PT  - JOURNAL ARTICLE
AU  - Käfer, Jos
AU  - Lartillot, Nicolas
AU  - Marais, Gabriel A.B.
AU  - Picard, Franck
TI  - Detecting sex-linked genes using genotyped individuals sampled in natural populations
AID  - 10.1101/2020.01.31.928291
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.01.31.928291
4099  - http://biorxiv.org/content/early/2020/07/22/2020.01.31.928291.short
4100  - http://biorxiv.org/content/early/2020/07/22/2020.01.31.928291.full
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.