Population bottleneck 900K years ago

Paper behind a paywall, but new genetic technique indicates our ancestors dropped to around 1,000 individuals

https://www.science.org/doi/10.1126/science.abq7487

Editor’s summary​

Today, there are more than 8 billion human beings on the planet. We dominate Earth’s landscapes, and our activities are driving large numbers of other species to extinction. Had a researcher looked at the world sometime between 800,000 and 900,000 years ago, however, the picture would have been quite different. Hu et al. used a newly developed coalescent model to predict past human population sizes from more than 3000 present-day human genomes (see the Perspective by Ashton and Stringer). The model detected a reduction in the population size of our ancestors from about 100,000 to about 1000 individuals, which persisted for about 100,000 years. The decline appears to have coincided with both major climate change and subsequent speciation events. —Sacha Vignieri

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.

BWV said:

1000 individuals

I wonder what the uncertainties are on that number, or would that number be a lower bound.

I would be cautious about making estimates or models based on 'found' fossil records. The absence of fossils doesn't necessarily mean humanoids didn't exist in some other area. After listening to discussions of the last 2000 - 3000 years, and the periodic annihilation of populations, who didn't leave skeletal remains, I would expect from 800k years ago, a lot went missing (got recycled by scavengers).

Astronuc said:

I wonder what the uncertainties are on that number, or would that number be a lower bound.

As I understand it from the description in Arstechnica, this number (about 1300) is the approximate number of individuals that contributed genetically to the population in a way that is reflected to our lineage today. Or, in other words, if you trace the ancestors of any human today back in time, it will eventually contain a subset of only those 1300 individuals. At least, that is how I understand it.

The accuracy of this number seems mostly to be determined by the accuracy of this new analysis model of which my understanding is very hazy. It is, again as I understand it, a new member of a family of models that look at the statistical variations of the genes in a population over time, but where older similar models see "no signal" around 900K this model apparently does.

if this is accurate, it’s hard to parse - the natural disasters don’t line up, Toba - the largest eruption of the last 25M years, was ~70K years ago and that population bottleneck theory has fallen out of favor. There was another VEI 8 Toba eruption around that time and also this impact event ,. 1 MYA had a homo erectus population spread out across Eurasia, so hard to picture a widespread extinction. The analysis cannot really estimate the total population, just the population of individuals that are ancestors of living humans - it could be that this coincides with a smaller group that spread through superior technology and did not interbreed with existing populations during the period in question

There have been 10 glacial-interglacial cycles in the last 800 millenia. Ostensibly, ocean levels fall during glacial periods (ice ages) and rise during interglacial periods. So, I'm guessing a lot got washed away, and some populations who lived by the shoreline might have been erased, not to mentioned whatever catastrophic flooding occurred.

https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2015RG000482

BWV said:

1 MYA had a homo erectus population spread out across Eurasia, so hard to picture a widespread extinction.

As I understand it, this bottleneck in the population on the African continent as detected up by the new analysis model is not (yet) correlated with any global change that has been picked up by other means or in other populations. Also, it is not clear to me if the new analysis "on purpose" has filtered out genetic "signals" from populations that already had left Africa around that time but later mixed back into the gene pool (e.g. Neanderthals) or not, but I did get away with a clear understanding this analysis only speaks about the African population at around 900k years ago, meaning if remaining global population had no such bottleneck the cause of an African bottleneck likely has to be fairly local.

Filip Larsen said:

As I understand it, this bottleneck in the population on the African continent as detected up by the new analysis model is not (yet) correlated with any global change that has been picked up by other means or in other populations. Also, it is not clear to me if the new analysis "on purpose" has filtered out genetic "signals" from populations that already had left Africa around that time but later mixed back into the gene pool (e.g. Neanderthals) or not, but I did get away with a clear understanding this analysis only speaks about the African population at around 900k years ago, meaning if remaining global population had no such bottleneck the cause of an African bottleneck likely has to be fairly local.

if you define ‘speciation’ as a branch where the new organism can no longer create fertile offspring with the old organism (like donkey and horse) - then perhaps some genetic change made a population of early humans no longer able to breed and create fertile offspring with the rest of the population at that time?