Analysis of Chimpanzee History Based on Genome Sequence Alignments
Publication Date
April 18, 2008
Journal
PLOS Genetics
Authors
Jennifer L. Caswell, Swapan Mallick, Daniel J. Richter, Julie Neubauer, et al
Volume
4
Issue
4
Pages
e1000057
DOI
https://dx.plos.org/10.1371/journal.pgen.1000057
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1000057
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/18421364
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278377
Europe PMC
http://europepmc.org/abstract/MED/18421364
Web of Science
000255407400011
Scopus
43249086697
Mendeley
http://www.mendeley.com/research/analysis-chimpanzee-history-based-genome-sequence-alignments
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Analysis of chimpanzee history based on genome sequence alignments", "type"=>"journal", "authors"=>[{"first_name"=>"Jennifer L.", "last_name"=>"Caswell", "scopus_author_id"=>"55929502800"}, {"first_name"=>"Swapan", "last_name"=>"Mallick", "scopus_author_id"=>"24339060900"}, {"first_name"=>"Daniel J.", "last_name"=>"Richter", "scopus_author_id"=>"36777932400"}, {"first_name"=>"Julie", "last_name"=>"Neubauer", "scopus_author_id"=>"16245897300"}, {"first_name"=>"Christine", "last_name"=>"Schirmer", "scopus_author_id"=>"16246484900"}, {"first_name"=>"Sante", "last_name"=>"Gnerre", "scopus_author_id"=>"6506778444"}, {"first_name"=>"David", "last_name"=>"Reich", "scopus_author_id"=>"7102313000"}], "year"=>2008, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"43249086697", "doi"=>"10.1371/journal.pgen.1000057", "pui"=>"351656698", "pmid"=>"18421364", "scopus"=>"2-s2.0-43249086697", "issn"=>"15537390", "isbn"=>"1553-7404 (Electronic)\\n1553-7390 (Linking)"}, "id"=>"9e59586a-5f97-3269-9ce8-ab64014382ed", "abstract"=>"Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated approximately 1,290,000 years ago, western and other common chimpanzees approximately 510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5-7 million years ago when the ancestors of humans separated from those of the chimpanzees.", "link"=>"http://www.mendeley.com/research/analysis-chimpanzee-history-based-genome-sequence-alignments", "reader_count"=>139, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>25, "Researcher"=>32, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>31, "Student > Postgraduate"=>5, "Student > Master"=>15, "Other"=>2, "Student > Bachelor"=>9, "Professor"=>15}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>25, "Researcher"=>32, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>31, "Student > Postgraduate"=>5, "Student > Master"=>15, "Other"=>2, "Student > Bachelor"=>9, "Professor"=>15}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Agricultural and Biological Sciences"=>98, "Business, Management and Accounting"=>3, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>7, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>10, "Mathematics"=>1, "Medicine and Dentistry"=>6, "Physics and Astronomy"=>1, "Social Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Social Sciences"=>{"Social Sciences"=>4}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>5}, "Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>7}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>98}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Netherlands"=>2, "South Korea"=>1, "Belgium"=>1, "United States"=>7, "Denmark"=>2, "United Kingdom"=>1, "Mexico"=>1, "France"=>1, "Switzerland"=>3, "Germany"=>2, "Spain"=>1}, "group_count"=>7}

CrossRef

Scopus | Further Information

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  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"1", "html_views"=>"8"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"3", "xml_views"=>"2", "html_views"=>"10"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"18"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"21"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"17", "xml_views"=>"0", "html_views"=>"38"}
  • {"month"=>"2", "year"=>"2019", "pdf_views"=>"0", "xml_views"=>"0", "html_views"=>"16"}
  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"6", "xml_views"=>"3", "html_views"=>"28"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"10"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"7"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"10"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"15"}
  • {"month"=>"8", "year"=>"2019", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"12"}
  • {"month"=>"9", "year"=>"2019", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"17"}
  • {"month"=>"10", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"23"}
  • {"month"=>"11", "year"=>"2019", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"22"}
