Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.30.229286v1?rss=1

Authors: Wang, S., Ge, S., Colijn, C., Wang, L., Elliott, L. T.

Abstract:

Genetic similarity is a measure for the genetic relatedness among individuals. The standard method for computing similarity matrices involves the inner product of observed genetic variant matrices. Such an approach is inaccurate or impossible if genotypes are not available, or not densely sampled, or of poor quality (for example, genetic analysis of extinct species). We provide a new method for computing genetic similarities among individuals using phylogenetic trees. Our method can supplement (or stand in for) computations based on genetic sequences. We show that the genetic similarity matrices computed from trees are consistent with those computed from genotypes. Quantitative analysis on genetic traits and analysis of heritability and co-heritability can be conducted directly using genetic similarity matrices and so in the absence of genotype data, and the presence of phylogenetic trees derived from morphological data or geological dates, such analyses can be undertaken using our methods. We use simulation studies to demonstrate the advantages of our method, and we provide an application to ancient hominin data.

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