13Genital divergence contributes to reproductive barriers between species. Emergence of a 14 novel accessory structure, the baculum, has independently evolved and been lost throughout 15 mammalian evolution, purportedly driven by sexual selection. In primates, the longest recorded 16 baculum belongs to Macaca arctoides, the bear macaque. This species has been proposed to be of 17 homoploid hybrid origin via ancient hybridization between representatives from the fascicularis 18 and sinica species groups. To investigate the evolutionary origins of the bear macaque and its 19 unique morphology, we used whole genome sequences to quantify gene flow and phylogenetic 20 relationships in 10 individuals from 5 species, including the bear macaque (n=3), and two species 21 each from the sinica (n=3) and fascicularis (n=4) species groups. The results of these analyses were 22 concordant, and identified 608 genes in the bear macaque that supported both clustering between 23 M. arctoides and the sinica group (topo2) and had shared derived alleles between species from the 24 two groups. Similarly, 361 genes supported both clustering between M. arctoides and the 25 fascicularis group (topo3) and had shared derived alleles between both groups. Further, sliding 26 window analysis of phylogenetic relationships revealed 53% of the genomic regions supported 27 placement of M. arctoides in the sinica species group (topo2), 16% supported placement in the 28 fascicularis species group (topo3), and 11% supported M. arctoides in a grouping distinct from the 29 sinica and fascicularis groups (topo1). Genomic regions with topo1 were intersected with 30 previously identified QTL for mouse baculum morphology, and 47 genes were found, including five 31 of sixteen major candidate loci that govern mouse baculum variation (KIF14, KIAA0586, RHOJ, 32 TGM2, and DACT1). Although baculum morphology in the bear macaque is diverged from its parent 33 taxa, it most closely resembles that of the fascicularis group. Outliers of shared ancestry from the 34 fascicularis species group located within these same QTL regions overlap with the gene BMP4, 35 which is an important component of the hedgehog signaling pathway that controls gonadogenesis. 36Two additional outlier genes (one shared with each species group) outside of the baculum QTL are 37 known to interact with BMP4, suggesting this pathway may be involved in baculum morphology in 38 primates. These results highlight how the mosaic ancestry of the bear macaque could explain its 39 unique baculum evolution and collectively contribute to reproductive isolation. 40
Introductory Paragraph 41In mammals, the baculum has extreme morphological variability, a dynamic evolutionary 42 history characterized by repeated gain and loss, and is often used in species identification. The bear 43 macaque has divergent genital morphology, including the longest baculum among all primates, and 44 is proposed to have evolved via ancient hybrid speciation. Here, population genetic and 45 phylogenomic approaches were used to e...