Human ancestors passed through a very serious bottleneck

This recently-published paper [see attached Hu et al. paper] has been all over the news this past week. Human ancestors (hominins) diverged from gorilla and chimpanzee ancestors between 8 million and 5.5 million years ago. One of these lineages ultimately evolved into present-day gorillas and chimps, whereas the other line evolved into early human ancestors (hominids). Further evolution of the latter continues to be studied with frequent new paleontological data, but it is clear [see figure below; H.denisova and H.floresiensis were not yet established when this graph was made] that there were many (at least 24) fits and starts in southwestern and southeastern Africa. The ultimate “survivors” that migrated out of Africa (in several “waves” before the successful wave ultimately survived) included Homo sapiens, Homo denisova and Homo neandertalensis (among a few other minor ones); there is evidence these three sublines interbred (as previously discussed in these GEITP pages).

It is now generally agreed upon that modern man (Homo sapiens) appeared some 300,000 years ago. The Pleistocene is the geological epoch that lasted from ~2.58 million to 11,700 years ago, spanning the Earth’s most recent Glacial Period (~110,000 to 11,700 years ago). From ice-core data over the last 800,000 years (in Antarctica and Greenland), we know there have been about ten Glacial Periods (~100,000 years) interspersed with Interglacial Periods (~15,000 years long). When Earth awakened from its last Glacial Period (11,700 years ago), the area we now call Cincinnati was under about 3 miles of glacier ice; obviously, it was cold and began to get warmer, as glaciers receded in both the north and south poles…

Earth’s climate system began to change during the Middle Pleistocene transition, which is associated with a severe cooling phase ~900,000 years ago. How this change might have affected human populations is difficult to determine, because human fossil and archaeological records are relatively sparse for this period and lie beyond the reach of ancient DNA recovery. Authors Hu et al. [see attached] used a new method of analysis called FitCoal to project current human genetic variation backwards in time — to estimate the size of populations at specific points in the past.

Their data suggest that human ancestors suffered a severe population bottleneck that started ~930,000 years ago and lasted for almost 120,000 years; this adversity is estimated to have reduced the number of breeding individuals to ~1,300(!!), bringing human ancestors close to extinction. Hu et al. postulate that the proposed bottleneck correlates with a chronological gap in the African and Eurasian fossil records that may have led to evolution of a new human species, ancestral to Homo sapiens. They favor H.heidelbergensis as this ancestral species, probably emerging in Africa by 800,000 years ago [depicted as #3 or #5 in the graph above].

Two lineages of large-brained humans have long been recognized in the later Pleistocene: H. sapiens and Neanderthals (H. neandertalensis). A third group — Denisovans — was identified more recently from ancient DNA in fossils and sediments at Denisova Cave in Siberian Russia. Considering how the inferred bottleneck might have affected human evolution, inevitably leads to debate about the nature of the last common ancestor of H. sapiens, Neanderthals, and Denisovans, and when and where this ancestor lived.

It is not yet clear whether the last common ancestor lived in Europe, Asia, or Africa. Authors attributed the East Asian fossil record from that time to the more ancient human species H.erectus. However, there is evidence from sites (e.g., Yunyang, China), of a distinct species that is morphologically closer to later humans from Eurasia and Africa such as H.sapiens and Neanderthals, suggesting their ancestral lineage(s) might already have diverged from H. erectus by the time of the Yunyang fossils — which are dated at 1,100,000 to 800,000 years ago.

Estimates using genomic data from H.sapiens, Neanderthals, and Denisovans calibrate the last common ancestor to have existed between ~700,000 and 500,000 years ago — which would relate the inferred bottleneck to this ancestral population (wherever it lived) — with comparable signals expected from Denisovan and Neanderthal genomes, as well as from those of H.sapiens.

However, some recent studies of dental and cranial variation in fossilized skulls place the last common ancestor earlier, between about 1,200,000 and 800,000 years ago — which might mean that already-separated basal lineages of Neanderthals and Denisovans avoided the bottleneck, or suffered it to a lesser extent. Morphological analysis of fossils suggests that the last common ancestor might be H.heidelbergensis (as favored by Hu et al.), H.rhodesiensis, H.antecessor, or H.bodoensis. 😊


Science 1 Sept 2023; 381: 979-984 & editorial pp 947-948

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