1
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Bergman J, Schierup MH. Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes. Genome Biol 2022; 23:215. [PMID: 36253794 PMCID: PMC9575207 DOI: 10.1186/s13059-022-02784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 09/30/2022] [Indexed: 12/03/2022] Open
Abstract
Background The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme recombination and mutation processes. We investigate PAR1 evolution using population genomic datasets of extant humans, eight populations of great apes, and two archaic human genome sequences. Results We find that PAR1 is fast evolving and closer to evolutionary nucleotide equilibrium than autosomal telomeres. We detect a difference between substitution patterns and extant diversity in PAR1, mainly driven by the conflict between strong mutation and recombination-associated fixation bias at CpG sites. We detect excess C-to-G mutations in PAR1 of all great apes, specific to the mutagenic effect of male recombination. Despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence. We find differences between substitution spectra of these archaics suggesting rapid evolution of PAR1 in recent hominin history. Frequency analysis of alleles segregating in females and males provided no evidence for recent sexual antagonism in this region. We study repeat content and double-strand break hotspot regions in PAR1 and find that they may play roles in ensuring the obligate X-Y recombination event during male meiosis. Conclusions Our study provides an unprecedented quantification of population genetic forces governing PAR1 biology across extant and extinct hominids. PAR1 evolutionary dynamics are predominantly governed by recombination processes with a strong impact on mutation patterns across all species. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02784-x.
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Affiliation(s)
- Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, DK-8000, Aarhus C, Denmark.
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2
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Santos C, Mendes T, Antunes A. The genes from the pseudoautosomal region 1 (PAR1) of the mammalian sex chromosomes: Synteny, phylogeny and selection. Genomics 2022; 114:110419. [PMID: 35753589 DOI: 10.1016/j.ygeno.2022.110419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 11/04/2022]
Abstract
Sex chromosomes recombine restrictly in their homologous area, the pseudoautosomal region (PAR), represented by PAR1 and PAR2, which behave like an autosome in both pairing and recombination. The PAR1, common to most of the eutherian mammals, is located at the terminus of the sex chromosomes short arm and exhibit recombination rates ~20 times higher than the autosomes. Here, we assessed the interspecific evolutionary genomic dynamics of 15 genes of the PAR1 across 41 mammalian genera (representing six orders). The strong negative selection detected in most of the assessed groups reinforces the presence of evolutionary constraints, imposed by the important function of the PAR1 genes. Indeed, mutations in these genes are associated with various diseases in humans, including stature problems (Klinefelter Syndrome), leukemia and mental diseases. Yet, a few genes exhibiting positive selection (ω-value >1) were depicted in Rodentia (ASMT and ZBED1) and Primates (CRLF2 and CSF2RA). Rodents have the smallest described PAR1, while that of simian primates/humans underwent a 3 to 5 fold size reduction. The assessment of the PAR1 genes synteny revealed differences among the mammalian species, especially in the Rodentia order where chromosomic translocations from the sex chromosomes to the autosomes were observed. Such syntenic changes may be an evidence of the rapid evolution in rodents, as previous referred in other papers, also depicted by their increased branch lengths in the phylogenetic analyses. Concluding, we suggest that genome migration is an important factor influencing the evolution of mammals and may result in changes of the selective pressures operating on the genome.
