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Recombination between the X and Y human sex chromosomes is limited to the two pseudoautosomal regions (PARs) that present quite distinct evolutionary origins. Despite the crucial importance for male meiosis, genetic diversity patterns and evolutionary dynamics of these regions are poorly understood. In the present study, we analyzed and compared the genetic diversity of the PAR regions using publicly available genomic sequences encompassing both PAR1 and PAR2. Comparisons were performed through allele diversities, linkage disequilibrium status and recombination frequencies within and between X and Y chromosomes. In agreement with previous studies, we confirmed the role of PAR1 as a male-specific recombination hotspot, but also observed similar characteristic patterns of diversity in both regions although male recombination occurs at PAR2 to a much lower extent (at least one recombination event at PAR1 and in ≈1% in normal male meioses at PAR2). Furthermore, we demonstrate that both PARs harbor significantly different allele frequencies between X and Y chromosomes, which could support that recombination is not sufficient to homogenize the pseudoautosomal gene pool or is counterbalanced by other evolutionary forces. Nevertheless, the observed patterns of diversity are not entirely explainable by sexually antagonistic selection. A better understanding of such processes requires new data from intergenerational transmission studies of PARs, which would be decisive on the elucidation of PARs evolution and their role in male-driven heterosomal aneuploidies., Author summary The pseudoautosomal regions (PAR1 and PAR2) of the human sex chromosomes contain the unique blocks of homologous sequences between the X and Y chromosomes that allow pairing and recombination during male meiosis. Both PARs present a distinctive transmission behavior that includes the properties of either sex-linked or autosomal regions (hence the pseudoautosomal status). However, the type and extent of evolutionary forces acting on these regions are, so far, not totally clear. In this work, we aimed to study the genetic diversity patterns in the human PARs, taking advantage of the publicly available resource of human genetic variation provided by the 1000 Genomes Project. Our results showed a higher frequency of recombination in PAR1 when compared to PAR2, as well as, a fairly uneven distribution of recombination throughout both regions. Moreover, in both PARs, low recombination segments are consistently associated with increased linkage disequilibrium and significantly different allele frequencies between the X and Y chromosomes. Despite the discrepancy of male recombination rates (obligatory at PAR1 and in ≅1% of meiosis at PAR2), both regions harbor highly enriched stretches with regard to allele frequency differences among sexes, which are not counterbalanced by recombination, raising questions about underlying evolutionary forces (e.g., selection). Since our results do not fit the expectations of a sexually antagonistic model, new data based on fast evolving markers from intergenerational transmission studies of PARs are required for the elucidation of the evolutionary behavior and crucial role of these regions in male-driven sex-chromosome aneuploidies.

Meiosis distinguishes cells in the germ line from their somatic counterparts. Part of meiosis involves a bizarre series of events in which cells deliberately damage their DNA and then repair it. Of the many double-strand breaks that are generated, a minority are resolved as reciprocal exchanges between homologous chromosomes [1]. In a wide variety of species, recombination diversifies genomes and is required for the formation of viable gametes. Although the functional role of crossing over should impose strong selective constraints, the rate of recombination varies among individuals. Recombination rate shows resemblance among relatives [2], differs among inbred strains raised in a common environment [3], and responds to artificial selection [4], demonstrating a genetic component to individual rate differences that remains mostly unexplained. A handful of genes responsible for variation in recombination rate have been identified, including modifiers of the total number of crossovers [5–8] and loci that determine the genomic placement of recombination events [9]. As a fundamental part of gametogenesis, meiosis also plays a role in speciation, the means by which one species becomes two. A common observation is that otherwise viable hybrids between genetically differentiated lineages suffer from reduced fertility up to the point of complete sterility—an important reproductive barrier that keeps species distinct [10]. One stage during which problems appear is meiosis, when hybrid gametogenesis sometimes arrests. According to an influential model, hybrid sterility arises from disrupted interactions between different genes that evolved in separate populations [11,12]. The search for incompatibility genes that cause hybrid sterility has so far yielded a short