Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals
@article{Chen2020IdentifyingAI, title={Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals}, author={Lu Chen and Aaron Wolf and Wenqing Fu and Liming Li and Joshua M. Akey}, journal={Cell}, year={2020}, volume={180}, pages={677-687.e16} }
102 Citations
Ancient Admixture into Africa from the ancestors of non-Africans
- BiologybioRxiv
- 2020
SMCSMC is presented, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events and indicates that the authors' species’ demographic history around the out-of-Africa event is more complex than previously appreciated.
Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage
- BiologyGenetics
- 2020
This study presents a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and shows that they can be traced back to multiple introgression events, in agreement with the emergent notion that various Neanderthal populations contributed to extant human genetic variation in a population-specific manner.
Statistics used to infer inter-breeding between humans and Neanderthals are strongly predicted by flanking sequence heterozygosity
- BiologybioRxiv
- 2020
A new model explains why introgression of haploid or semi-haploid regions is essentially lacking and whyintrogression is often inferred around immune genes and other regions under strong selection and raises the possibility that reported legacies are largely an artefact arising out of the false assumption that mutation rate is constant.
Global Picture of Genetic Relatedness and the Evolution of Humankind
- BiologyBiology
- 2020
The entire picture of relatedness of all the studied populations presents itself in the form of shared number/size of IBDs, providing novel insights into geographical admixtures and genetic contributions that shaped human ancestry into what it is today.
Selection against admixture and gene regulatory divergence in a long-term primate field study
- BiologybioRxiv
- 2021
Significant signatures of selection against introgression are identified that are strikingly similar to those described for archaic hominins4–6, supporting the importance of gene regulation in primate evolution and the idea that selection targeted large regulatory effects following archaichominin admixture.
Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations
- BiologyNature Ecology & Evolution
- 2020
The authors show that Neanderthal introgression reintroduced thousands of lost ancestral variants with gene regulatory activity and that these RAs were more tolerated by modern humans than introgressed Neanderthal-derived alleles.
An ancestral recombination graph of human, Neanderthal, and Denisovan genomes
- BiologyScience Advances
- 2021
A new heuristic ARG inference tool maps archaic hominin admixture and highlights genomic regions unique to modern humans and finds that only 1.5 to 7% of the modern human genome is uniquely human.
Inferring archaic introgression from hominin genetic data
- BiologyEvolutionary anthropology
- 2021
How technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus on whether or not Homo sapiens interbred with other hominin groups is outlined.
The Genomic History of the Middle East
- Biology
- 2020
All populations suffered a bottleneck overlapping documented aridification events, while regional migrations increased genetic structure, and may have contributed to the spread of the Semitic languages.
Apportioning archaic variants among modern populations
- BiologyPhilosophical Transactions of the Royal Society B
- 2022
It is found that archaic ancestry coverage at the individual- and population-level present distinct patterns in modern human populations: South Asians have nearly twice the number of population-unique archaic alleles compared with Europeans or East Asians, indicating that these populations experienced differing demographic and archaic admixture events.
References
SHOWING 1-10 OF 63 REFERENCES
Complex history of admixture between modern humans and Neandertals.
- BiologyAmerican journal of human genetics
- 2015
Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from Non-African Populations
- Geography, BiologyGenome biology and evolution
- 2013
An alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African modern humans who were the ancestors of those involved in the OOA migration is examined.
Possible Ancestral Structure in Human Populations
- BiologyPLoS genetics
- 2006
Using sequence data from the Environmental Genome Project, strong evidence is found for ancient admixture in both a European and a West African population, with contributions to the modern gene pool of at least 5%.
Multiple episodes of interbreeding between Neanderthals and modern humans
- BiologyNature Ecology & Evolution
- 2018
A simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations, indicating a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.
Model‐based detection and analysis of introgressed Neanderthal ancestry in modern humans
- BiologyMolecular ecology
- 2018
Evidence that selection against Neanderthal ancestry was due to higher genetic load in Neanderthals resulting from small effective population size, rather than widespread Dobzhansky–Müller incompatibilities (DMIs) that could contribute to reproductive isolation is found.
North African Populations Carry the Signature of Admixture with Neandertals
- BiologyPloS one
- 2012
It is found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans, a fact that can be interpreted as a sign of Ne andertal admixture.
The landscape of Neandertal ancestry in present-day humans
- BiologyNature
- 2014
The results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.
Functional implications of Neandertal introgression in modern humans
- BiologyGenome Biology
- 2017
It is shown that gene expression changes are more often associated with Neandertal ancestry than expected, and that the introgressed non-synonymous variants tend to have less predicted functional effect on modern human proteins than mutations that arose on the human lineage.
Ancient gene flow from early modern humans into Eastern Neanderthals
- Biology, HistoryNature
- 2016
It is concluded that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
The Strength of Selection against Neanderthal Introgression
- BiologyPLoS genetics
- 2016
A novel method is developed for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans, suggesting that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.