Abstract
Since the migrations that led humans to colonize Earth, our species has faced frequent adaptive challenges that have left signatures in the landscape of genetic variation and that we can identify in our today’s genomes. Here, we (i) perform an outlier approach on eight different population genetic statistics for 22 non-admixed human populations of the Phase III of the 1000 Genomes Project to detect selective sweeps at different historical ages, as well as events of recurrent positive selection in the human lineage; and (ii) create PopHumanScan, an online catalog that compiles and annotates all candidate regions under selection to facilitate their validation and thoroughly analysis. Well-known examples of human genetic adaptation published elsewhere are included in the catalog, as well as hundreds of other attractive candidates that will require further investigation. Designed as a collaborative database, PopHumanScan aims to become a central repository to share information, guide future studies and help advance our understanding of how selection has modeled our genomes as a response to changes in the environment or lifestyle of human populations. PopHumanScan is open and freely available at https://pophumanscan.uab.cat.
Highlights
Since the split with chimpanzees, and especially since the migrations that led humans to colonize almost every single place on Earth, our species has faced frequent environmental and social changes that have shaped the variation patterns of our genomes through the action of natural selection [1]. These environmental challenges include, for example, extreme cold temperatures in much of the Americas and Eurasia during the last ice age, limiting exposure to sunlight as we moved to higher latitudes or contact with new pathogens
PopHumanScan reports each evidence of selection with the empirical distributions of the corresponding DNA diversity statistic across the human genome and among populations, structural and functional annotations of the region, links to external databases, as well as cross-references to 268 publications
The information displayed in each row includes: (i) the genomic coordinates of the candidate locus, (ii) genes contained in or partially overlapping the region, (iii) the most extreme value for each of the eight statistics considered (i.e. most extreme value in any 10-kb window included in the region, for any population or population pair; green and red values are outliers (P < 0.0005) in the corresponding empirical distribution), (iv) color-coded dots depicting different types of selection signatures (i.e. Linkage Disequilibrium (LD), Site Frequency Spectrum (SFS) and/or Protein Changes), (v) color-coded dots depicting the meta-population(s) that show signatures of selection (i.e. Europe (EUR), Africa (AFR), South-Asia (SAS) and/or East-Asia (EAS)) and (vi) the source that contributed the candidate region under selection
Summary
Since the split with chimpanzees, and especially since the migrations that led humans to colonize almost every single place on Earth, our species has faced frequent environmental and social changes that have shaped the variation patterns of our genomes through the action of natural selection [1]. In addition to the exhaustive genome-wide selection scan that has been performed, we have created PopHumanScan, a collaborative, online database that is aimed at compiling and annotating adaptation events along the human evolutionary history (Figure 2).
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