Present-Day DNA Contamination in Ancient DNA Datasets.

Area of Science:

• Genetics
• Bioinformatics
• Archaeology

Background:

• Ancient DNA (aDNA) studies are crucial for understanding past populations and evolutionary history.
• Contamination from present-day DNA is a significant challenge, potentially leading to erroneous conclusions in aDNA research.
• Reliable estimation of contamination is essential for the validity of aDNA studies.

Purpose of the Study:

• To provide a comprehensive overview of existing methods for estimating contamination in ancient DNA.
• To classify these methods based on the signals they utilize.
• To guide researchers in selecting appropriate contamination estimation methods for their specific datasets.

Main Methods:

• Review and synthesis of current contamination estimation techniques for ancient DNA.
• Classification of methods based on underlying signals (e.g., sequence characteristics, allele frequency differences).
• Highlighting the strengths and weaknesses of each method in relation to different data types.

Main Results:

• A structured overview of various contamination estimation methods is presented.
• Methods are categorized based on the type of molecular or genetic signal used.
• Strengths and limitations of each approach are discussed in the context of different ancient DNA data.

Conclusions:

• Researchers can use the proposed classification to choose optimal contamination estimation strategies.
• Understanding method-specific signals is key to accurate contamination assessment.
• Identifying current limitations paves the way for developing improved future methods for ancient DNA contamination control.