Phylogenetic Network of HSA Sequences in Humans and Great Apes
Phylogenetic split network (based on alignment shown in Figure S2) showing the relationships between HSA segments, produced with SplitsTree4 22 via the “NeighborNet” method and the “uncorrectedP” distance. Lengths of edges represent the proportion of sites at which sequences differ, as indicated by the scale-bar. The reticulated structure indicates a history of gene conversion. Abbreviations are as follows: Hu, human; Ch, chimpanzee; and Go, gorilla.

XY Translocations between PRKX and PRKY, the PRKY Gene Region, and Gametologous Sequence Variants and Conversions around Translocation Hotspot A
(A) Idiograms of the sex chromosomes (not to scale) showing the pseudoautosomal regions (PAR1, PAR2), the SRY gene, and the PRKX and PRKY gene pair.
(B) The PRKY gene region, showing positions of exons and HSA. Exon numbering is based on PRKX 13 , so exon 6 is absent. Gene orientation varies as a result of a polymorphic Yp inversion 14 , and the orientation shown is that permissive for XY translocation 15 (opposite to the Y reference sequence 7 ). There is no reason to expect orientation to influence the probability of conversion.
(C) Sequence states of GSVs in the Y- and X-chromosomal reference sequences of an ∼1.9 kb region encompassing HSA. The positions of 66 surveyed gametologous sequence variants (GSVs) are indicated by circles (see key below figure), and some are numbered sequentially. Y- and X-specific primers (arrows) cover the proximal- and distal-most four GSVs.
(D) Sequence states of GSVs in Y-chromosomal copies of part of the region. Names of DNA samples and their Y-chromosomal haplogroups 8 are given to the left. Samples with the prefix “YCC” are from the Y Chromosome Consortium, and haplogroup information is as described. 8,21 Other human samples of known haplogroup are from collections of the authors. Below is shown the shorter region surveyed in the Y chromosome of sample YCC4.
(E) Sequence states of GSVs in X-chromosomal copies; DNA sample names and their populations of origin are given to the left. Haplotypes (ht) are numbered to the right.