NEW YORK – New research suggests humans had a close brush with extinction during an extended population bottleneck that took place on the order of 900,000 years ago during the early to mid-Pleistocene.
"From a technical perspective, obtaining detailed information on population sizes becomes increasingly challenging as we explore deeper into ancient demographic history," co-senior and co-corresponding author Yi-Hsuan Pan, a researcher at East China Normal University, said in an email. "Whereas many previous methods have primarily focused on recent demographic events, our methodology is anchored in fundamental theoretical demographic models. This guarantees unbiased calculations and enables us to extract more detailed data about ancient populations."
As they reported in Science on Thursday, Pan and colleagues from the Chinese Academy of Sciences, East China Normal University, and other centers in China, Italy, and the US relied on a new analytical tool called the "fast infinitesimal time coalescent process," or FitCoal, to assess genome sequences from present-day individuals participating in the 1000 Genomes Project or the Human Genome Diversity Project.
The FitCoal approach calculates anticipated branch lengths for each "site frequency spectrum," or allele frequency distribution, category under arbitrary demographic models, co-first author Wangjie Hu, a computational biology researcher affiliated with the Chinese Academy of Sciences and the East China Normal University, explained in an email.
"The efficacy of FitCoal is underscored by its consistent results, which align closely with the true model," Hu said, "displaying narrower confidence intervals in simulated data than those observed with previous methods."
When they used FitCoal to analyze genome sequence data for 3,154 individuals from 10 African and 40 non-African populations, the investigators found evidence for a severe and extended population bottleneck that nearly wiped out ancestors of modern humans in Africa.
"The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction," the researchers reported, noting that it "is congruent with a substantial chronological gap in the available African and Eurasian fossil record."
The population crash was missed in previous analyses, the team explained, but supported by subsequent validation modeling and analyses using an extended version of the FitCoal approach.
"We established several models to validate the existence of this bottleneck and determined that the out-of-Africa dispersal could influence its identification when analyzing non-African populations," Hu said.
The team estimated that the population bottleneck — which reached an estimated minimum of some 1,280 breeding individuals — occurred roughly 813,000 to 930,000 years ago at around the same time as climate changes that marked the mid-Pleistocene transition, wiping out nearly 99 percent of the human ancestors that existed at the start of the bottleneck.
"Many questions remain unanswered, such as where these individuals lived, how they overcame the catastrophic climate changes, and how the ancient population remained so small for so long," the authors wrote, noting that "[f]urther studies are warranted to investigate these matters to obtain a more detailed picture of human evolution during the early to middle Pleistocene transition."
The bottleneck appeared to occur at around the same time that the human chromosome 2 formed through the fusion of two ancestral chromosomes, the team noted, and may have influenced the evolution of a shared common ancestor of modern humans, Denisovans, and Neanderthals.
"This population bottleneck had a critical impact on human evolution" and likely determined the formation of many important phenotypes in modern humans, co-first author Ziqian Hao, a researcher focusing on artificial intelligence and big data for medical sciences at Shandong Academy of Medical Sciences, said in an email.
In a related perspectives article in Science, Chris Stringer, a scientist at the Natural History Museum in London, and Nick Ashton, a researcher at the British Museum, argued that "[i]t is not yet clear whether the last common ancestor lived in Europe, Asia, or Africa."
"If methods such as FitCoal can be further applied to growing data from the genomes of H. sapiens, Neanderthals, Denisovans, and hopefully others, this should clarify ancient bottlenecks, and which regions under habitation might have been the most or least affected," they suggested. "However, the genomic data must also be tested against the fossil and archaeological records of early human populations, records that need further enhancement from many regions of the ancient world."