Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes

Abstract

Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.

Sex-mediated gene flow of grayfoot chacma baboons (Papio ursinus griseipes) in a highly seasonal habitat in Gorongosa National Park

“…Further works could investigate the origin of immigrants reaching CFR and the implications of gene flow for the phenotypic variation of baboons observed in the region. The analysis of a larger set of Y chromosome microsatellite loci is expected to generate informative haplotypes and enable a more detailed reconstruction of the relationships among males within and across populations (Mutti et al, 2023). We found molecular evidence for "historical" male-biased dispersal and female philopatry for the grayfoot chacma baboon across 140 km in the Gorongosa region (e.g., dispersal over several generations, Lawson Handley & Perrin 2007).…”

Insights into the Geographical Origins of the Cabo Verde Green Monkey

“…To address the limitations of this work, future work should use variable autosomal and Y chromosome-linked loci (not yet available), in combination with mtDNA data, to investigate the geographic origin of introduced populations of green monkeys in Atlantic islands, which could be developed using genome-wide data from wild individuals [27] and searching algorithms used in closely-related Cercopithecine species (see [42]).…”