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Affiliation(s)
- Carla Santos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Porto, Portugal; Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Portugal
| | - Tito Mendes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Porto, Portugal
| | - Agostinho Antunes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
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3
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Wang Z, Sun L, Paterson AD. Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD. PLoS Genet 2022; 18:e1010231. [PMID: 35639794 PMCID: PMC9187127 DOI: 10.1371/journal.pgen.1010231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 06/10/2022] [Accepted: 05/03/2022] [Indexed: 12/19/2022] Open
Abstract
An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF). sdMAF persisted for many of these SNPs in the recently released high coverage whole genome sequence of the 1000 Genomes Project that was aligned to GRCh38, and it was consistent between the five super-populations. Among the 245,825 common (MAF>5%) biallelic X-chromosomal SNPs in the phase 3 data presumed to be of high quality, 2,039 have genome-wide significant sdMAF (p-value <5e-8). sdMAF varied by location: non-pseudo-autosomal region (NPR) = 0.83%, pseudo-autosomal regions (PAR1) = 0.29%, PAR2 = 13.1%, and X-transposed region (XTR)/PAR3 = 0.85% of SNPs had sdMAF, and they were clustered at the NPR-PAR boundaries, among others. sdMAF at the NPR-PAR boundaries are biologically expected due to sex-linkage, but have generally been ignored in association studies. For comparison, similar analyses found only 6, 1 and 0 SNPs with significant sdMAF on chromosomes 1, 7 and 22, respectively. Similar sdMAF results for the X chromosome were obtained from the high coverage whole genome sequence data from gnomAD V 3.1.2 for both the non-Finnish European and African/African American samples. Future X chromosome analyses need to take sdMAF into account. The human X chromosome contains over 800 genes and is the 8th largest human chromosome. Genome-wide associations studies have generally failed to examine variants on the X chromosome for association with diseases and traits, partly due to complexities of the data analysis, and challenges with genotype imputation. We examined X chromosomal variants from the 1000 Genomes Project for sex differences in allele frequency and found that many variants showed significant differences. These variants cluster at the centromeric parts of the pseudoautosomal regions 1 and 2, as well as the putative pseudo-autosomal region 3 (also termed X-transposed region). This pattern was observed in high coverage whole genome sequence data from the same subjects that was aligned to GRCh38, suggesting that is not an artefact of low coverage sequencing or problems specific to GRCh37. In addition, we replicated this phenomenon in high coverage whole genome sequence aligned to GRCh38 from the gnomAD database in both the non-Finnish European and African/African American samples. These findings have implications for the analysis of X chromosomal variants for disease and trait associations.
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Affiliation(s)
- Zhong Wang
- Department of Statistics and Data Science, Faculty of Science, National University of Singapore, Singapore
| | - Lei Sun
- Department of Statistic Sciences, Faculty of Arts and Science, University of Toronto, Ontario, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
- * E-mail: (LS); (ADP)
| | - Andrew D. Paterson
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
- Genetics and Genome Biology, The Hospital for Sick Children, Ontario, Canada
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
- * E-mail: (LS); (ADP)
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4
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Fukami M, Fujisawa Y, Ono H, Jinno T, Ogata T. Human Spermatogenesis Tolerates Massive Size Reduction of the Pseudoautosomal Region. Genome Biol Evol 2021; 12:1961-1964. [PMID: 32785664 PMCID: PMC7608489 DOI: 10.1093/gbe/evaa168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 01/21/2023] Open
Abstract
Mammalian male meiosis requires homologous recombination between the X and Y chromosomes. In humans, such recombination occurs exclusively in the short arm pseudoautosomal region (PAR1) of 2.699 Mb in size. Although it is known that complete deletion of PAR1 causes spermatogenic arrest, no studies have addressed to what extent male meiosis tolerates PAR1 size reduction. Here, we report two families in which PAR1 partial deletions were transmitted from fathers to their offspring. Cytogenetic analyses revealed that a ∼400-kb segment at the centromeric end of PAR1, which accounts for only 14.8% of normal PAR1 and 0.26% and 0.68% of the X and Y chromosomes, respectively, is sufficient to mediate sex chromosomal recombination during spermatogenesis. These results highlight the extreme recombinogenic activity of human PAR1. Our data, in conjunction with previous findings from animal studies, indicate that the minimal size requirement of mammalian PARs to maintain male fertility is fairly small.