list [13–15]. The fact that only a small number of genes are known to control variation in recombination rate or to contribute to hybrid sterility makes the discovery that one gene mediates both traits especially noteworthy. Prdm9 encodes a histone methyltransferase that modifies chromatin and is essential for meiosis in mice [16]. Decades of persistent effort from the group of Jiri Forejt demonstrated that incompatibility between Prdm9 and other loci causes sterility in F1 hybrid males formed by crossing two subspecies of house mice [17]. Subsequently, genetic mapping in crosses, population genetic analysis, bioinformatic prediction of DNA binding sites, and association studies jointly identified Prdm9 as a primary determinant of recombination hotspot location (short stretches of sequence within which most crossovers occur) in mice and humans [9,18–20]. The dual roles of Prdm9 reveal a tantalizing link between recombination and speciation at the genetic level and motivate the search for other genes that affect both processes. Now, progress from Jiri Forejt’s lab provides fresh evidence for a genetic connection between recombination and hybrid sterility. Balcova et al. (2016) [21] profile the genome-wide recombination rate by visualizing the immunolocalization pattern of the MLH1 mismatch repair protein that resolves double-strand breaks into crossovers (Fig 1). This powerful approach enables the total number of recombination events to be counted in individual spermatocytes. The authors first use the MLH1 technique to confirm that the genome of an inbred strain representing the house mouse subspecies Mus musculus musculus experiences an average of 4.7 more crossovers than the genome of an inbred strain descended primarily from M. m. domesticus (a 19% increase). Next, Balcova et al. (2016) measure recombination rates in a panel of inbred strains, each of which harbors single chromosomes from the M. m. musculus strain on the genomic background of the M. m. domesticus strain. By comparing rates in chromosome substitution strains with the appropriate parental strain, the authors identify three chromosomes that affect the genome-wide crossover number. The locus with the largest phenotypic effect is located on the X chromosome. Rate differences among substitution strains carrying pieces of the chromosome further localize the position of this modifier of the global recombination rate to a 4.7 Mb interval (nicknamed Meir1 by the authors). This locus lies within a broader part of the X chromosome previously shown to modulate recombination in crosses involving other subspecies of mice [22,23]. Fig 1 Image illustrating immunofluorescent cytology approach to measuring the genome-wide recombination rate (from Balcova et al., 2016). Several lines of evidence suggest that this region of the X chromosome genetically links recombination and speciation. First, the same interval is associated with multiple correlates of hybrid sterility. Small testes, low sperm count, and morphological abnormalities in sperm observed in F1 males from crosses between M. m. musculus mothers and M. m. domesticus fathers all map to this genomic location [24,25]. Second, hybrid male sterility due to one of the loci in this X-linked region (Hstx2) involves an incompatibility with Prdm9 [25]. Finally, the effects of this piece of the X chromosome on recombination and sterility show similar properties, including male specificity. The findings of Balcova et al. (2016), along with previous discoveries about Prdm9, raise the intriguing possibility that recombination and speciation are mechanistically coupled. Remarkably, both the fine-scale placement of crossovers (mediated by Prdm9) and the global recombination rate (controlled by Meir1) seem to be associated with hybrid sterility. The authors propose that the incompatibility between Prdm9 and Hstx2 could inhibit the repair of double-strand breaks, which could in turn lead to the disrupted synapsis of chromosomes and meiotic arrest observed in sterile F1 males [26,27]. Regardless of the mechanism, the larger implication is that evolutionary divergence in recombination genes can generate a frequently observed form of reproductive isolation. Once the causative gene(s) and mutation(s) corresponding to Meir1 and Hstx2 are identified in this system, important remaining questions can be answered. Do the joint effects on recombination and hybrid sterility reflect the pleiotropic activities of a single gene or multiple linked genes? What are the molecular, cellular, and developmental bases of these phenotypes? What is the evolutionary history of the causative mutations? Did natural selection drive phenotypic divergence, as seems to be the case for the rapidly evolving Prdm9 [28]? The results from Balcova et al. (2016) should also motivate similar studies in other organisms. The observations that recombination rate evolves and that hybrid sterility is a key reproductive barrier are phylogenetically widespread, leaving no obvious reason that the emerging connection between recombination and speciation should be restricted to mice.

Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination., Author Summary Previous studies on cattle recombination largely focused on males. Using a large Holstein sample from the USDA national database, we studied both male and female recombination by assembling paternal and maternal recombination events in at least three generations. This unique data set provides unprecedented statistical power to study cattle genome recombination in the two sexes: (1) We report for the first time that bulls have more recombination than cows, contrary to the common perception that females have more recombination than males as observed in many mammalian species including humans and mice, and that the sex difference in recombination primarily occurs near the subtelomeric regions of all bovine autosomes; (2) We identify several genes associated with cattle recombination in both females and males, and genes affecting female recombination only; (3) We define putative recombination hotspots and find the cattle PRDM9 gene to be associated with recombination hotspot usage. These results provide new insights for understanding cattle and mammalian genome recombination.

Upon entering a Regency-era ball, a Jane Austen heroine might ask herself, “Do I stay with my sister, or attempt to secure a partner?” The homologous recombination events that occur during meiosis need to make a similar decision, and how they do so is investigated in papers by Doug Bishop, Neil Hunter, and colleagues [1] and Nancy Hollingsworth and colleagues [2] in PLOS Genetics. The authors define the interplay between the strand exchange proteins Dmc1 and Rad51 in partner choice during meiotic double-strand break (DSB) repair and reveal that when the delicate balance between their activities is manipulated, partner choice is disrupted. However, like the plot twists that bring partners together to enforce happy endings in Austen's novels, robust buffering of recombination counteracts the deleterious effect of eschewing a partner in favor of your sister (chromatid). For many organisms, accurate segregation of homologous chromosomes of different parental origin (homologs) in meiosis depends upon interhomolog crossovers. Crossovers are formed by the repair of programmed DSBs induced by Spo11 [3] and involve the exchange of genetic information flanking the initiating break. DSB ends are processed into 3′ single-stranded tails encased by a nucleoprotein filament, which contains strand exchange factors that are used to invade an intact homologous duplex to initiate recombination. Recombination intermediates can be resolved to form crossovers or noncrossovers, the latter of which do not involve exchange of flanking information. Failure to form crossovers leads to aneuploidy or gamete death; as such, crossover frequency and distribution is tightly controlled to ensure at least one crossover occurs between each pair of homologs (crossover assurance), that crossovers do not form in close juxtaposition (crossover interference), and that crossover numbers are maintained despite perturbations in the number of DSBs (crossover homeostasis) [4]. Recent studies of crossover control have revealed feedback regulation occurring at multiple steps during recombination progression—including DSB formation [5]–[7] and the crossover-noncrossover decision [8]—to provide robust homeostatic control. Critical questions remain: what intermediates are sensed by homeostatic mechanisms, and how do these mechanisms interact to execute crossover regulation? Like DSB formation, the strand exchange reaction is a potential target of homeostatic control. The Rad51 strand exchange factor mediates recombination during the mitotic cell cycle, which preferentially utilizes the sister chromatid to template repair. While Rad51 also has a critical role in meiosis, its own strand exchange activity is not required. Instead, Rad51 functions as a cofactor for a meiosis-specific strand exchange factor, Dmc1 [9]. When Rad51 and Dmc1 act together, they exhibit homolog bias, directing strand exchange between homologs rather than sister chromatids. However, loss of Rad51 does not phenocopy loss of Dmc1 [3]. In the absence of Rad51, interhomolog recombination is reduced, and intersister recombination predominates. In the absence of Dmc1, all DSB repair is dramatically reduced, a recombination checkpoint is activated, and the strand exchange activity of Rad51 is inhibited by the Hed1 protein and by an effector kinase, Mek1. Removing this inhibition allows efficient recombination, although interhomolog crossovers are reduced compared to wild type. Lao, Cloud, et al. [1] asked how well budding yeast dmc1 hed1 mutants, which use Rad51 alone, complete meiosis. Using assays that differentiate template choice in recombination intermediates, they observed a five-fold reduction in homolog bias in dmc1 hed1 and a two-fold reduction in hed1 alone. This implies that Dmc1 executes template choice by inhibiting the strand exchange activity of