Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe
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{"title"=>"Mutation rate switch inside eurasian mitochondrial haplogroups: Impact of selection and consequences for dating settlement in europe", "type"=>"journal", "authors"=>[{"first_name"=>"Denis", "last_name"=>"Pierron", "scopus_author_id"=>"24067448500"}, {"first_name"=>"Ivan", "last_name"=>"Chang", "scopus_author_id"=>"43561050100"}, {"first_name"=>"Amal", "last_name"=>"Arachiche", "scopus_author_id"=>"25421156300"}, {"first_name"=>"Margit", "last_name"=>"Heiske", "scopus_author_id"=>"25721946300"}, {"first_name"=>"Olivier", "last_name"=>"Thomas", "scopus_author_id"=>"54584567800"}, {"first_name"=>"Marine", "last_name"=>"Borlin", "scopus_author_id"=>"54583145600"}, {"first_name"=>"Erwan", "last_name"=>"Pennarun", "scopus_author_id"=>"8790154200"}, {"first_name"=>"Pacal", "last_name"=>"Murail", "scopus_author_id"=>"6603224146"}, {"first_name"=>"Didier", "last_name"=>"Thoraval", "scopus_author_id"=>"6602520974"}, {"first_name"=>"Christophe", "last_name"=>"Rocher", "scopus_author_id"=>"6603960770"}, {"first_name"=>"Thierry", "last_name"=>"Letellier", "scopus_author_id"=>"6603672495"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0021543", "issn"=>"19326203", "sgr"=>"79959575355", "scopus"=>"2-s2.0-79959575355", "pui"=>"362022061", "pmid"=>"21738700", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"3f6d4ef8-5804-3c2a-8931-d6b12cf1650e", "abstract"=>"R-lineage mitochondrial DNA represents over 90% of the European population and is significantly present all around the planet (North Africa, Asia, Oceania, and America). This lineage played a major role in migration \"out of Africa\" and colonization in Europe. In order to determine an accurate dating of the R lineage and its sublineages, we analyzed 1173 individuals and complete mtDNA sequences from Mitomap. This analysis revealed a new coalescence age for R at 54.500 years, as well as several limitations of standard dating methods, likely to lead to false interpretations. These findings highlight the association of a striking under-accumulation of synonymous mutations, an over-accumulation of non-synonymous mutations, and the phenotypic effect on haplogroup J. Consequently, haplogroup J is apparently not a Neolithic group but an older haplogroup (Paleolithic) that was subjected to an underestimated selective force. These findings also indicated an under-accumulation of synonymous and non-synonymous mutations localized on coding and non-coding (HVS1) sequences for haplogroup R0, which contains the major haplogroups H and V. These new dates are likely to impact the present colonization model for Europe and confirm the late glacial resettlement scenario.", "link"=>"http://www.mendeley.com/research/mutation-rate-switch-inside-eurasian-mitochondrial-haplogroups-impact-selection-consequences-dating", "reader_count"=>28, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Materials Science"=>1, "Agricultural and Biological Sciences"=>21, "Arts and Humanities"=>1, "Social Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>21}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>1, "France"=>1, "Germany"=>1}, "group_count"=>0}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/761421"], "description"=>"<p>Individuals belonging to U, T, R2 and Other were included in a single category: “GLOBAL”. The data are based on the dataset published by Richard <i>et al.</i> and the phylogenetic distance was calculated by determining the number of synonymous mutations separating haplotypes belonging to haplogroup R from MRCA-R (based on Mitomap data).</p>", "links"=>[], "tags"=>["accumulated", "mutations", "hvs1", "haplotypes"], "article_id"=>431779, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.g006", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_accumulated_mutations_on_HVS1_between_present_haplotypes_R0_J_and_Global_and_the_most_recent_common_ancestor_of_the_R_haplogroup_/431779", "title"=>"Distribution of accumulated mutations on HVS1 between present haplotypes (R0, J, and Global) and the most recent common ancestor of the R haplogroup.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-28 00:29:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/760872"], "description"=>"<p>The phylogenetic distance was calculated by determining the number of synonymous mutation separating 1173 haplotypes belonging to haplogroup R from MRCA-R (based on Mitomap data).</p>", "links"=>[], "tags"=>["haplotypes"], "article_id"=>431239, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_distance_distribution_between_present_haplotypes_and_the_most_recent_common_ancestor_of_the_R_haplogroup_/431239", "title"=>"Phylogenetic distance distribution between present haplotypes and the most recent common ancestor of the R haplogroup.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-28 00:20:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/761511"], "description"=>"<p>The data are based on the Mitomap dataset and the phylogenetic distance was calculated by determining the number of synonymous mutations separating haplotypes belonging to haplogroups N and M from MRCA-L3 (based on Mitomap data).</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>431879, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.g007", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_distance_distribution_of_R0_N_and_M_haplotypes_/431879", "title"=>"Phylogenetic distance distribution of R0, N, and M haplotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-28 00:31:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/761335"], "description"=>"<p>Mutation events are in red, the green star is the MRCA lineage. Present haplotypes are shown as triangles. The green triangle is the Living Fossil Sequence with no mutation event on this lineage since MRCA. Db is the phylogenic distance between the AS and MRCA of the superlineage. Da is the phylogenic distance between AS and the present related haplotype. Phylogenetic distance is the average number of synonymous mutations accumulated between individuals.</p>", "links"=>[], "tags"=>["phylogenic", "ancestral"], "article_id"=>431701, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.g005", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hypothetical_phylogenic_tree_with_an_Ancestral_Sequence_still_present_in_the_population_/431701", "title"=>"Hypothetical phylogenic tree with an Ancestral Sequence still present in the population.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-28 00:28:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/761667"], "description"=>"<p>Phylogenetic distance between present haplotypes and MRCA-R.