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Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yasuko Fujisawa
- Department of Pediatrics, Hamamatsu University School of Medicine, Japan
| | - Hiroyuki Ono
- Department of Pediatrics, Hamamatsu University School of Medicine, Japan
| | - Tomoko Jinno
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Japan
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5
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Ralf A, Lubach D, Kousouri N, Winkler C, Schulz I, Roewer L, Purps J, Lessig R, Krajewski P, Ploski R, Dobosz T, Henke L, Henke J, Larmuseau MHD, Kayser M. Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers. Hum Mutat 2020; 41:1680-1696. [DOI: 10.1002/humu.24068] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/05/2020] [Accepted: 06/22/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Delano Lubach
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Nefeli Kousouri
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | | | - Iris Schulz
- Institut für Blutgruppenforschung LGC GmbH Cologne Germany
| | - Lutz Roewer
- Abteilung für Forensische Genetik, Institut für Rechtsmedizin und Forensische Wissenschaften Charite ́‐Universitätsmedizin Berlin Berlin Germany
| | - Josephine Purps
- Abteilung für Forensische Genetik, Institut für Rechtsmedizin und Forensische Wissenschaften Charite ́‐Universitätsmedizin Berlin Berlin Germany
| | - Rüdiger Lessig
- Institut für Rechtsmedizin Universitätsklinikum Halle Halle/Saale Germany
| | - Pawel Krajewski
- Department of Medical Genetics and Department of Forensic Medicine Medical University Warsaw Warsaw Poland
| | - Rafal Ploski
- Department of Medical Genetics and Department of Forensic Medicine Medical University Warsaw Warsaw Poland
| | - Tadeusz Dobosz
- Department of Forensic Medicine Wroclaw Medical University Wroclaw Poland
| | - Lotte Henke
- Institut für Blutgruppenforschung LGC GmbH Cologne Germany
| | - Jürgen Henke
- Institut für Blutgruppenforschung LGC GmbH Cologne Germany
| | | | - Manfred Kayser
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
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6
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Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination. Chromosoma 2019; 128:279-296. [PMID: 31332531 DOI: 10.1007/s00412-019-00718-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 02/01/2023]
Abstract
During meiosis, DNA double-strand breaks are initiated by the topoisomerase-like enzyme SPO11 and are repaired by inter-sister chromatid and inter-homologue DNA repair pathways. Genome-wide maps of initiating DNA double-strand breaks and inter-homologue repair events are now available for a number of mammalian, fungal and plant species. In mammals, PRDM9 specifies the location of meiotic recombination initiation via recognition of specific DNA sequence motifs by its C2H2 zinc finger array. In fungi and plants, meiotic recombination appears to be initiated less discriminately in accessible chromatin, including at gene promoters. Generally, meiotic crossover is suppressed in highly repetitive genomic regions that are made up of transposable elements (TEs), to prevent deleterious non-allelic homologous recombination events. However, recent and older studies have revealed intriguing relationships between meiotic recombination initiation and repair, and transposable elements. For instance, gene conversion events have been detected in maize centromeric retroelements, mouse MULE-MuDR DNA transposons undergo substantial meiotic recombination initiation, Arabidopsis Helitron TEs are among the hottest of recombination initiation hotspots, and human TE sequences can modify the crossover rate at adjacent PRDM9 motifs in cis. Here, we summarize the relationship between meiotic recombination and TEs, discuss recent insights from highly divergent eukaryotes and highlight outstanding questions in the field.
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7
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Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 2019; 46:2159-2168. [PMID: 29401301 PMCID: PMC5861413 DOI: 10.1093/nar/gky066] [Citation(s) in RCA: 383] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/23/2018] [Indexed: 12/30/2022] Open
Abstract
Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing.
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Affiliation(s)
- Simon Ardui
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala 75108, Sweden.,School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | | | - Matthew S Hestand
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium.,Department of Clinical Genetics, VU University Medical Center, Amsterdam 1081 BT, The Netherlands
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8
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Morgan AP, Bell TA, Crowley JJ, Pardo-Manuel de Villena F. Instability of the Pseudoautosomal Boundary in House Mice. Genetics 2019; 212:469-487. [PMID: 31028113 PMCID: PMC6553833 DOI: 10.1534/genetics.119.302232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
Faithful segregation of homologous chromosomes at meiosis requires pairing and recombination. In taxa with dimorphic sex chromosomes, pairing between them in the heterogametic sex is limited to a narrow interval of residual sequence homology known as the pseudoautosomal region (PAR). Failure to form the obligate crossover in the PAR is associated with male infertility in house mice (Mus musculus) and humans. Yet despite this apparent functional constraint, the boundary and organization of the PAR is highly variable in mammals, and even between subspecies of mice. Here, we estimate the genetic map in a previously documented expansion of the PAR in the M. musculus castaneus subspecies and show that the local recombination rate is 100-fold higher than the autosomal background. We identify an independent shift in the PAR boundary in the M. musculus musculus subspecies and show that it involves a complex rearrangement, but still recombines in heterozygous males. Finally, we demonstrate pervasive copy-number variation at the PAR boundary in wild populations of M. m. domesticus, M. m. musculus, and M. m. castaneus Our results suggest that the intensity of recombination activity in the PAR, coupled with relatively weak constraints on its sequence, permit the generation and maintenance of unusual levels of polymorphism in the population of unknown functional significance.