Rad51. In a complementary study, Liu et al. [2] took a different approach by generating a hypomorphic allele, dmc1-T159A. They then tweaked the balance of power between Rad51 and Dmc1 by introducing dmc1-T159A into strains lacking Hed1 and/or a bypass of Mek1 repression of Rad51. While dmc1-T159A showed no reduction in homolog bias on its own, coupling it with increased Rad51 activity led to a synergistic eight-fold reduction in homolog bias, inferring that inhibition of Rad51 strand exchange is required to favor interhomolog strand exchange by Dmc1. Intriguingly, regardless of the extent of reduction in homolog bias, there was a much milder effect on ultimate crossover formation. Lao, Cloud, et al. found that dmc1 hed1 exhibited nearly wild-type crossover levels and distributions on chromosome III, suggesting that a highly effective compensatory mechanism is invoked. One such mechanism could be the maintenance of crossovers at the expense of noncrossovers [8]; indeed, the authors observed an increase in the crossover-to-noncrossover ratio in dmc1 hed1. To test the extent of this compensation, they coupled dmc1 hed1 with spo11 alleles that reduce global DSB numbers. Decreasing DSBs did not cause a further increase in the crossover-to-noncrossover ratio, implying that the dmc1 hed1 strain has maximized the buffering capacity afforded by the crossover-noncrossover decision. While this analysis by Lao, Cloud, et al. was limited to a single recombination hotspot, Liu et al. directly measured genome-wide recombination by whole-genome sequencing of tetrads from strains with altered interhomolog bias. Although crossover number in dmc1-T159A was equivalent to wild type, noncrossovers were significantly reduced. In hed1 alone or in hed1 dmc1-T159A double mutants, crossovers were significantly reduced, but noncrossovers were reduced to the same extent as that observed in dmc1-T159A alone. Despite the fact that the number of sequenced tetrads was low, these findings indicate that any compensatory mechanisms that work on the crossover-noncrossover decision are already maximized by the mild reduction in interhomolog bias observed in hed1. Remarkably, the spacing of crossovers was unaffected in all three strains, indicating that reduced interhomolog interactions do not alter crossover interference. What mechanisms maintain crossover numbers genome-wide? Lao, Cloud, et al. argue that a second homeostatic mechanism—continued formation of DSBs—must account for the high levels of crossovers observed when interhomolog bias is disrupted (Figure 1). In support of this view, while crossovers were reduced locally in dmc1 hed1 at a hotspot that is saturated for DSB formation, crossovers increased in a larger adjacent chromosomal region. They propose that larger chromosomal regions retain a higher potential for receiving additional DSBs through this second homeostatic mechanism. Figure 1 Homeostatic regulation of meiotic recombination. An important insight gleaned from these studies is that successful interhomolog interactions are a critical gauge by which homeostatic regulation is effected. Thus, homeostatic sensing must occur between chromosomes (in trans) in response to interhomolog interactions, which may or may not be independent from sensing along a chromosome (in cis) in response to DSB formation [7]. Recent evidence of multiple types of feedback regulation of Spo11-mediated DSB formation will likely provide a key component to a synthetic model that can explain local, regional, and global regulation of meiotic recombination [5]–[7]. It is notable in this context that the mutants analyzed in the current studies show a delay in meiotic progression, suggesting that they activate the meiotic recombination checkpoint. One recently identified pathway for Spo11-mediated DSB feedback involves the recombination checkpoint preventing expression of proteins that shut off DSB formation [10], [11]. In the template choice mutants studied here, the prophase delay could lead to increased formation of DSBs, which eventually provoke enough interhomolog interactions to disengage the checkpoint and complete meiosis. Recent work in mouse spermatocytes indicates that DSB formation is significantly increased when chromosomes have failed to synapse in this organism, as well [12]. Taken together, these findings in yeast and in mice suggest the existence of highly tuned compensatory mechanisms able to target de novo DSB formation specifically to regions of the genome where more recombination is needed. These two manuscripts have clarified the competitive relationship between Rad51 and Dmc1 during meiotic strand exchange and leveraged this relationship to investigate how interhomolog interactions are integrated into homeostatic regulation. Identifying all of the various components of the multilayered feedback mechanisms inherent to recombination homeostasis, and especially understanding how they crosstalk with one another, will continue to be a stimulating area of research.

