Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition

Abstract

Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.

Demography as a confounding factor to explain highly diverged loci between cultivated and wild rice

“…Moreover, the confounding effects of demography can be addressed by controlling its false-positive rate, which is generally composed by two-step analysis (Li and Stephan, 2006;Koropoulis et al, 2020). Genome-wide DNA polymorphism is used to infer the demography (Speidel et al, 2019;Hu et al, 2023) and the detection of positive selection is followed conditional on the inferred demography. The alternative approaches could be to use neutrality tests that are insensitive to demographic events (Li, 2011;Hunter-Zinck and Clark, 2015).…”

Quantifying hominin morphological diversity at the end of the middle Pleistocene: Implications for the origin of Homo sapiens

“…700 ka; Dean et al, 2015) and the subsequent opening of migration corridors from East Africa in particular (Abbate & Sagri, 2012;Beyin et al, 2019;Head & Gibbard, 2015). In Africa, hominin populations may have suffered a major bottleneck between approximately 930 to 810 ka, leading to a dramatic loss of genetic diversity (Hu et al, 2023). In Eurasia, some regions, such as Iberia, the Italian peninsula, and the Balkans, might have served as refugia zones during periods of climatic deterioration, favoring bottleneck effects and sometimes leading to extinctions (Dennell et al, 2011).…”

Is leadership the solution to the wicked problem of climate change?

“…3. There are suggestions that the ancestors of modern humans sank to as few as 1300 individuals around 800, 000 years ago (Hu et al, 2023). 4. https://atmosphere.copernicus.eu/copernicus-cams-forecast-shows-large-ozone-hole-early-december Retrieved 3 December 2023.…”

“…3.There are suggestions that the ancestors of modern humans sank to as few as 1300 individuals around 800,000 years ago (Hu et al, 2023). …”