Biology subjects

Rogers, A. R.

Publications and source records attributed to Rogers, A. R..

10 recordsLinked to original sources

bioRxiv2026

Human ancestors interbred with two distinct populations of distant relatives

Ancient DNA has shown that a distantly-related "superarchaic" population interbred first with the ancestors of Neanderthals and Denisovans and later with Denisovans themselves. Other work has shown that a superarchaic population interbred with the African ancestors of all modern humans. But it is not yet clear whether these events involved the same superarchaic population. Here, we use the distribution of derived alleles among populations to evaluate hypotheses about superarchaics and their relationship to other hominins of the Pleistocene and Holocene. We find evidence for at least two distinct superarchaic populations. The one contributing to archaic Eurasian populations (Denisovans and Neanderthal-Denisovan ancestors) diverged earlier from the human lineage than did the one contributing to early moderns in Africa. This latter superarchaic contributed a large fraction--about 20%--to the ancestry of modern humans. These findings reveal previously unrecognized structure among hominin populations in the Pleistocene. Significance statementGenetic data have shown that all human populations are mixtures. Since the last ice age, the populations mixing have been relatively close relatives--separated by a few tens of thousands of years or less. Earlier in the Pleistocene, there was mixing between more distantly-related populations, with separation times in excess of a million years. Here, we document admixture events involving two distinct populations, each of which had separated from the human lineage well over a million years ago. One of these was apparently Eurasian, because it mixed with archaic Eurasian populations. The other was apparently African, because it mixed with the African ancestors of modern humans. This latter event was remarkable, because the distant relative contributed such a large fraction--about 20%--to the ancestry of modern humans. These results show that during the Pleistocene, the earth was home to hominin populations far more distantly related than any pair of modern human populations, with separation times similar to that of bonobos and chimpanzees. These distantly-related pairs existed not only on separate continents, but also within the African continent. And in spite of the large differences between them, these populations were able to interbreed.

evolutionary biology↗

bioRxiv2023

Declines in Neanderthal and Denisovan population sizes are probably not an artifact of subdivision

PSMC estimates of Neanderthal effective population size (Ne) exhibit a roughly 5-fold decline across the most recent 20 ky before the death of each fossil. To explain this pattern, this article develops new theory relating genetic variation to geographic population structure and local extinction. It argues that the observed pattern results from subdivision and gene flow. If two haploid genomes are sampled from the same subpopulation, their recent ancestors are likely to be geographic neighbors and therefore coalesce rapidly. By contrast, remote ancestors are likely to be far apart, and their coalescent rate is lower. Consequently, Ne is larger in the distant past than in the recent past. New theoretical results show that modest rates of extinction cause substantial reductions in heterozygosity, Wrights FST, and Ne.

evolutionary biology↗

bioRxiv2022

Estimating Pan evolutionary history from nucleotide site patterns

Introgression appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. However, accurately estimating introgression is difficult, particularly when 1) there are many parameters, 2) multiple models fit the data well, and 3) parameters are not simultaneously estimated. Here, we use the software Legofit to investigate the evolutionary history of bonobos (Pan paniscus) and chimpanzees (P. troglodytes) using whole genome sequences. This approach 1) ignores within-population variation, reducing the number of parameters requiring estimation, 2) allows for model selection, and 3) simultaneously estimates all parameters. We tabulated site patterns from the autosomes of 71 bonobos and chimpanzees representing all five extant Pan lineages. We then compared previously proposed demographic models and estimated parameters using a deterministic approach. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. Introgression from bonobos into the ancestor of eastern and central chimpanzees and from western into eastern chimpanzees best explained the autosomal site patterns. This second event was substantial with an estimated 0.21 admixture proportion. Estimates of effective population size and most divergence dates are consistent with previous findings; however, we observe a deeper divergence within chimpanzees at 987 ka. Finally, we identify male-biased reproduction in Pan evolutionary history and suggest that western to eastern chimpanzee introgression was driven by western males mating with eastern females.

