RT Journal Article
SR Electronic
T1 Detecting sex-linked genes using genotyped individuals sampled in natural populations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.01.31.928291
DO 10.1101/2020.01.31.928291
A1 Käfer, Jos
A1 Lartillot, Nicolas
A1 Marais, Gabriel A.B.
A1 Picard, Franck
YR 2020
UL http://biorxiv.org/content/early/2020/07/22/2020.01.31.928291.abstract
AB We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows to statistically test for the presence or absence of sex chromosomes, and to infer sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between both. We test the method using simulated and human sequencing data, and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.Competing Interest StatementThe authors have declared no competing interest.