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Affiliation(s)
- Andrew P Morgan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27514
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27514
| | - James J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27514
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27514
- Department of Clinical Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27514
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9
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Lee YQ, Storry JR, Karamatic Crew V, Halverson GR, Thornton N, Olsson ML. A large deletion spanning
XG
and
GYG2
constitutes a genetic basis of the Xg
null
phenotype, underlying anti‐Xg
a
production. Transfusion 2019; 59:1843-1849. [DOI: 10.1111/trf.15242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/15/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Yan Quan Lee
- Division of Hematology and Transfusion Medicine, Department of Laboratory MedicineLund University Lund Sweden
| | - Jill R. Storry
- Division of Hematology and Transfusion Medicine, Department of Laboratory MedicineLund University Lund Sweden
- Department of Clinical Immunology and Transfusion MedicineOffice of Medical Services Lund Sweden
| | - Vanja Karamatic Crew
- International Blood Group Reference Laboratory, NHS Blood and Transplant Bristol United Kingdom
| | | | - Nicole Thornton
- International Blood Group Reference Laboratory, NHS Blood and Transplant Bristol United Kingdom
| | - Martin L. Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory MedicineLund University Lund Sweden
- Department of Clinical Immunology and Transfusion MedicineOffice of Medical Services Lund Sweden
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10
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Poriswanish N, Neumann R, Wetton JH, Wagstaff J, Larmuseau MHD, Jobling MA, May CA. Recombination hotspots in an extended human pseudoautosomal domain predicted from double-strand break maps and characterized by sperm-based crossover analysis. PLoS Genet 2018; 14:e1007680. [PMID: 30296256 PMCID: PMC6193736 DOI: 10.1371/journal.pgen.1007680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/18/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023] Open
Abstract
The human X and Y chromosomes are heteromorphic but share a region of homology at the tips of their short arms, pseudoautosomal region 1 (PAR1), that supports obligate crossover in male meiosis. Although the boundary between pseudoautosomal and sex-specific DNA has traditionally been regarded as conserved among primates, it was recently discovered that the boundary position varies among human males, due to a translocation of ~110 kb from the X to the Y chromosome that creates an extended PAR1 (ePAR). This event has occurred at least twice in human evolution. So far, only limited evidence has been presented to suggest this extension is recombinationally active. Here, we sought direct proof by examining thousands of gametes from each of two ePAR-carrying men, for two subregions chosen on the basis of previously published male X-chromosomal meiotic double-strand break (DSB) maps. Crossover activity comparable to that seen at autosomal hotspots was observed between the X and the ePAR borne on the Y chromosome both at a distal and a proximal site within the 110-kb extension. Other hallmarks of classic recombination hotspots included evidence of transmission distortion and GC-biased gene conversion. We observed good correspondence between the male DSB clusters and historical recombination activity of this region in the X chromosomes of females, as ascertained from linkage disequilibrium analysis; this suggests that this region is similarly primed for crossover in both male and female germlines, although sex-specific differences may also exist. Extensive resequencing and inference of ePAR haplotypes, placed in the framework of the Y phylogeny as ascertained by both Y microsatellites and single nucleotide polymorphisms, allowed us to estimate a minimum rate of crossover over the entire ePAR region of 6-fold greater than genome average, comparable with pedigree estimates of PAR1 activity generally. We conclude ePAR very likely contributes to the critical crossover function of PAR1. 95% of our genome is contained in 22 pairs of chromosomes shared by all humans. However, women and men differ in their sex chromosomes: while women have two X chromosomes, men have an X and a smaller, sex-determining Y chromosome. To ensure correct partition of X and Y into sperm, genetic exchange (crossover) must occur between these very different chromosomes in a short, shared region. The location of the boundary of this region was thought to have been conserved since before the divergence from old world monkeys at least 27 million years ago, but recently it has been shown that some human males carry an extended version on their Y chromosomes, thanks to the transposition of a piece of DNA from the X chromosome. Here, we asked if genetic exchange occurs in this newly extended region. To do this, we used previously published information that signposted the positions within the X chromosome segment which exhibit the hallmarks of crossover initiation. We then sought direct evidence of crossover in the sperm of men carrying the extension. This work showed that the signposts were accurate, pointing to frequent crossover in this novel shared sex-chromosomal domain.
