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Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains

Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains

Published on: November 30, 2021

Statistical guidelines for detecting past population shifts using ancient DNA.

Tobias Mourier¹, Simon Y W Ho, M Thomas P Gilbert

¹Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. tmourier@snm.ku.dk

Molecular Biology and Evolution

|March 20, 2012

Summary

Ancient DNA analysis reveals nuclear single-nucleotide polymorphisms (SNPs) are more powerful than mitochondrial sequences for detecting past population bottlenecks, especially those with rapid recovery. Mitochondrial data alone may lack power for moderate demographic shifts.

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Area of Science:

Population Genetics
Paleogenomics
Evolutionary Biology

Background:

Genetic variation within populations reflects their demographic history.
Ancient DNA (aDNA) data significantly enhances the inference of past population dynamics.
Detecting historical population bottlenecks is crucial for understanding evolutionary processes.

Purpose of the Study:

To evaluate the efficacy of ancient mitochondrial DNA (mtDNA) sequences versus nuclear single-nucleotide polymorphisms (SNPs) in detecting past population bottlenecks.
To assess the impact of different sampling schemes on the power to infer demographic history from aDNA.
To provide guidelines for optimizing aDNA sampling strategies for demographic inference.

Main Methods:

Utilized serial-coalescent simulations to model population histories.
Incorporated both quantitative and temporal sampling schemes for ancient DNA data.
Compared the detection power of ancient mtDNA sequences and nuclear SNPs for population bottlenecks.

Main Results:

Ancient mtDNA sequences exhibit limited power to detect subtle bottlenecks or rapid post-bottleneck recoveries.
Nuclear SNPs demonstrate greater power in detecting bottlenecks, particularly when followed by rapid recovery.
Bottlenecks involving population reductions of less than 50% are challenging to detect with low power, requiring extensive ancient nuclear data.

Conclusions:

Nuclear SNPs are superior to mtDNA sequences for inferring population bottlenecks, especially in scenarios with dynamic demographic changes.
Sole reliance on mitochondrial information in aDNA studies may lead to underestimation of moderate demographic collapses.
The findings offer practical guidance for designing effective sampling strategies in paleogenomic research.