Present-Day DNA Contamination in Ancient DNA Datasets

Abstract Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.1. Introduction 2. Classification of Signals Used to Estimate Contamination 2.1. Differences in the DNA Sequence 2.2. Deviation from the Expected Ploidy 2.3. Ancient DNA Degradation Patterns 3. Methods to Estimate Contamination 3.1. Mitochondrial DNA 3.1.1. Methods Based on Differences in the DNA Sequence 3.1.2. Methods Based on Deviations from the Expected Ploidy 3.2. Sex Chromosomes 3.2.1. Methods Based on Differences in the DNA Sequence 3.2.2. Methods Based on Deviations from the Expected Ploidy 3.3. Autosomal DNA 3.3.1. Methods Based on Differences in the DNA Sequence 3.3.2. Methods Based on Deviations from the Expected Ploidy 3.3.3. Methods Based on Patterns of Ancient DNA Damage 4. Perspectives 4.1. Methods Based on Differences in the DNA Sequence 4.2. Methods Based on Deviations from the Expected Ploidy 4.3. Methods Based on Characteristics of Ancient DNA 5. Conclusio