The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques
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{"title"=>"The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques", "type"=>"journal", "authors"=>[{"first_name"=>"Sergio", "last_name"=>"Cardoso", "scopus_author_id"=>"7102228014"}, {"first_name"=>"Laura", "last_name"=>"Valverde", "scopus_author_id"=>"24729671000"}, {"first_name"=>"Miguel A.", "last_name"=>"Alfonso-Sánchez", "scopus_author_id"=>"6601976010"}, {"first_name"=>"Leire", "last_name"=>"Palencia-Madrid", "scopus_author_id"=>"35725994700"}, {"first_name"=>"Xabier", "last_name"=>"Elcoroaristizabal", "scopus_author_id"=>"35745928800"}, {"first_name"=>"Jaime", "last_name"=>"Algorta", "scopus_author_id"=>"24330801400"}, {"first_name"=>"Susana", "last_name"=>"Catarino", "scopus_author_id"=>"55315055600"}, {"first_name"=>"David", "last_name"=>"Arteta", "scopus_author_id"=>"16023763700"}, {"first_name"=>"Rene J.", "last_name"=>"Herrera", "scopus_author_id"=>"7103233331"}, {"first_name"=>"María Teresa", "last_name"=>"Zarrabeitia", "scopus_author_id"=>"7004208162"}, {"first_name"=>"José A.", "last_name"=>"Peña", "scopus_author_id"=>"7402535346"}, {"first_name"=>"Marian M.", "last_name"=>"de Pancorbo", "scopus_author_id"=>"6701536373"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23844106", "doi"=>"10.1371/journal.pone.0067835", "sgr"=>"84879752699", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84879752699", "issn"=>"19326203", "pui"=>"369253433"}, "id"=>"f49981fd-2ce2-3482-aa01-406e9ba4d60e", "abstract"=>"The European genetic landscape has been shaped by several human migrations occurred since Paleolithic times. The accumulation of archaeological records and the concordance of different lines of genetic evidence during the last two decades have triggered an interesting debate concerning the role of ancient settlers from the Franco-Cantabrian region in the postglacial resettlement of Europe. Among the Franco-Cantabrian populations, Basques are regarded as one of the oldest and more intriguing human groups of Europe. Recent data on complete mitochondrial DNA genomes focused on macrohaplogroup R0 revealed that Basques harbor some autochthonous lineages, suggesting a genetic continuity since pre-Neolithic times. However, excluding haplogroup H, the most representative lineage of macrohaplogroup R0, the majority of maternal lineages of this area remains virtually unexplored, so that further refinement of the mtDNA phylogeny based on analyses at the highest level of resolution is crucial for a better understanding of the European prehistory. We thus explored the maternal ancestry of 548 autochthonous individuals from various Franco-Cantabrian populations and sequenced 76 mitogenomes of the most representative lineages. Interestingly, we identified three mtDNA haplogroups, U5b1f, J1c5c1 and V22, that proved to be representative of Franco-Cantabria, notably of the Basque population. The seclusion and diversity of these female genetic lineages support a local origin in the Franco-Cantabrian area during the Mesolithic of southwestern Europe, ~10,000 years before present (YBP), with signals of expansions at ~3,500 YBP. These findings provide robust evidence of a partial genetic continuity between contemporary autochthonous populations from the Franco-Cantabrian region, specifically the Basques, and Paleolithic/Mesolithic hunter-gatherer groups. Furthermore, our results raise the current proportion (≈ 15%) of the Franco-Cantabrian maternal gene pool with a putative pre-Neolithic origin to ≈ 35%, further supporting the notion of a predominant Paleolithic genetic substrate in extant European populations.", "link"=>"http://www.mendeley.com/research/expanded-mtdna-phylogeny-francocantabrian-region-upholds-preneolithic-genetic-substrate-basques", "reader_count"=>47, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>11, "Other"=>2, "Student > Master"=>8, "Student > Bachelor"=>4, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1109464", "https://ndownloader.figshare.com/files/1109465", "https://ndownloader.figshare.com/files/1109466", "https://ndownloader.figshare.com/files/1109467"], "description"=>"<div><p>The European genetic landscape has been shaped by several human migrations occurred since Paleolithic times. The accumulation of archaeological records and the concordance of different lines of genetic evidence during the last two decades have triggered an interesting debate concerning the role of ancient settlers from the Franco-Cantabrian