NEW YORK (GenomeWeb) – Researchers have developed a method for teasing out populations' demographic histories from their genomes.
A University of Washington-led team of researchers devised a way to estimate not only current effective population sizes, but also historical effective population sizes, from genome-wide genetic data. As they reported today in PLOS Genetics, they applied this method to admixed populations, including Latino-American and African-American populations in the US, to gauge the size of ancestral populations and delve into their demographic histories.
"Admixed populations in the Americas are like ropes constructed by braiding together several different fibers, with the fibers representing different ancestral population groups," first author Sharon Browning from the University of Washington said in a statement. "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.
In particular, in the Americas, populations' ancestries may be a combination of ancestry from indigenous groups, European settlers, and enslaved Africans. Because this admixture took place fairly recently, long chromosomal segments within individuals' genomes can be traced back to ancestral populations.
The method developed by Browning and her colleagues, dubbed IBDNe, relies on uncovering these identity-by-descent segments within populations' genomes and local ancestry calls from genome-wide data. This, they said, allows them to make certain inferences about the ancestral populations. For instance, if the number of IBD segments is high, then the effective population size is low, and vice versa, they said.
After testing their method using simulated data, Browning and her colleagues applied IBDNe to data from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), which they divided based on where participants said their grandparents were from.
Using that data, collected from people living in four US cities, Browning and her colleagues estimated the effective population sizes of nine Latin American populations for the past 100 generations. Most of the populations, the researchers reported, experienced a population bottleneck about 12 generations ago — around the time of colonization — that varied in size, ranging from an effective population size of 1,000 in Puerto Rico to 60,000 in Mexico.
Similarly, Browning and her colleagues used their approach to study the demographic history of African-American populations in Memphis and Pittsburgh using data from the Healthy Aging and Body Composition study.
Both populations also experienced bottlenecks around the same time with effective population sizes of between 130,000 and 190,000.
In addition, for both the Memphis and Pittsburgh African-American populations, the researchers estimated a pre-admixture, Africa-specific population size of between 1 million and 2 million. They noted that the African-American populations in Memphis and Pittsburgh have similar estimated demographic histories, which the researchers said could reflect historical mixing,
At the same time, Browning and her colleagues also found similarities in the European ancestry component of the two Memphis and Pittsburgh African-American populations as well as of the Memphis European-American population. They estimated that the pre-admixture, Europe-specific population size of the two African-American populations to be about 1 million, as was the pre-admixture Memphis European-American population size. This suggested to the researchers that the European ancestors of these populations might have come from the same source.
This, along with previous data, supports the view that most of the European admixture in African-American populations occurred in the South, prior to the Great Migration.
These differences in historical effective populations sizes could help explain why some populations have different health and disease risks, the researchers said. Populations with small founder sizes, such as Puerto Rico, they noted, can harbor important medical genetic variants at a moderate frequency that would otherwise be rare in other populations.