genomics↗

bioRxiv2021

An efficient algorithm for estimating population history from genetic data

The Legofit statistical package uses genetic data to estimate parameters describing population history. Previous versions used computer simulations to estimate probabilities, an approach that limited both speed and accuracy. This article describes a new deterministic algorithm, which makes Legofit faster and more accurate. The speed of this algorithm declines as model complexity increases. With very complex models, the deterministic algorithm is slower than the stochastic one. In an application to simulated data sets, the estimates produced by the deterministic and stochastic algorithms were essentially identical. Reanalysis of a human data set replicated the findings of a previous study and provided increased support for the hypotheses that (a) early modern humans contributed genes to Neanderthals, and (b) a "superarchaic" population (which separated from all other humans early in the Pleistocene) was either large or deeply subdivided.

evolutionary biology↗

bioRxiv2020

Beating your neighbor to the berrypatch

Foragers often compete for resources that ripen (or otherwise improve) gradually. What strategy is optimal in this situation? It turns out that there is no optimal strategy. There is no evolutionarily stable strategy (ESS), and the only Nash equilibrium (NE) is unstable: strategies similar to the NE can always invade. But in spite of this instability, the NE is predictive. If harvesting attempts are costly or there are many competitors, the process tends to remain near the unstable NE. In this case, the resource often goes unharvested. Harvesting attempts--when they happen at all--usually occur when the resource is barely ripe enough to offset costs. The more foragers there are, the lower the chance that the resource will be harvested and the greater its mean value when harvested. This counterintuitive behavior is exhibited not only by theoretical models and computer simulations, but also by human subjects in an experimental game.

evolutionary biology↗

bioRxiv2020

Sharing of weak signals of positive selection across the genome

Selection in humans often leaves subtle signatures at individual loci. Few studies have measured the extent to which these signals are shared among human populations. Here a new method is developed to compare weak signals of selection in aggregate across the genome using the 1000 Genomes Phase 3 Data. Results presented here show that selection producing weak selection serves to increase population differences around coding areas of the genome.

genomics↗

bioRxiv2020

Genomic regions linked to soft sweeps approximate neutrality when inferring population history from site pattern frequencies

Recent studies have suggested that selection is widespread throughout the genome and largely uncompensated for in inferences of population history. To address this potential issue, we estimated site pattern frequencies for neutral and selection associated areas of the genome. There are notable differences in these frequencies between neutral regions and those affected by selection. However, these differences have relatively small effects when inferring population history.

genomics↗

bioRxiv2020

Detecting shared independent selection

Signals of selection are not often shared between populations. When a mutual signal is detected, it is often not known if selection occurred before or after populations split. Here we develop a method to detect genomic regions at which selection has favored different haplotypes in two populations. This method is verified through simulations and tested on small regions of the genome. This method was then expanded to scan the phase 3 genomes of the 1000 Genomes Project populations for regions in which the evidence for independent selection is strongest. We identify several genes which likely underwent selection independently in different populations.

genomics↗

bioRxiv2019

Neanderthal-Denisovan ancestors interbred with a distantly-related hominin

Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors--members of a \"superarchaic\" population that separated from other humans about 2 mya. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that: (1) Denisovans also interbred with superarchaics, (2) Neanderthals and Denisovans separated early in the middle Pleistocene, (3) their ancestors endured a bottleneck of population size, and (4) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (5) Neanderthals interbred with the ancestors of modern humans.\n\nOne-sentence summaryWe document the earliest known interbreeding between ancient human populations and an expansion out of Africa early in the middle Pleistocene.

evolutionary biology↗

bioRxiv2019

Legofit: Estimating Population History from Genetic Data

BackgroundOur current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these biases, it is necessary to estimate these parameters simultaneously with those describing admixture. Genetic estimates of population histories also confront problems of statistical identifiability: different models or different combinations of parameter values may fit the data equally well. To deal with this problem, we need methods of model selection and model averaging, which are lacking from most existing software.\n\nResultsThe Legofit software package allows simultaneous estimation of parameters describing admixture and other aspects of population history. It includes facilities for data manipulation, estimation, model selection, and model averaging. It outperforms several statistical methods that have been widely used to study archaic admixture in humans.

evolutionary biology↗