The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
By Swapan Mallick, Heng Li, Mark Lipson, I. Mathieson, M. Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon and 69 more. Nature, 2016
1,396 citations recorded by the source corpus.
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
Subfields: Genetics
View Paper: https://www.semanticscholar.org/paper/b20616b0b707175d638cfdac4ac57640227efffb
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Genetics
- Oliver Stegle
- John A. Kamm
- Ira M. Hall
- Aaron R. Quinlan
- Mark J. P. Chaisson
- Evan E. Eichler
- Richard Durbin
- Paul Flicek
Citations in the corpus
- Mosdepth: quick coverage calculation for genomes and exomes (2017, methodology): “6) on a BAM with about 30X coverage from the Simon’s Genome Diversity Panel (Mallick et al., 2016) (Supplemental Info).”
- A high-coverage Neandertal genome from Vindija Cave in Croatia (2017, neutral): “A proportion of the genomes of all present-day people whose roots are outside Africa derives from Neandertals (2, 3, 22).”
- Haplotype-resolved diverse human genomes and integrated analysis of structural variation (2021, methodology): “We applied amachine-learningmethod( 47 )anddeveloped a hidden Markov model to identify ancestry-informative SNVs and to assign ancestral segments per block on the basis of population genetic data from the Simons Genome Diversity Project (SGDP) ( 18 , 48 ).”
- Insights into human genetic variation and population history from 929 diverse genomes (2019, methodology): “Outside of Africa, the time depths of population splits are in line with previous estimates (3, 4, 21), with all populations sharing most of their ancestry within the last 70 kya (Fig.”