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Affiliation(s)
- Nitikorn Poriswanish
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Forensic Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Jon H. Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - John Wagstaff
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Maarten H. D. Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology, Department of Imaging and Pathology, KU Leuven, Belgium
| | - Mark A. Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Celia A. May
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
- * E-mail:
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11
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Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
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Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
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12
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Frans G, Meert W, Van der Werff Ten Bosch J, Meyts I, Bossuyt X, Vermeesch JR, Hestand MS. Conventional and Single-Molecule Targeted Sequencing Method for Specific Variant Detection in IKBKG while Bypassing the IKBKGP1 Pseudogene. J Mol Diagn 2018; 20:195-202. [DOI: 10.1016/j.jmoldx.2017.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/09/2017] [Accepted: 10/25/2017] [Indexed: 12/30/2022] Open
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13
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Dosage compensation in the process of inactivation/reactivation during both germ cell development and early embryogenesis in mouse. Sci Rep 2017. [PMID: 28623283 PMCID: PMC5473838 DOI: 10.1038/s41598-017-03829-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ohno proposed that dosage compensation in mammals evolved as a two-step mechanism involving X-inactivation and X-upregulation. While X-inactivation is well characterized, it remains to further analysis whether upregulation of the single activated X chromosome in mammals occurs. We obtained RNA-seq data, including single-cell RNA-seq data, from cells undergoing inactivation/reactivation in both germ cell development and early embryogenesis stages in mouse and calculated the X: A ratio from the gene expression. Our results showed that the X: A ratio is always 1, regardless of the number of X chromosomes being transcribed for expressed genes. Furthermore, the single-cell RNA-seq data across individual cells of mouse preimplantation embryos of mixed backgrounds indicated that strain-specific SNPs could be used to distinguish transcription from maternal and paternal chromosomes and further showed that when the paternal was inactivated, the average gene dosage of the active maternal X chromosome was increased to restore the balance between the X chromosome and autosomes. In conclusion, our analysis of RNA-seq data (particularly single-cell RNA-seq) from cells undergoing the process of inactivation/reactivation provides direct evidence that the average gene dosage of the single active X chromosome is upregulated to achieve a similar level to that of two active X chromosomes and autosomes present in two copies.
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14
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Meiotic Consequences of Genetic Divergence Across the Murine Pseudoautosomal Region. Genetics 2017; 205:1089-1100. [PMID: 28100589 PMCID: PMC5340325 DOI: 10.1534/genetics.116.189092] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023] Open
Abstract
The production of haploid gametes during meiosis is dependent on the homology-driven processes of pairing, synapsis, and recombination. On the mammalian heterogametic sex chromosomes, these key meiotic activities are confined to the pseudoautosomal region (PAR), a short region of near-perfect sequence homology between the X and Y chromosomes. Despite its established importance for meiosis, the PAR is rapidly evolving, raising the question of how proper X/Y segregation is buffered against the accumulation of homology-disrupting mutations. Here, I investigate the interplay of PAR evolution and function in two interfertile house mouse subspecies characterized by structurally divergent PARs, Mus musculus domesticus and M. m. castaneus. Using cytogenetic methods to visualize the sex chromosomes at meiosis, I show that intersubspecific F1 hybrids harbor an increased frequency of pachytene spermatocytes with unsynapsed sex chromosomes. This high rate of asynapsis is due, in part, to the premature release of synaptic associations prior to completion of prophase I. Further, I show that when sex chromosomes do synapse in intersubspecific hybrids, recombination is reduced across the paired region. Together, these meiotic defects afflict ∼50% of spermatocytes from F1 hybrids and lead to increased apoptosis in meiotically dividing cells. Despite flagrant disruption of the meiotic program, a subset of spermatocytes complete meiosis and intersubspecific F1 males remain fertile. These findings cast light on the meiotic constraints that shape sex chromosome evolution and offer initial clues to resolve the paradox raised by the rapid evolution of this functionally significant locus.
