Genome study presents new way to track historical demographics of US populations
Sharon Browning of the University of Washington and colleagues developed a method to estimate historical effective population size, which is the number of individuals who pass on their genes to the next generation, to reveal the shifting demographic history of U.S. populations during the last several thousand years. They report their findings in a new study published May 24th, 2018 in PLOS Genetics.
Many populations in the U.S. are mixed, with ancestry from Europe, Africa, and the Americas. By looking at genome-wide data from several hundred individuals from a population, scientists can learn not only the current effective population size, but also the sizes of the ancestral populations that once contributed their genes. In the current study, researchers developed a method for estimating past effective population size and used it to analzye data from nine populations enrolled in a Latino health study, and from African-American and European-American populations in Pittsburgh and Memphis. They estimate that overall effective population sizes dropped substantially after the start of European and African immigration, reaching a minimum around 12 generations ago, but rebounded a few generations later. Researchers investigated these population size reductions, also known as bottlenecks, and found that the smallest bottleneck occurred in Puerto Rico, where the effective size at one point fell to just one thousand people.
The differences in historical effective sizes between these populations can be useful for understanding why individual groups face different health and disease risks. They can also be useful for scientists in selecting populations that will be most useful for studies that identify the genes linked to specific diseases.
Sharon Browning adds: "Admixed populations in the Americas are like ropes constructed by braiding together several different fibers, with the fibers representing different ancestral population groups. The genetic composition of those different groups is overall very similar, but is different enough so that we can distinguish the genetic material from each ancestry group and study its properties, which tells us about the histories of those populations.
We found that around 100 generations ago, which is approximately several thousand years ago, the effective sizes of the ancestral European, African and indigenous American populations contributing to current-day American populations were around several tens of thousands of individuals each. We also found clear signatures of the effects of migration and colonization, with reduced effective population sizes around 12 generations ago, which is approximately 300 years ago."
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Citation: Browning SR, Browning BL, Daviglus ML, Durazo-Arvizu RA, Schneiderman N, Kaplan RC, et al. (2018) Ancestry-specific recent effective population size in the Americas. PLoS Genet 14(5): e1007385. https://doi.org/10.1371/journal.pgen.1007385
Image Credit: Sharon R. Browning and colleagues
Image Caption: In the African component, we see smaller estimated pre-admixture effective sizes for Cuba (150,000) and Mexico (100,000) than for the Dominican Republic (700,000), suggesting that the African ancestors of the former two populations came from smaller sub-populations of Africa than the African ancestors of the latter two populations. In the European component we see smaller estimated pre-admixture effective sizes for Cuba (200,000), Mexico (150,000), and Nicaragua (120,000) than for the Dominican Republic (400,000). In the American ancestral component, the estimated pre-admixture effective sizes are similar between Nicaragua (400,000), Ecuador (700,000), and Mexico (600,000).
Funding: The analyses in this study were supported by NIH research grants GM099568 and HG005701 (funding received by SRB). Funding support for the CIDR Visceral Adiposity Study which generated the Health ABC GWAS data was provided through the Division of Aging Biology and the Division of Geriatrics and Clinical Gerontology, NIA. The baseline examination of HCHS/SOL was carried out as a collaborative study supported by contracts from the National Heart, Lung, and Blood Institute (NHLBI) to the University of North Carolina (N01-HC65233), University of Miami (N01-HC65234), Albert Einstein College of Medicine (N01-HC65235), Northwestern University (N01-HC65236), and San Diego State University (N01-HC65237). The following Institutes/Centers/Offices contributed to the first phase of HCHS/SOL through a transfer of funds to the NHLBI: National Institute on Minority Health and Health Disparities, National Institute on Deafness and Other Communication Disorders, National Institute of Dental and Craniofacial Research (NIDCR), National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, NIH Institution-Office of Dietary Supplements. The Genetic Analysis Center at Washington University was supported by NHLBI and NIDCR contracts (HHSN268201300005C AM03 and MOD03). Additional analysis support was provided by 1R01DK101855-01 and 13GRNT16490017. Genotyping efforts were supported by NHLBI HSN 26220/20054C, NCATS CTSI grant UL1TR000123, and NIDDK Diabetes Research Center (DRC) grant DK063491. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
<h4>Related Journal Article</h4>http://dx.doi.org/10.1371/journal.pgen.1007385