  • {"month"=>"12", "year"=>"2019", "pdf_views"=>"0", "xml_views"=>"0", "html_views"=>"1"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/933653"], "description"=>"<p>We targeted up to 5 kb centered on each of these regions for PCR-based resequencing, and only analyzed divergent sites that were independent of those found in the shotgun analysis (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057.s015\" target=\"_blank\">Text S9</a>). We found an excess of CH sites and BH sites in regions previously identified as clustering these pairs of species (∼22 times the genome average), as would be expected if these regions have the genealogies inferred in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen-1000057-t004\" target=\"_blank\">Table 4</a>. Chimpanzee-bonobo genetic divergence divided by human-orangutan genetic divergence is 38.4%, about three times the observed genome-wide rate of 12.2%, as expected if chimpanzees and bonobos share a common ancestor so long ago that it occurred prior to human-chimpanzee speciation. Both patterns attenuate with distance, as expected if the genealogies cover only a limited physical distance span.</p>", "links"=>[], "tags"=>["validate", "regions", "incomplete", "lineage", "carried", "laboratory-based", "follow-up", "11", "genealogy", "chimpanzees", "bonobos"], "article_id"=>604077, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.g005", "stats"=>{"downloads"=>3, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_To_validate_regions_of_incomplete_lineage_sorting_we_carried_out_laboratory_based_follow_up_of_11_regions_where_our_main_analysis_found_strong_evidence_in_favor_of_a_genealogy_where_chimpanzees_and_bonobos_are_not_most_closely_related_likelihood_ratio_of/604077", "title"=>"To validate regions of incomplete lineage sorting, we carried out laboratory-based follow-up of 11 regions where our main analysis found strong evidence in favor of a genealogy where chimpanzees and bonobos are not most closely related (likelihood ratio of >20,000:1).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-04-18 01:07:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/933883"], "description"=>"<p>Note: Estimates of six parameters of demographic history with 90% credible intervals from bootstrap analysis (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057.s010\" target=\"_blank\">Text S4</a>). Estimates of absolute ages (in years) and population sizes are all based on assuming that human-chimpanzee genetic divergence occurred 7 Mya, and assume 20 years per generation. For comparison, we also present estimates of the same parameters from two previous studies of chimpanzee history <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057-Won1\" target=\"_blank\">[11]</a>,<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057-Becquet2\" target=\"_blank\">[12]</a>. The fact that the previous studies jointly estimated migration rate along with the other parameters means that our credible intervals are not fully comparable with the previous studies, which had to estimate more complex models. The only credible intervals that are fully appropriate to compare are those for t<sub>ECWB</sub> and N<sub>ECWB</sub>, since we found that they are not substantially affected by assumptions about the central-western migration rate (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen-1000057-g002\" target=\"_blank\">Figure 2</a>).</p>*<p>To make our estimates comparable to the other studies, we multiplied all the ages and population size estimates from the Won and Hey analysis <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057-Won1\" target=\"_blank\">[11]</a> by 7/6 (since they used 6 rather than 7 Mya for human-chimpanzee genetic divergence), and further multiplied population sizes by 15/20 (since they assumed 15 not 20 years per generation). We did not rescale the estimates from the Becquet and Przeworski analysis <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057-Becquet2\" target=\"_blank\">[12]</a>, since they used the same estimate of 20 years per generation as we did, and assumed a mutation rate of μ = 1.0×10<sup>−9</sup> per base pair per year, which corresponds to a calibration date of 7 Mya for human-chimpanzee genetic divergence and 0.0128 differences between these two species per base pair.</p>", "links"=>[], "tags"=>["chimpanzee"], "article_id"=>604329, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.t002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_key_parameters_of_chimpanzee_history_/604329", "title"=>"Estimates of key parameters of chimpanzee history.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-04-18 01:12:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/933803"], "description"=>"<p>Notes: All data sets are restricted to the autosomes, and all estimates are given as a fraction of human-chimpanzee genetic divergence within the same alignment. For the 5-group alignments, we present in parentheses estimates correcting for recurrent mutation (calculated by EM analysis as described in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057.s009\" target=\"_blank\">Text S3</a>).</p>*<p>The CBHOM data set adds to the 9 data sets that are the focus of most of this study. It consists of an alignment of chimpanzee-bonobo-human-orangutan-macaque, using the specialized alignment procedure described in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057.s014\" target=\"_blank\">Text S8</a>. The estimate of chimpanzee-bonobo divergence is consistent with the other alignments.