Background: Schizophrenia is a major disorder with complex genetic mechanisms. Earlier, population genetic studies revealed the occurrence of strong positive selection in the GABRB2 gene encoding the β2 subunit of GABAA receptors, within a segment of 3,551 bp harboring twenty-nine single nucleotide polymorphisms (SNPs) and containing schizophrenia-associated SNPs and haplotypes. Methodology/Principal Findings:In the present study, the possible occurrence of recombination in this 'S1-S29' segment was assessed. The occurrence of hotspot recombination was indicated by high resolution recombination rate estimation, haplotype diversity, abundance of rare haplotypes, recurrent mutations and torsos in haplotype networks, and experimental haplotyping of somatic and sperm DNA. The sub-segment distribution of relative recombination strength, measured by the ratio of haplotype diversity (Hd) over mutation rate (θ), was indicative of a human specific Alu-Yi6 insertion serving as a central recombining sequence facilitating homologous recombination. Local anomalous DNA conformation attributable to the Alu-Yi6 element, as suggested by enhanced DNase I sensitivity and obstruction to DNA sequencing, could be a contributing factor of the increased sequence diversity. Linkage disequilibrium (LD) analysis yielded prominent low LD points that supported ongoing recombination. LD contrast revealed significant dissimilarity between control and schizophrenic cohorts. Among the large array of inferred haplotypes, H26 and H73 were identified to be protective, and H19 and H81 risk-conferring, toward the development of schizophrenia. Conclusions/Significance: The co-occurrence of hotspot recombination and positive selection in the S1-S29 segment of GABRB2 has provided a plausible contribution to the molecular genetics mechanisms for schizophrenia. The present findings therefore suggest that genome regions characterized by the co-occurrence of positive selection and hotspot recombination, two interacting factors both affecting genetic diversity, merit close scrutiny with respect to the etiology of common complex disorders. © 2010 Ng et al.

Genomic regions participating in recombination events may support distinct topologies, and phylogenetic analyses should incorporate this heterogeneity. Existing phylogenetic methods for recombination detection are challenged by the enormous number of possible topologies, even for a moderate number of taxa. If, however, the detection analysis is conducted independently between each putative recombinant sequence and a set of reference parentals, potential recombinations between the recombinants are neglected. In this context, a recombination hotspot can be inferred in phylogenetic analyses if we observe several consecutive breakpoints. We developed a distance measure between unrooted topologies that closely resembles the number of recombinations. By introducing a prior distribution on these recombination distances, a Bayesian hierarchical model was devised to detect phylogenetic inconsistencies occurring due to recombinations. This model relaxes the assumption of known parental sequences, still common in HIV analysis, allowing the entire dataset to be analyzed at once. On simulated datasets with up to 16 taxa, our method correctly detected recombination breakpoints and the number of recombination events for each breakpoint. The procedure is robust to rate and transitionratiotransversion heterogeneities for simulations with and without recombination. This recombination distance is related to recombination hotspots. Applying this procedure to a genomic HIV-1 dataset, we found evidence for hotspots and de novo recombination.

Recent experiments using sperm typing have demonstrated that, in several regions of the human genome, recombination does not occur uniformly but instead is concentrated in “hotspots” of 1–2 kb. Moreover, the crossover asymmetry observed in a subset of these has led to the suggestion that hotspots may be short-lived on an evolutionary time scale. To test this possibility, we focused on a region known to contain a recombination hotspot in humans, TAP2, and asked whether chimpanzees, the closest living evolutionary relatives of humans, harbor a hotspot in a similar location. Specifically, we used a new statistical approach to estimate recombination rate variation from patterns of linkage disequilibrium in a sample of 24 western chimpanzees (Pan troglodytes verus). This method has been shown to produce reliable results on simulated data and on human data from the TAP2 region. Strikingly, however, it finds very little support for recombination rate variation at TAP2 in the western chimpanzee data. Moreover, simulations suggest that there should be stronger support if there were a hotspot similar to the one characterized in humans. Thus, it appears that the human TAP2 recombination hotspot is not shared by western chimpanzees. These findings demonstrate that fine-scale recombination rates can change between very closely related species and raise the possibility that rates differ among human populations, with important implications for linkage-disequilibrium based association studies.