Related Experiment Video
Updated: May 8, 2026
06:18
Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains
Published on: November 30, 2021
Local ancestry inference identifies robust evidence of selection in Neolithic Europe
Georgia Mies1, Iain Mathieson1
1Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Biorxiv : the Preprint Server for Biology
|May 7, 2026
Summary
Local ancestry inference methods show variable performance on ancient DNA. Validating across multiple methods is crucial for robustly identifying genetic adaptations in Neolithic European genomes.
Area of Science:
- Population genetics
- Ancient genomics
- Human evolution
Background:
- The European Neolithic transition involved admixture between Anatolian farmers and local hunter-gatherers, driving significant evolutionary changes.
- Local ancestry inference is vital for detecting natural selection after admixture but its efficacy in ancient DNA is uncertain.
Purpose of the Study:
- To benchmark six local ancestry inference methods using imputed Neolithic genomes.
- To assess method performance regarding ancestry proportions, tract lengths, and selection signatures in ancient DNA.
Main Methods:
- Benchmarking six local ancestry inference methods on 176 imputed Neolithic genomes.
- Comparing ancestry estimates, tract length distributions, and selection signatures.
- Replicating findings across methods and in two independent ancient DNA datasets (n=378 and 1,121).
Main Results:
- Individual ancestry estimates were highly correlated across methods, but tract lengths and admixture times varied significantly.
- Robust signals of adaptation were identified at SLC24A5 (pigmentation) and FADS1/2 (metabolism).
- Candidate loci PER3 (circadian rhythm) and IRAK4 (innate immunity) showed less consistent signals; HLA region results were method-dependent.
Conclusions:
- Local ancestry inference can detect meaningful biological signals in ancient genomes, but results are sensitive to the chosen method.
- Multi-method validation is essential for reliable inference of ancestry patterns and selection signals in ancient DNA.
- Methodological choices critically impact the interpretation of genetic adaptation in past populations.
More Related Videos
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:55The Evidence for Evolution
Genetic variations accumulating within populations over generations give rise to biological evolution. Evolutionary changes can result in the formation of novel varieties and entire new species. These changes are responsible for the diverse forms of life inhabiting the planet. The evidence for evolution suggests that all living organisms descended from common ancestors.
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
02:16Genetics of Speciation
Speciation is the evolutionary process resulting in the formation of new, distinct species—groups of reproductively isolated populations.
01:24Eukaryotic Evolution
The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the nucleus-first hypothesis, the ancestral prokaryote first evolved a membrane to enclose DNA and form the nucleus. Conversely, the mitochondria-first hypothesis suggests that the nucleus was formed after endosymbiosis of mitochondria.
Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and...
Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and...