region in the postglacial resettlement of Europe. Among the Franco-Cantabrian populations, Basques are regarded as one of the oldest and more intriguing human groups of Europe. Recent data on complete mitochondrial DNA genomes focused on macrohaplogroup R0 revealed that Basques harbor some autochthonous lineages, suggesting a genetic continuity since pre-Neolithic times. However, excluding haplogroup H, the most representative lineage of macrohaplogroup R0, the majority of maternal lineages of this area remains virtually unexplored, so that further refinement of the mtDNA phylogeny based on analyses at the highest level of resolution is crucial for a better understanding of the European prehistory. We thus explored the maternal ancestry of 548 autochthonous individuals from various Franco-Cantabrian populations and sequenced 76 mitogenomes of the most representative lineages. Interestingly, we identified three mtDNA haplogroups, U5b1f, J1c5c1 and V22, that proved to be representative of Franco-Cantabria, notably of the Basque population. The seclusion and diversity of these female genetic lineages support a local origin in the Franco-Cantabrian area during the Mesolithic of southwestern Europe, ∼10,000 years before present (YBP), with signals of expansions at ∼3,500 YBP. These findings provide robust evidence of a partial genetic continuity between contemporary autochthonous populations from the Franco-Cantabrian region, specifically the Basques, and Paleolithic/Mesolithic hunter-gatherer groups. Furthermore, our results raise the current proportion (≈15%) of the Franco-Cantabrian maternal gene pool with a putative pre-Neolithic origin to ≈35%, further supporting the notion of a predominant Paleolithic genetic substrate in extant European populations.</p></div>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary systematics", "phylogenetics", "population genetics", "Gene flow", "Genetic polymorphism", "haplotypes", "Evolutionary genetics", "Population biology", "expanded", "mtdna", "phylogeny", "franco-cantabrian", "upholds", "pre-neolithic", "substrate"], "article_id"=>738088, "categories"=>["Biological Sciences"], "users"=>["Sergio Cardoso", "Laura Valverde", "Miguel A. Alfonso-Sánchez", "Leire Palencia-Madrid", "Xabier Elcoroaristizabal", "Jaime Algorta", "Susana Catarino", "David Arteta", "Rene J. Herrera", "Maria Teresa Zarrabeitia", "José A. Peña", "Marian M. de Pancorbo"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067835.s001", "https://dx.doi.org/10.1371/journal.pone.0067835.s002", "https://dx.doi.org/10.1371/journal.pone.0067835.s003", "https://dx.doi.org/10.1371/journal.pone.0067835.s004"], "stats"=>{"downloads"=>17, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Expanded_mtDNA_Phylogeny_of_the_Franco_Cantabrian_Region_Upholds_the_Pre_Neolithic_Genetic_Substrate_of_Basques_/738088", "title"=>"The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-07-03 01:35:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/1109460"], "description"=>"<p>N: number of complete mtDNA sequences used for the age estimates. Calculations were performed based on the mitogenomes from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone-0067835-g001\" target=\"_blank\">Fig. 1</a> rho: average distance to the most recent common ancestor <sup>56</sup> sigma: standard error <sup>57</sup>.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary systematics", "phylogenetics", "population genetics", "Gene flow", "Genetic polymorphism", "haplotypes", "Evolutionary genetics", "Population biology", "estimates", "franco-cantabrian", "autochthonous", "haplogroups", "rho"], "article_id"=>738083, "categories"=>["Biological Sciences"], "users"=>["Sergio Cardoso", "Laura Valverde", "Miguel A. Alfonso-Sánchez", "Leire Palencia-Madrid", "Xabier Elcoroaristizabal", "Jaime Algorta", "Susana Catarino", "David Arteta", "Rene J. Herrera", "Maria Teresa Zarrabeitia", "José A. Peña", "Marian M. de Pancorbo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067835.t001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Age_estimates_for_three_Franco_Cantabrian_autochthonous_haplogroups_by_using_rho_r_statistics_/738083", "title"=>"Age estimates for three Franco-Cantabrian autochthonous haplogroups by using rho (r) statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-03 01:35:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/1109457"], "description"=>"<p>These trees are extracted from the maximum parsimony phylogenetic tree of 76 complete mtDNA sequences of the Franco-Cantabrian