</p>", "links"=>[], "tags"=>["divergence", "pairs", "chimpanzee"], "article_id"=>604245, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_divergence_between_pairs_of_chimpanzee_populations_/604245", "title"=>"Genetic divergence between pairs of chimpanzee populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-04-18 01:10:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/933724"], "description"=>"<p>Note: Results of resequencing of 11 candidate regions of incomplete lineage sorting. We targeted up to 5 kb for resequencing in 4 chimpanzees, 3 bonobos, 3 humans, and 3 orangutans. Divergent sites were filtered to remove sites that overlapped with the ones used to discoverer the regions (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057.s015\" target=\"_blank\">Text S9</a>). The counts of the 7 possible classes of divergent sites can be non-integer due to within-species polymorphism.</p>*<p>We observe an excess of CH sites in regions where chimpanzees and humans cluster, and BH sites in regions where bonobos and humans cluster (6.6% vs. the genome-wide average of 0.3%). Chimpanzee-bonobo genetic divergence in these regions is also inflated: 38.4% on average versus the average of 12.2%.</p>†<p>Resequencing of region 1298 provided substantially less data than the other 10 regions. Nevertheless, the data showed a substantial excess of BH (n = 6) over CH (n = 2) sites at this locus, supporting the presence of incomplete lineage sorting.</p>", "links"=>[], "tags"=>["11", "regions", "chimp-bonobo-human", "incomplete", "lineage"], "article_id"=>604163, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.t005", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_of_11_candidate_regions_of_chimp_bonobo_human_incomplete_lineage_sorting_/604163", "title"=>"Validation of 11 candidate regions of chimp-bonobo-human incomplete lineage sorting.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-04-18 01:09:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/933771"], "description"=>"*<p>Each divergent site class is designated by a string of 0's and 1's, the bases seen in chimp/bonobo/human/orangutan/macaque. The macaque allele is defined as state “0”.</p>†<p>Under a model of incomplete lineage sorting, our EM analysis (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057.s009\" target=\"_blank\">Text S3</a>) obtains a good fit between observed and expected, with nominal χ<sup>2</sup> = 9, and a prediction that 27% of CH sites and 30% of BH sites are due to recurrent mutation. These results are concordant with our observation (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen-1000057-g004\" target=\"_blank\">Fig. 4</a>) that very close to CB sites, the rate of CH and BH sites is reduced to 26±6% of the average. If we only allow a model with genealogies clustering chimpanzees and bonobos, the best fit has a nominal χ<sup>2</sup> = 673.</p>‡<p>We examined all 18,985 alignments, looking for ones where genealogical trees clustering CH or BH are favored over those clustering CB (>20,000:1 likelihood ratio), and in which the counts fit the proposed genealogies well (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057.s014\" target=\"_blank\">Text S8</a>). Although these alignments should be treated with caution as they are extremes from a distribution, they are strong prospects for loci where chimpanzees and bonobos not being most closely related (alignment details are at genepath.med.harvard.edu/∼reich/Data%20Sets.htm).</p>", "links"=>[], "tags"=>["chimp-bonobo-human", "incomplete", "lineage"], "article_id"=>604212, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.t004", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evidence_for_chimp_bonobo_human_incomplete_lineage_sorting_/604212", "title"=>"Evidence for chimp-bonobo-human incomplete lineage sorting.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-04-18 01:10:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/933848"], "description"=>"<p>Demographic estimates that are unaffected by calibrations to the fossil record.</p>", "links"=>[], "tags"=>["estimates", "unaffected", "calibrations", "fossil"], "article_id"=>604290, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.t003", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Demographic_estimates_that_are_unaffected_by_calibrations_to_the_fossil_record_/604290", "title"=>"Demographic estimates that are unaffected by calibrations to the fossil record.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-04-18 01:11:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/933203"], "description"=>"<p>(A) Each five-group alignment has divergent site types that correspond to a branch in the tree: the lengths of branches are estimated from the observed numbers of the corresponding types of sites. The larger tree shows five possible types of sites (using the CWBH alignment as an example), and how they would be generated by single historical mutations. The smaller tree corresponds to one of the two rarer divergent site types that can arise when the genes from the two most closely related groups (central and western chimpanzee) share a common ancestor prior to the separation of the less closely related population (bonobo). (B) In the six-parameter model of chimpanzee evolution, the separation time of central chimpanzees and western chimpanzees is t<sub>ECW</sub>, the separation time of chimpanzees and bonobos is t<sub>ECWB</sub>, N<sub>C</sub> and N<sub>W</sub> specify the modern effective sizes of the central and western chimpanzee populations, and N<sub>ECW</sub> and N<sub>ECWB</sub> the effective sizes in the two earlier epochs. Although we do not include eastern chimpanzee in this analysis, the notations for t<sub>ECW</sub>, t<sub>ECWB</sub>, N<sub>ECW</sub>, and N<sub>ECWB</sub> refer to eastern chimpanzee because eastern form a clade with central chimpanzees.