</p>", "links"=>[], "tags"=>["haplotypes"], "article_id"=>432038, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.t001", "stats"=>{"downloads"=>3, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_distance_between_present_haplotypes_and_MRCA_R_/432038", "title"=>"Phylogenetic distance between present haplotypes and MRCA-R.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-28 00:33:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/382924", "https://ndownloader.figshare.com/files/382952", "https://ndownloader.figshare.com/files/382979", "https://ndownloader.figshare.com/files/382985", "https://ndownloader.figshare.com/files/383019"], "description"=>"<div><p>R-lineage mitochondrial DNA represents over 90% of the European population and is significantly present all around the planet (North Africa, Asia, Oceania, and America). This lineage played a major role in migration “out of Africa” and colonization in Europe. In order to determine an accurate dating of the R lineage and its sublineages, we analyzed 1173 individuals and complete mtDNA sequences from Mitomap. This analysis revealed a new coalescence age for R at 54.500 years, as well as several limitations of standard dating methods, likely to lead to false interpretations. These findings highlight the association of a striking under-accumulation of synonymous mutations, an over-accumulation of non-synonymous mutations, and the phenotypic effect on haplogroup J. Consequently, haplogroup J is apparently not a Neolithic group but an older haplogroup (Paleolithic) that was subjected to an underestimated selective force. These findings also indicated an under-accumulation of synonymous and non-synonymous mutations localized on coding and non-coding (HVS1) sequences for haplogroup R0, which contains the major haplogroups H and V. These new dates are likely to impact the present colonization model for Europe and confirm the late glacial resettlement scenario.</p> </div>", "links"=>[], "tags"=>["mutation", "eurasian", "mitochondrial", "consequences", "dating", "europe"], "article_id"=>135623, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021543.s001", "https://dx.doi.org/10.1371/journal.pone.0021543.s002", "https://dx.doi.org/10.1371/journal.pone.0021543.s003", "https://dx.doi.org/10.1371/journal.pone.0021543.s004", "https://dx.doi.org/10.1371/journal.pone.0021543.s005"], "stats"=>{"downloads"=>13, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Mutation_Rate_Switch_inside_Eurasian_Mitochondrial_Haplogroups_Impact_of_Selection_and_Consequences_for_Dating_Settlement_in_Europe/135623", "title"=>"Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-06-28 01:33:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/761590"], "description"=>"<p>Estimated date of the MRCA of the R lineage and sublineages.</p>", "links"=>[], "tags"=>["mrca", "lineage"], "article_id"=>431953, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.t005", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimated_date_of_the_MRCA_of_the_R_lineage_and_sublineages_/431953", "title"=>"Estimated date of the MRCA of the R lineage and sublineages.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-28 00:32:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/761206"], "description"=>"<p>Individuals belonging to U, T, R2 and Other were included in a single category: “GLOBAL”. The data are based on the Mitomap dataset and the phylogenetic distance was calculated by determining the number of synonymous mutations separating haplotypes belonging to haplogroup R from MRCA-R (based on Mitomap data).</p>", "links"=>[], "tags"=>["haplotypes"], "article_id"=>431576, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_distance_distribution_between_R0_J_and_Global_haplotypes_and_the_most_recent_common_ancestor_of_the_R_haplogroup_/431576", "title"=>"Phylogenetic distance distribution between R0, J, and Global haplotypes and the most recent common ancestor of the R haplogroup.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-28 00:26:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/760988"], "description"=>"<p>The data are based on the Mitomap dataset and the phylogenetic distance was calculated by determining the number of synonymous mutations separating haplotypes belonging to haplogroup R from MRCA-R (based on Mitomap data).</p>", "links"=>[], "tags"=>["haplotypes", "monophyletic", "lineages"], "article_id"=>431355, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_distance_distribution_of_present_haplotypes_in_the_4_major_monophyletic_lineages_R0_R2JT_U_and_B_and_the_OTHER_category_/431355", "title"=>"Phylogenetic distance distribution of present haplotypes in the 4 major monophyletic lineages (R0, R2JT, U, and B) and the OTHER category.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-28 00:22:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/761758"], "description"=>"<p>Average posterior probability distribution of distance to the root for GLOBAL, R0 and J individuals, set by set.</p>", "links"=>[], "tags"=>["posterior", "probability", "r0"], "article_id"=>432124, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_posterior_probability_distribution_of_distance_to_the_root_for_GLOBAL_R0_and_J_individuals_set_by_set_/432124", "title"=>"Average posterior probability distribution of distance to the root for GLOBAL, R0 and J individuals, set by set.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-28 00:35:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/761103"], "description"=>"<p>The data and tree topology are based on the PhyloTree dataset and branch lengths reflect the differential accumulation of mutations along different lineages.</p>", "links"=>[], "tags"=>["phylogeny"], "article_id"=>431469, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.g003", "stats"=>{"downloads"=>5, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_phylogeny_of_the_R_haplogroup_/431469", "title"=>"Schematic phylogeny of the R haplogroup.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-28 00:24:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/761629"], "description"=>"<p>Oldest Ancestral Sequences (AS) still present in each haplogroup.</p>", "links"=>[], "tags"=>["ancestral", "sequences"], "article_id"=>431992, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Denis Pierron", "Ivan Chang", "Amal Arachiche", "Margit Heiske", "Olivier Thomas", "Marine Borlin", "Erwan Pennarun", "Pacal Murail", "Didier Thoraval", "Christophe Rocher", "Thierry Letellier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021543.t004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Oldest_Ancestral_Sequences_AS_still_present_in_each_haplogroup_/431992", "title"=>"Oldest Ancestral Sequences (AS) still present in each haplogroup.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-28 00:33:12"}

PMC Usage Stats | Further Information

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