Absence of the TAP2 Human Recombination Hotspot in Chimpanzees
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{"title"=>"Absence of the TAP2 human recombination hotspot in chimpanzees", "type"=>"journal", "authors"=>[{"first_name"=>"Susan E.", "last_name"=>"Ptak", "scopus_author_id"=>"6603656066"}, {"first_name"=>"Amy D.", "last_name"=>"Roeder", "scopus_author_id"=>"7003386551"}, {"first_name"=>"Matthew", "last_name"=>"Stephens", "scopus_author_id"=>"7201574987"}, {"first_name"=>"Yoav", "last_name"=>"Gilad", "scopus_author_id"=>"6602166624"}, {"first_name"=>"Svante", "last_name"=>"Pääbo", "scopus_author_id"=>"7006151134"}, {"first_name"=>"Molly", "last_name"=>"Przeworski", "scopus_author_id"=>"6603966439"}], "year"=>2004, "source"=>"PLoS Biology", "identifiers"=>{"issn"=>"15449173", "isbn"=>"1545-7885 (Electronic)", "pmid"=>"15208713", "scopus"=>"2-s2.0-16344392281", "doi"=>"10.1371/journal.pbio.0020155", "sgr"=>"16344392281", "pui"=>"39234450"}, "id"=>"33dd8b91-e554-3a0c-93e2-60a1181b8860", "abstract"=>"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.", "link"=>"http://www.mendeley.com/research/absence-tap2-human-recombination-hotspot-chimpanzees", "reader_count"=>60, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>7, "Student > Doctoral Student"=>3, "Researcher"=>12, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>13}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>7, "Student > Doctoral Student"=>3, "Researcher"=>12, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>13}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>12, "Mathematics"=>1, "Agricultural and Biological Sciences"=>37, "Medicine and Dentistry"=>3, "Neuroscience"=>1, "Physics and Astronomy"=>1, "Psychology"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>37}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"New Zealand"=>1, "Austria"=>1, "Sweden"=>1, "United States"=>4, "Brazil"=>1, "Australia"=>1, "Germany"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/964518"], "description"=>"<p>The positions of sites that differ between humans and chimpanzees are shown on the first line, while the positions of sites polymorphic in humans from the UK or in western chimpanzees are shown on the next two lines. The human hotspot region is underlined. The dashed lines indicate regions not surveyed for variation in western chimpanzees (see <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020155#s4\" target=\"_blank\">Materials and Methods</a>).</p>", "links"=>[], "tags"=>["sites", "genomic"], "article_id"=>634452, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Susan E Ptak", "Amy D Roeder", "Matthew Stephens", "Yoav Gilad", "Svante Pääbo", "Molly Przeworski"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020155.g004", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Variable_Sites_in_the_Genomic_Region_/634452", "title"=>"Distribution of Variable Sites in the Genomic Region", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:19:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/964451"], "description"=>"<p>In this model, there is at most one hotspot in the region, the location and width of which are unknown and estimated along with <i>λ</i> and <i>ρ.</i> On the <i>y</i>-axis is an estimate of the posterior probability of elevated recombination, Pr(<i>λ</i> > 1), between each pair of consecutive SNPs (plotted at the midpoint position).</p>", "links"=>[], "tags"=>["recombination", "humans"], "article_id"=>634386, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Susan E Ptak", "Amy D Roeder", "Matthew Stephens", "Yoav Gilad", "Svante Pääbo", "Molly Przeworski"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020155.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_Recombination_Rate_Variation_in_Humans_and_Western_Chimpanzees_/634386", "title"=>"Estimates of Recombination Rate Variation in Humans and Western Chimpanzees", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:18:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/473684"], "description"=>"<div><p>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 <em>(Pan troglodytes verus).</em> 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.</p> </div>", "links"=>[], "tags"=>["tap2", "recombination", "hotspot", "chimpanzees"], "article_id"=>153339, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Susan E Ptak", "Amy D Roeder", "Matthew Stephens", "Yoav Gilad", "Svante Pääbo", "Molly Przeworski"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020155", "stats"=>{"downloads"=>4, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Absence_of_the_TAP2_Human_Recombination_Hotspot_in_Chimpanzees/153339", "title"=>"Absence of the TAP2 Human Recombination Hotspot in Chimpanzees", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-20 11:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/964355"], "description"=>"<p>We assumed that, if the hotspot is present, it is in the same location as estimated by sperm typing in humans (see <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020155#s4\" target=\"_blank\">Materials and Methods</a>). A <i>λ</i> value of one corresponds to the absence of recombination rate variation, while values of <i>λ</i> greater than one indicate a hotspot. The estimates for humans from the UK are shown in blue and those for western chimpanzees in orange.</p>", "links"=>[], "tags"=>["recombination", "hotspot", "genotype"], "article_id"=>634292, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Susan E Ptak", "Amy D Roeder", "Matthew Stephens", "Yoav Gilad", "Svante Pääbo", "Molly Przeworski"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020155.g002", "stats"=>{"downloads"=>5, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_the_Recombination_Hotspot_Intensity_955_Based_on_Genotype_Data_/634292", "title"=>"Estimates of the Recombination Hotspot Intensity, <i>λ,</i> Based on Genotype Data", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:17:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/964318"], "description"=>"<p>Only SNPs with minor allele frequencies above 0.1 are included. The rows correspond to the consecutive SNPs in the region, as do the columns. Each cell indicates the extent of LD between a pair of sites, as measured by |<i>D</i>′| (estimated using the Expectation Maximization algorithm, as implemented by Arlequin: <a href=\"http://lgb.unige.ch/arlequin/\" target=\"_blank\">http://lgb.unige.ch/arlequin/</a>).</p>", "links"=>[], "tags"=>["pairwise", "ld", "humans"], "article_id"=>634254, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Susan E Ptak", "Amy D Roeder", "Matthew Stephens", "Yoav Gilad", "Svante Pääbo", "Molly Przeworski"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020155.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Patterns_of_Pairwise_LD_in_Humans_and_Chimpanzees_/634254", "title"=>"Patterns of Pairwise LD in Humans and Chimpanzees", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:17:29"}

PMC Usage Stats | Further Information

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