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15
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The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research. Hum Genet 2016; 136:559-573. [DOI: 10.1007/s00439-016-1740-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
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Masset H, Hestand MS, Van Esch H, Kleinfinger P, Plaisancié J, Afenjar A, Molignier R, Schluth-Bolard C, Sanlaville D, Vermeesch JR. A Distinct Class of Chromoanagenesis Events Characterized by Focal Copy Number Gains. Hum Mutat 2016; 37:661-8. [DOI: 10.1002/humu.22984] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/24/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Heleen Masset
- Department of Human Genetics; KU Leuven; Leuven Belgium
| | | | | | - Pascale Kleinfinger
- Laboratoire Cerba; Département de Génétique Humaine; Saint-Ouen l'Aumône France
| | - Julie Plaisancié
- Service de Génétique Médicale; Hôpital Purpan; CHU Toulouse France
| | - Alexandra Afenjar
- APHP; Hôpital Armand-Trousseau; Service de Génétique Clinique; Paris France
- APHP; Hôpital Armand-Trousseau; Service de Neuropédiatrie; Paris France
| | - Romain Molignier
- Laboratoire de Biologie Clinique; Clinique Saint Jean Languedoc; Toulouse France
| | - Caroline Schluth-Bolard
- Laboratoire de Cytogénétique Constitutionnelle; Hospices Civils de Lyon; France
- Lyon Neuroscience Research Center; CNRS UMR5292, INSERM U1028, UCBL Lyon France
| | - Damien Sanlaville
- Laboratoire de Cytogénétique Constitutionnelle; Hospices Civils de Lyon; France
- Lyon Neuroscience Research Center; CNRS UMR5292, INSERM U1028, UCBL Lyon France
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Genetic Diversity on the Human X Chromosome Does Not Support a Strict Pseudoautosomal Boundary. Genetics 2016; 203:485-92. [PMID: 27010023 PMCID: PMC4858793 DOI: 10.1534/genetics.114.172692] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/11/2016] [Indexed: 11/18/2022] Open
Abstract
Unlike the autosomes, recombination between the X chromosome and the Y chromosome is often thought to be constrained to two small pseudoautosomal regions (PARs) at the tips of each sex chromosome. PAR1 spans the first 2.7 Mb of the proximal arm of the human sex chromosomes, whereas the much smaller PAR2 encompasses the distal 320 kb of the long arm of each sex chromosome. In addition to PAR1 and PAR2, there is a human-specific X-transposed region that was duplicated from the X to the Y chromosome. The X-transposed region is often not excluded from X-specific analyses, unlike the PARs, because it is not thought to routinely recombine. Genetic diversity is expected to be higher in recombining regions than in nonrecombining regions because recombination reduces the effect of linked selection. In this study, we investigated patterns of genetic diversity in noncoding regions across the entire X chromosome of a global sample of 26 unrelated genetic females. We found that genetic diversity in PAR1 is significantly greater than in the nonrecombining regions (nonPARs). However, rather than an abrupt drop in diversity at the pseudoautosomal boundary, there is a gradual reduction in diversity from the recombining through the nonrecombining regions, suggesting that recombination between the human sex chromosomes spans across the currently defined pseudoautosomal boundary. A consequence of recombination spanning this boundary potentially includes increasing the rate of sex-linked disorders (e.g., de la Chapelle) and sex chromosome aneuploidies. In contrast, diversity in PAR2 is not significantly elevated compared to the nonPARs, suggesting that recombination is not obligatory in PAR2. Finally, diversity in the X-transposed region is higher than in the surrounding nonPARs, providing evidence that recombination may occur with some frequency between the X and Y chromosomes in the X-transposed region.
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Hestand MS, Van Houdt J, Cristofoli F, Vermeesch JR. Polymerase specific error rates and profiles identified by single molecule sequencing. Mutat Res 2016; 784-785:39-45. [PMID: 26829216 DOI: 10.1016/j.mrfmmm.2016.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 12/16/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
DNA polymerases have an innate error rate which is polymerase and DNA context specific. Historically the mutational rate and profiles have been measured using a variety of methods, each with their own technical limitations. Here we used the unique properties of single molecule sequencing to evaluate the mutational rate and profiles of six DNA polymerases at the sequence level. In addition to accurately determining mutations in double strands, single molecule sequencing also captures direction specific transversions and transitions through the analysis of heteroduplexes. Not only did the error rates vary, but also the direction specific transitions differed among polymerases.
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Affiliation(s)
- Matthew S Hestand
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium
| | - Jeroen Van Houdt
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium
| | - Francesca Cristofoli
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium
| | - Joris R Vermeesch
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium.