</p>", "links"=>[], "tags"=>["six-parameter"], "article_id"=>603645, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.g001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_of_our_six_parameter_model_for_analysis_of_the_history_of_bonobos_central_and_western_chimpanzees_/603645", "title"=>"Schematic of our six-parameter model for analysis of the history of bonobos, central, and western chimpanzees.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-04-18 01:00:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/933537"], "description"=>"<p>(A) The most common is on the left, but if there is incomplete lineage sorting, different tree topologies such as the two on the right can occur. These should be detectable from CH sites that cluster chimpanzee and human to the exclusion of the other species, or BH sites that cluster bonobo and human. (B) In the subset of the CBHOM data that is within 40 base pairs of a CH or BH site, we observe a ∼38-fold excess of sites of the same class, a deficiency in CB sites typical of the standard genealogy (∼25% of the average), and a ∼3.3-fold excess of sites that differ between chimpanzee and bonobo, exactly as would be expected if in these regions, chimpanzees and bonobos are not most closely related and only share a common ancestor prior to human-chimpanzee speciation. (C) By contrast, very near to CB sites typical of the standard genealogy, we observe few CH or BH sites (∼26% of the genome average). These results confirm that the majority (∼74%) of CH and BH sites are marking out genuine regions where the genealogy is different from the species relationships. All bars in this figure correspond to one standard error.</p>", "links"=>[], "tags"=>["trees", "relating", "macaque"], "article_id"=>603979, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genealogical_trees_relating_chimpanzee_bonobo_human_orangutan_and_macaque_CBHOM_vary_in_shape_across_the_genome_/603979", "title"=>"Genealogical trees relating chimpanzee, bonobo, human, orangutan, and macaque (CBHOM) vary in shape across the genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-04-18 01:06:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/459952", "https://ndownloader.figshare.com/files/459990", "https://ndownloader.figshare.com/files/460035", "https://ndownloader.figshare.com/files/460073", "https://ndownloader.figshare.com/files/460112", "https://ndownloader.figshare.com/files/460153", "https://ndownloader.figshare.com/files/460199", "https://ndownloader.figshare.com/files/460257", "https://ndownloader.figshare.com/files/460349", "https://ndownloader.figshare.com/files/460424", "https://ndownloader.figshare.com/files/460512", "https://ndownloader.figshare.com/files/460574", "https://ndownloader.figshare.com/files/460618", "https://ndownloader.figshare.com/files/460662", "https://ndownloader.figshare.com/files/460737", "https://ndownloader.figshare.com/files/460782"], "description"=>"<div><p>Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated ∼1,290,000 years ago, western and other common chimpanzees ∼510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5–7 million years ago when the ancestors of humans separated from those of the chimpanzees.</p></div>", "links"=>[], "tags"=>["chimpanzee", "based", "genome", "alignments"], "article_id"=>150620, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000057.s001", "https://dx.doi.org/10.1371/journal.pgen.1000057.s002", "https://dx.doi.org/10.1371/journal.pgen.1000057.s003", "https://dx.doi.org/10.1371/journal.pgen.1000057.s004", "https://dx.doi.org/10.1371/journal.pgen.1000057.s005", "https://dx.doi.org/10.1371/journal.pgen.1000057.s006", "https://dx.doi.org/10.1371/journal.pgen.1000057.s007", "https://dx.doi.org/10.1371/journal.pgen.1000057.s008", "https://dx.doi.org/10.1371/journal.pgen.1000057.s009", "https://dx.doi.org/10.1371/journal.pgen.1000057.s010", "https://dx.doi.org/10.1371/journal.pgen.1000057.s011", "https://dx.doi.org/10.1371/journal.pgen.1000057.s012", "https://dx.doi.org/10.1371/journal.pgen.1000057.s013", "https://dx.doi.org/10.1371/journal.pgen.1000057.s014", "https://dx.doi.org/10.1371/journal.pgen.1000057.s015", "https://dx.doi.org/10.1371/journal.pgen.1000057.s016"], "stats"=>{"downloads"=>39, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Analysis_of_Chimpanzee_History_Based_on_Genome_Sequence_Alignments/150620", "title"=>"Analysis of Chimpanzee History Based on Genome Sequence Alignments", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-04-18 00:10:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/933316"], "description"=>"<p>All plots consider the full range of migration rates for which we could obtain a reasonable fit to the data (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057.s013\" target=\"_blank\">Text S7</a>), with the values matching those