Improved Models of Coalescence Ages of Y-DNA Haplogroups

Abstract

Databases of commercial DNA-testing companies now contain more customers with sequenced DNA than any completed academic study, leading to growing interest from academic and forensic entities. An important result for both these entities and the test takers themselves is how closely two individuals are related in time, as calculated through one or more molecular clocks. For Y-DNA, existing interpretations of these clocks are insufficiently accurate to usefully measure relatedness in historic times. In this article, I update the methods used to calculate coalescence ages (times to most-recent common ancestor, or TMRCAs) using a new, probabilistic statistical model that includes Y-SNP, Y-STR and ancilliary historical data, and provide examples of its use.

Keywords: human Y chromosome; male history; molecular clock; time estimation.

Figure 1

A schematic representation of the example given in Section 3.1.

Figure 2

A schematic representation of the example given in Section 3.2.

Figure 3

A schematic representation of the example given in Section 3.3.

Figure 4

A schematic representation of the example given in Section 3.4. Individual testers and the haplogroups they form are shown as the interconnected grey boxes. Participants are listed using the identifier assigned by their testing company. Measured or estimated coverage, in millions of base pairs, is shown to their upper-right; restrictions known from paper genealogies are shown to their lower-right. Between testers and haplogroups, in brackets, are shown the number of STR mutations that have occurred (g), the number of STR markers tested, and the number of SNP mutations that have occurred within the region of testing used for the parent haplogroup ($\overline{b}$). Note that the mutation at GRCh38 position 17651002 is sometimes designated A22007; R-A309 is labelled by Family Tree DNA by the alternative name R-A306. The asterisked genetic distances cannot be uniquely placed in the tree, due to lack of STR results for some testers: these are discarded for this calculation.