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Abstract
Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.
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Johansson MM, Van Geystelen A, Larmuseau MHD, Djurovic S, Andreassen OA, Agartz I, Jazin E. Microarray Analysis of Copy Number Variants on the Human Y Chromosome Reveals Novel and Frequent Duplications Overrepresented in Specific Haplogroups. PLoS One 2015; 10:e0137223. [PMID: 26322892 PMCID: PMC4554990 DOI: 10.1371/journal.pone.0137223] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/13/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The human Y chromosome is almost always excluded from genome-wide investigations of copy number variants (CNVs) due to its highly repetitive structure. This chromosome should not be forgotten, not only for its well-known relevance in male fertility, but also for its involvement in clinical phenotypes such as cancers, heart failure and sex specific effects on brain and behaviour. RESULTS We analysed Y chromosome data from Affymetrix 6.0 SNP arrays and found that the signal intensities for most of 8179 SNP/CN probes in the male specific region (MSY) discriminated between a male, background signals in a female and an isodicentric male containing a large deletion of the q-arm and a duplication of the p-arm of the Y chromosome. Therefore, this SNP/CN platform is suitable for identification of gain and loss of Y chromosome sequences. In a set of 1718 males, we found 25 different CNV patterns, many of which are novel. We confirmed some of these variants by PCR or qPCR. The total frequency of individuals with CNVs was 14.7%, including 9.5% with duplications, 4.5% with deletions and 0.7% exhibiting both. Hence, a novel observation is that the frequency of duplications was more than twice the frequency of deletions. Another striking result was that 10 of the 25 detected variants were significantly overrepresented in one or more haplogroups, demonstrating the importance to control for haplogroups in genome-wide investigations to avoid stratification. NO-M214(xM175) individuals presented the highest percentage (95%) of CNVs. If they were not counted, 12.4% of the rest included CNVs, and the difference between duplications (8.9%) and deletions (2.8%) was even larger. CONCLUSIONS Our results demonstrate that currently available genome-wide SNP platforms can be used to identify duplications and deletions in the human Y chromosome. Future association studies of the full spectrum of Y chromosome variants will demonstrate the potential involvement of gain or loss of Y chromosome sequence in different human phenotypes.
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Affiliation(s)
- Martin M. Johansson
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
- * E-mail: (MMJ); (EJ)
| | - Anneleen Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Maarten H. D. Larmuseau
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole A. Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Agartz
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
- * E-mail: (MMJ); (EJ)
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Qiu S, Bergero R, Guirao-Rico S, Campos JL, Cezard T, Gharbi K, Charlesworth D. RAD mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region. Mol Ecol 2015; 25:414-30. [PMID: 26139514 DOI: 10.1111/mec.13297] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/10/2023]
Abstract
How loss of genetic exchanges (recombination) evolves between sex chromosomes is a long-standing question. Suppressed recombination may evolve when a sexually antagonistic (SA) polymorphism occurs in a partially sex-linked 'pseudoautosomal' region (or 'PAR'), maintaining allele frequency differences between the two sexes, and creating selection for closer linkage with the fully sex-linked region of the Y chromosome in XY systems, or the W in ZW sex chromosome systems. Most evidence consistent with the SA polymorphism hypothesis is currently indirect, and more studies of the genetics and population genetics of PAR genes are clearly needed. The sex chromosomes of the plant Silene latifolia are suitable for such studies, as they evolved recently and the loss of recombination could still be ongoing. Here, we used RAD sequencing to genetically map sequences in this plant, which has a large genome (c. 3 gigabases) and no available whole-genome sequence. We mapped 83 genes on the sex chromosomes, and comparative mapping in the related species S. vulgaris supports previous evidence for additions to an ancestral PAR and identified at least 12 PAR genes. We describe evidence that recombination rates have been reduced in meiosis of both sexes, and differences in recombination between S. latifolia families suggest ongoing recombination suppression. Large allele frequency differences between the sexes were found at several loci closely linked to the PAR boundary, and genes in different regions of the PAR showed striking sequence diversity patterns that help illuminate the evolution of the PAR.
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Affiliation(s)
- S Qiu
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - R Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S Guirao-Rico
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - T Cezard
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - K Gharbi
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - D Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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