in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen-1000057-t002\" target=\"_blank\">Tables 2</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen-1000057-t003\" target=\"_blank\">3</a> for the zero-migration rate scenarios. (A) In the presence of migration, central-western population separation time t<sub>ECW</sub> increases relative to the zero-migration scenario, but (B) the bonobo-common chimpanzee separation time estimate t<sub>ECWB</sub> is unchanged. (C,D) Migration rate has a variable effect on our estimates of western and central population size, depending on the direction of the migration, but (E) increasing migration rate always decreases our estimate of N<sub>ECW</sub>, and (F) our estimate of ancestral bonobo-chimpanzee population size is unaffected by migration rate assumptions. (G) For all migration rates consistent with the data, we infer that the western population size contracted relative to the ancestral size by at least 1.8-fold (panel f divided by e), and (H) that the ratio of central to western size has been >4.1 (d divided by e).</p>", "links"=>[], "tags"=>["chimpanzee", "ratios", "assumptions", "chimpanzees", "western-central"], "article_id"=>603755, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inferred_values_of_the_six_parameters_of_chimpanzee_demographic_history_and_key_ratios_of_population_sizes_for_various_assumptions_about_the_migration_rate_per_generation_between_western_and_central_chimpanzees_since_the_western_central_population_split_/603755", "title"=>"Inferred values of the six parameters of chimpanzee demographic history and key ratios of population sizes, for various assumptions about the migration rate per generation between western and central chimpanzees since the western-central population split.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-04-18 01:02:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/933459"], "description"=>"<p>We ran our computer simulation of chimpanzee history using the six demographic parameters that were the best fits to our data under the assumption of no western-central migration (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen-1000057-t002\" target=\"_blank\">Table 2</a>). We then varied the time t<sub>EC</sub> of eastern-central separation and the modern eastern population size N<sub>E</sub>, exploring the full range of parameters consistent with three statistics of interest that we measured using data from ref. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000057#pgen.1000057-Fischer2\" target=\"_blank\">[9]</a>: the F<sub>ST</sub> value between eastern and central chimpanzees, the ratio of eastern to central chimpanzee genetic diversity, and the average heterozygosity of SNPs discovered as polymorphic within ten eastern chimpanzees. We found an excellent fit to our data for the parameters N<sub>E</sub> = 30,078 and t<sub>EC</sub> = 13,672 generations (∼273,000 years assuming 20 years per generation). The values in the cells give -log<sub>10</sub> of the P-value for a χ<sup>2</sup> statistic with three degrees of freedom. We indicate the 95% credible interval (gray) as the region where this is within 0.86 of the maximum (a likelihood ratio test, which is only approximate since the three statistics that we use to assess the fit are not fully independent). This analysis implies that, with approximately 95% probability, eastern and central chimpanzees split at least 50,000 years ago.</p>", "links"=>[], "tags"=>["chimpanzee"], "article_id"=>603903, "categories"=>["Evolutionary Biology"], "users"=>["Jennifer L. Caswell", "Swapan Mallick", "Daniel J. Richter", "Julie Neubauer", "Christine Schirmer", "Sante Gnerre", "David Reich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000057.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inferences_about_parameters_of_eastern_chimpanzee_history_/603903", "title"=>"Inferences about parameters of eastern chimpanzee history.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-04-18 01:05:03"}

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  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
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  • {"unique-ip"=>"10", "full-text"=>"14", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"3"}
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  • {"unique-ip"=>"29", "full-text"=>"40", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"19", "full-text"=>"12", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"16", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"11", "full-text"=>"13", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
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  • {"unique-ip"=>"37", "full-text"=>"42", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
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  • {"unique-ip"=>"42", "full-text"=>"78", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
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  • {"unique-ip"=>"35", "full-text"=>"47", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"57", "full-text"=>"54", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2019", "month"=>"9"}
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Relative Metric

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