A Three-Stage Colonization Model for the Peopling of the Americas
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{"title"=>"A three-stage colonization model for the peopling of the Americas", "type"=>"journal", "authors"=>[{"first_name"=>"Andrew", "last_name"=>"Kitchen", "scopus_author_id"=>"23489084200"}, {"first_name"=>"Michael M.", "last_name"=>"Miyamoto", "scopus_author_id"=>"7402577551"}, {"first_name"=>"Connie J.", "last_name"=>"Mulligan", "scopus_author_id"=>"8077054400"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"18270583", "doi"=>"10.1371/journal.pone.0001596", "sgr"=>"45449118538", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-45449118538", "issn"=>"19326203", "pui"=>"351850573"}, "id"=>"90bedd6a-774e-3faf-8165-93837ce75561", "abstract"=>"BACKGROUND: We evaluate the process by which the Americas were originally colonized and propose a three-stage model that integrates current genetic, archaeological, geological, and paleoecological data. Specifically, we analyze mitochondrial and nuclear genetic data by using complementary coalescent models of demographic history and incorporating non-genetic data to enhance the anthropological relevance of the analysis.\\n\\nMETHODOLOGY/FINDINGS: Bayesian skyline plots, which provide dynamic representations of population size changes over time, indicate that Amerinds went through two stages of growth approximately 40,000 and approximately 15,000 years ago separated by a long period of population stability. Isolation-with-migration coalescent analyses, which utilize data from sister populations to estimate a divergence date and founder population sizes, suggest an Amerind population expansion starting approximately 15,000 years ago.\\n\\nCONCLUSIONS/SIGNIFICANCE: These results support a model for the peopling of the New World in which Amerind ancestors diverged from the Asian gene pool prior to 40,000 years ago and experienced a gradual population expansion as they moved into Beringia. After a long period of little change in population size in greater Beringia, Amerinds rapidly expanded into the Americas approximately 15,000 years ago either through an interior ice-free corridor or along the coast. This rapid colonization of the New World was achieved by a founder group with an effective population size of approximately 1,000-5,400 individuals. Our model presents a detailed scenario for the timing and scale of the initial migration to the Americas, substantially refines the estimate of New World founders, and provides a unified theory for testing with future datasets and analytic methods.", "link"=>"http://www.mendeley.com/research/threestage-colonization-model-peopling-americas", "reader_count"=>231, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>14, "Researcher"=>51, "Student > Doctoral Student"=>16, "Student > Ph. D. Student"=>61, "Student > Postgraduate"=>8, "Student > Master"=>21, "Other"=>13, "Student > Bachelor"=>20, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>3, "Professor"=>18}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>14, "Researcher"=>51, "Student > Doctoral Student"=>16, "Student > Ph. D. Student"=>61, "Student > Postgraduate"=>8, "Student > Master"=>21, "Other"=>13, "Student > Bachelor"=>20, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>3, "Professor"=>18}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Agricultural and Biological Sciences"=>111, "Arts and Humanities"=>20, "Philosophy"=>1, "Business, Management and Accounting"=>3, "Chemistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>13, "Economics, Econometrics and Finance"=>1, "Engineering"=>1, "Environmental Science"=>8, "Biochemistry, Genetics and Molecular Biology"=>9, "Materials Science"=>1, "Medicine and Dentistry"=>6, "Physics and Astronomy"=>1, "Psychology"=>1, "Social Sciences"=>41, "Immunology and Microbiology"=>1, "Linguistics"=>4}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Social Sciences"=>{"Social Sciences"=>41}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>8}, "Arts and Humanities"=>{"Arts and Humanities"=>20}, "Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>13}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>111}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>3}, "Linguistics"=>{"Linguistics"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Ecuador"=>1, "Colombia"=>2, "United States"=>20, "Uruguay"=>1, "Japan"=>1, "United Kingdom"=>1, "Malaysia"=>1, "Switzerland"=>2, "Spain"=>1, "New Zealand"=>1, "Canada"=>2, "Sweden"=>1, "Brazil"=>5, "Denmark"=>1, "Mexico"=>2, "Chile"=>3, "Australia"=>1, "Germany"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/937422"], "description"=>"<p>This plot follows the conventions of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001596#pone-0001596-g001\" target=\"_blank\">Figure 1</a>. Its estimates of coalescent time and N<sub>ef</sub> at the coalescence and today are in agreement with the coding mtDNA skyline plot (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001596#pone-0001596-g001\" target=\"_blank\">Figure 1</a>). In contrast, this HVRI+II plot provides little resolution for other population size changes, most likely because of mutational saturation in the non-coding control region (see text).</p>", "links"=>[], "tags"=>["skyline", "mtdna", "hvr"], "article_id"=>607872, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Andrew Kitchen", "Michael M. Miyamoto", "Connie J. Mulligan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001596.g002", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayesian_skyline_plot_for_the_mtDNA_HVR_I_II_datasets_/607872", "title"=>"Bayesian skyline plot for the mtDNA HVR I+II datasets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-02-13 02:11:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/937356"], "description"=>"<p>The curve plots median N<sub>ef</sub> with its 95% CI indicated by the light gray lines. The calculated N<sub>ef</sub> assumes a generation time of 20 years following Hey <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001596#pone.0001596-Hey1\" target=\"_blank\">[16]</a>; alternatively, using a generation time of 25 years <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001596#pone.0001596-Fenner1\" target=\"_blank\">[55]</a> would uniformly decrease all estimates of N<sub>ef</sub> by 20%. “X” marks the median coalescent time with its 95% CI given in brackets. The shaded regions highlight two periods of substantial population growth. This skyline plot provides the principal evidence for our three-stage model of New World colonization, i.e. the three stages that are depicted and labeled here.</p>", "links"=>[], "tags"=>["skyline", "mtdna", "coding", "genome"], "article_id"=>607798, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Andrew Kitchen", "Michael M. Miyamoto", "Connie J. Mulligan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001596.