole genome scans for footprints of selection using statistics related to Extended Haplotype Homozygosity (EHH) (Sabeti et al. 2002) - https://cran.r-project.org/web/packages/rehh/vignettes/rehh.html
• RegulomeDB - indetify DNA features and regulatory elements in non-coding regions of the human genome - https://regulomedb.org/regulome-search/
• BioMart - Tables of Ensembl data can be downloaded via the highly customisable BioMart data mining tool - https://useast.ensembl.org/info/data/biomart/index.html
• SNP-db - database of SNPs from NIH - https://www.ncbi.nlm.nih.gov/snp/
• Ensemble genome browswer - genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. -https://useast.ensembl.org/index.html
• TimeTree - TimeTree is a public knowledge-base for information on the evolutionary timescale of life - http://www.timetree.org/
• phangorn - phangorn is a package for phylogenetic reconstruction and analysis in the R language - https://github.com/KlausVigo/phangorn
• PopArt - PopART (Population Analysis with Reticulate Trees) is free population genetics software that was developed as part of the Allan Wilson Centre Imaging Evolution Initiative - http://popart.otago.ac.nz/index.shtml
• Neale Lab GWAS of UK BioBank - http://www.nealelab.is/uk-biobank
• GWAS Catalog - repository of GWAS summary statistics - https://www.ebi.ac.uk/gwas/
• Mequite - DNA sequence and alignment visualization - https://github.com/MesquiteProject/MesquiteCore
• iTOL - For visualizing and annotating phylogenetic trees - https://itol.embl.de/