region shown in detail in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone.0067835.s001\" target=\"_blank\">Fig. S1</a>. Mutations are displayed along the branches. All mutations are transitions unless a suffix specifies a transversion (A, C, G, T). Recurrent mutations within the complete phylogeny of the Franco-Cantabrian area are underlined. The prefix ‘‘@’’ indicates a back mutation. Mutational hotspot variants such as 16182, 16183, or 16519, or a variation around position 310 or 523–524, as well as length heteroplasmies were not considered for the phylogenetic reconstruction. All the samples are colored according to their geographic origin, as shown in the legend. For phylogeny construction, five previously published mitogenomes belonging to subhaplogroups U5b1f (JX286537 and DQ156208), J1c5c1 (JQ702776 and JQ704051) and V22 (HQ384212) were included (GenBank accession numbers in the tree). German ethnicity was declared for sample JX286537 in GenBank; however, maternal ancestry in southwestern Europe cannot be ruled out owing to the absence of lineage U51bf in populations outside the Franco Cantabrian area (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone.0067835.s003\" target=\"_blank\">Tables S2</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone.0067835.s004\" target=\"_blank\">S3</a>). French B.C. refers to samples from the French Basque Country.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary systematics", "phylogenetics", "population genetics", "Gene flow", "Genetic polymorphism", "haplotypes", "Evolutionary genetics", "Population biology", "parsimony", "trees", "haplogroups", "j1c", "autochthonous", "lineages", "j1c5c1"], "article_id"=>738081, "categories"=>["Biological Sciences"], "users"=>["Sergio Cardoso", "Laura Valverde", "Miguel A. Alfonso-Sánchez", "Leire Palencia-Madrid", "Xabier Elcoroaristizabal", "Jaime Algorta", "Susana Catarino", "David Arteta", "Rene J. Herrera", "Maria Teresa Zarrabeitia", "José A. Peña", "Marian M. de Pancorbo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067835.g001", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_parsimony_trees_of_haplogroups_U5b_J1c_and_V_including_the_three_autochthonous_lineages_U5b1f_J1c5c1_and_V22_/738081", "title"=>"Maximum parsimony trees of haplogroups U5b, J1c and V including the three autochthonous lineages U5b1f, J1c5c1 and V22.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-03 01:35:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/1109458"], "description"=>"<p>A) Geographic locations of populations surveyed for haplogroup U5b1f (1. Guipuzcoa, 2. South-West Guipuzcoa, 3. Biscay, 4. West Biscay, 5. Alava, 6. South Alava, 7. Northern Navarre, 8. Central-West Navarre, 9. North-East Navarre, 10. North-West Navarre, 11. Lower Navarre, 12. Labourdin, 13. Soule, 14. Bearn, 15. Bigorre, 16. Chalosse, 17. La Rioja, 18. Burgos, 19. Pas Valley, 20. Cantabria, 21. Aragon, 22. Zaragoza, 23. North-East Spain, 24. Madrid and 25. Périgord-Limousin). Frequency values are shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone.0067835.s004\" target=\"_blank\">Table S3</a>. B) Grayscale represents spatial variation in haplogroup frequency, with a peak between northeastern Navarre and Iparralde (French Basque Country), and a gradual decreasing trend towards the borders of the distribution. In evolutionary terms, differences in grayscale within the same geographic territory (e.g. Basque area) imply local genetic differentiation.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary systematics", "phylogenetics", "population genetics", "Gene flow", "Genetic polymorphism", "haplotypes", "Evolutionary genetics", "Population biology", "haplogroup", "u5b1f", "franco-cantabrian"], "article_id"=>738082, "categories"=>["Biological Sciences"], "users"=>["Sergio Cardoso", "Laura Valverde", "Miguel A. Alfonso-Sánchez", "Leire Palencia-Madrid", "Xabier Elcoroaristizabal", "Jaime Algorta", "Susana Catarino", "David Arteta", "Rene J. Herrera", "Maria Teresa Zarrabeitia", "José A. Peña", "Marian M. de Pancorbo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067835.g002", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_map_of_haplogroup_U5b1f_within_the_Franco_Cantabrian_region_/738082", "title"=>"Distribution map of haplogroup U5b1f within the Franco-Cantabrian region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-03 01:35:22"}

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Relative Metric

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