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayesian_skyline_plot_for_the_mtDNA_coding_genome_sequences_/607798", "title"=>"Bayesian skyline plot for the mtDNA coding genome sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-02-13 02:09:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/937545"], "description"=>"<p>(A) Divergence, then gradual population expansion of the Amerind ancestors from their East Central Asian gene pool (blue arrow). (B) Proto-Amerind occupation of Beringia with little to no population growth for ≈20,000 years. (C) Rapid colonization of the New World by a founder group migrating southward through the ice free, inland corridor between the eastern Laurentide and western Cordilleran Ice Sheets (green arrow) and/or along the Pacific coast (red arrow). In (B), the exposed seafloor is shown at its greatest extent during the last glacial maximum at ≈20–18 kya <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001596#pone.0001596-Hopkins1\" target=\"_blank\">[25]</a>. In (A) and (C), the exposed seafloor is depicted at ≈40 kya and ≈16 kya, when prehistoric sea levels were comparable <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001596#pone.0001596-Elias1\" target=\"_blank\">[24]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001596#pone.0001596-Hopkins1\" target=\"_blank\">[25]</a>. Because of the earth's curvature, the km scale (which is based on the straight line distance at the equator) provides only an approximation of the same distance between two points on these maps. In addition, a scaled-down version of Beringia today (60% reduction of A–C) is presented in the lower left corner. This smaller map highlights the Bering Strait that has geographically separated the New World from Asia since ≈11–10 kya.</p>", "links"=>[], "tags"=>["depicting", "three-step", "colonization", "peopling"], "article_id"=>607991, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Andrew Kitchen", "Michael M. Miyamoto", "Connie J. Mulligan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001596.g004", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maps_depicting_each_phase_of_our_three_step_colonization_model_for_the_peopling_of_the_Americas_/607991", "title"=>"Maps depicting each phase of our three-step colonization model for the peopling of the Americas.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-02-13 02:13:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/937483"], "description"=>"<p>The plot depicts mean N<sub>e</sub> for the Amerind founder population (y-axis) as a product of increasing the constraint on the upper bound of the priors for the migration rates (x-axis). In these analyses, the prior on the lower bound of the divergence time was uniformly set to 15 kya on the basis of known archaeological materials for human occupation in the New World (see text). Each point is based on the average of the estimated medians for ten independent replicate analyses, with the bars corresponding to ± 1 standard deviation. These standard deviations are often small (with coefficients of variation less than 0.01), since their Markov chains were run for 100 million generations each.</p>", "links"=>[], "tags"=>["im", "mitochondrial", "coding", "dna"], "article_id"=>607934, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Andrew Kitchen", "Michael M. Miyamoto", "Connie J. Mulligan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001596.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graph_of_IM_results_for_the_combined_nuclear_and_mitochondrial_coding_DNA_dataset_/607934", "title"=>"Graph of IM results for the combined nuclear and mitochondrial coding DNA dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-02-13 02:12:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/462015", "https://ndownloader.figshare.com/files/462032"], "description"=>"<div><h3>Background</h3><p>We evaluate the process by which the Americas were originally colonized and propose a three-stage model that integrates current genetic, archaeological, geological, and paleoecological data. Specifically, we analyze mitochondrial and nuclear genetic data by using complementary coalescent models of demographic history and incorporating non-genetic data to enhance the anthropological relevance of the analysis.</p><h3>Methodology/Findings</h3><p>Bayesian skyline plots, which provide dynamic representations of population size changes over time, indicate that Amerinds went through two stages of growth ≈40,000 and ≈15,000 years ago separated by a long period of population stability. Isolation-with-migration coalescent analyses, which utilize data from sister populations to estimate a divergence date and founder population sizes, suggest an Amerind population expansion starting ≈15,000 years ago.</p><h3>Conclusions/Significance</h3><p>These results support a model for the peopling of the New World in which Amerind ancestors diverged from the Asian gene pool prior to 40,000 years ago and experienced a gradual population expansion as they moved into Beringia. After a long period of little change in population size in greater Beringia, Amerinds rapidly expanded into the Americas ≈15,000 years ago either through an interior ice-free corridor or along the coast. This rapid colonization of the New World was achieved by a founder group with an effective population size of ≈1,000–5,400 individuals. Our model presents a detailed scenario for the timing and scale of the initial migration to the Americas, substantially refines the estimate of New World founders, and provides a unified theory for testing with future datasets and analytic methods.</p></div>", "links"=>[], "tags"=>["three-stage", "colonization", "peopling", "americas"], "article_id"=>151055, "categories"=>["Evolutionary Biology", "Cancer"], "users"=>["Andrew Kitchen", "Michael M. Miyamoto", "Connie J. Mulligan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0001596.s001", "https://dx.doi.org/10.1371/journal.pone.0001596.s002"], "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Three_Stage_Colonization_Model_for_the_Peopling_of_the_Americas/151055", "title"=>"A Three-Stage Colonization Model for the Peopling of the Americas", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-02-13 00:17:35"}

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  • {"unique-ip"=>"96", "full-text"=>"112", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"70", "full-text"=>"82", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"94", "full-text"=>"110", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"115", "full-text"=>"130", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"113", "full-text"=>"132", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"114", "full-text"=>"135", "pdf"=>"11", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
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Relative Metric

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