Beyond Reasonable Doubt: Evolution from DNA Sequences
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{"title"=>"Beyond Reasonable Doubt: Evolution from DNA Sequences", "type"=>"journal", "authors"=>[{"first_name"=>"W. Timothy J.", "last_name"=>"White", "scopus_author_id"=>"22954832300"}, {"first_name"=>"Bojian", "last_name"=>"Zhong", "scopus_author_id"=>"26535367700"}, {"first_name"=>"David", "last_name"=>"Penny", "scopus_author_id"=>"35230726200"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23950906", "doi"=>"10.1371/journal.pone.0069924", "sgr"=>"84881332753", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84881332753", "issn"=>"19326203", "pui"=>"369535467"}, "id"=>"22c505d1-413c-355f-be52-dd092569aece", "abstract"=>"We demonstrate quantitatively that, as predicted by evolutionary theory, sequences of homologous proteins from different species converge as we go further and further back in time. The converse, a non-evolutionary model can be expressed as probabilities, and the test works for chloroplast, nuclear and mitochondrial sequences, as well as for sequences that diverged at different time depths. Even on our conservative test, the probability that chance could produce the observed levels of ancestral convergence for just one of the eight datasets of 51 proteins is ≈1×10⁻¹⁹ and combined over 8 datasets is ≈1×10⁻¹³². By comparison, there are about 10⁸⁰ protons in the universe, hence the probability that the sequences could have been produced by a process involving unrelated ancestral sequences is about 10⁵⁰ lower than picking, among all protons, the same proton at random twice in a row. A non-evolutionary control model shows no convergence, and only a small number of parameters are required to account for the observations. It is time that that researchers insisted that doubters put up testable alternatives to evolution.", "link"=>"http://www.mendeley.com/research/beyond-reasonable-doubt-evolution-dna-sequences", "reader_count"=>41, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>10, "Student > Ph. D. Student"=>11, "Student > Master"=>7, "Other"=>1, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>10, "Student > Ph. D. Student"=>11, "Student > Master"=>7, "Other"=>1, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>2, "Agricultural and Biological Sciences"=>27, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"New Zealand"=>1, "Colombia"=>1, "United States"=>2, "Brazil"=>1, "United Kingdom"=>4, "Italy"=>1, "Belize"=>1, "Germany"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1146796"], "description"=>"<p>Separately, we measure the alignment score between each pair of sequences (s(<sub>i,j</sub>)) with one member in each of the two subsets, for example, s(<sub>a,k</sub>), s(<sub>a,l</sub>), s(<sub>a,m</sub>), and so on.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Molecular genetics", "Sequence analysis", "systems biology", "Evolutionary biology", "Forms of evolution", "Convergent evolution", "macroevolution", "Evolutionary genetics", "evolutionary theory", "Plant science", "Plant evolution", "subgroups", "independently", "align", "sequences", "optimal", "infer", "ancestral", "subtrees", "nearest", "node", "subtree", "pairwise", "alignment"], "article_id"=>767380, "categories"=>["Biological Sciences"], "users"=>["W. Timothy J. White", "Bojian Zhong", "David Penny"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069924.g001", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_We_use_two_natural_subgroups_X_and_Y_independently_align_the_sequences_for_the_species_in_each_subgroup_independently_determine_the_optimal_tree_for_each_subgroup_independently_infer_the_ancestral_sequences_a_x_and_a_y_on_the_optimal_subtrees_in_practice/767380", "title"=>"We use two natural subgroups (X and Y), independently align the sequences for the species in each subgroup, independently determine the optimal tree for each subgroup, independently infer the ancestral sequences a<sub>x</sub> and a<sub>y</sub> on the optimal subtrees (in practice the sequence at the nearest node to the root of the subtree is estimated), and finally measure the pairwise alignment score between the ancestral sequences, s(a<sub>x</sub>,a<sub>y</sub>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 01:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1146797"], "description"=>"<p>The example is the monocot/eudicot chloroplast dataset and for the short protein psbF (<b>2A</b>), a longer protein atpA (<b>2B</b>), and the 51 concatenated genes (<b>2C</b>). The x-axis shows the alignment score, which increases with the length of the protein(s), and is largest for the 51 concatenated proteins. There are 1056 s(<i>i</i>,<i>j</i>) scores between pairs of 24 monocots and 44 eudicots, and the y-axis indicates where the s(a<sub>x,</sub>a<sub>y</sub>) fits as a proportion of this number. For some short proteins in particular, multiple s(<i>i</i>,<i>j</i>) values equal the ancestral score s(a<sub>x</sub>,a<sub>y</sub>), and in this case our test conservatively places the ancestral score below the rest (as in psbF in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069924#pone-0069924-g002\" target=\"_blank\">Fig 2A</a>).</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Molecular genetics", "Sequence analysis", "systems biology", "Evolutionary biology", "Forms of evolution", "Convergent evolution", "macroevolution", "Evolutionary genetics", "evolutionary theory", "Plant science", "Plant evolution", "comparing", "alignment", "ancestral", "sequences", "scores", "pairs"], "article_id"=>767381, "categories"=>["Biological Sciences"], "users"=>["W. Timothy J. White", "Bojian Zhong", "David Penny"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069924.g002", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cumulative_frequency_plots_comparing_the_alignment_score_for_the_ancestral_sequences_s_a_x_a_y_small_circle_with_the_alignment_scores_of_all_pairs_of_proteins_s_i_j_/767381", "title"=>"Cumulative frequency plots comparing the alignment score for the ancestral sequences (s(a<sub>x,</sub>a<sub>y</sub>), small circle) with the alignment scores of all pairs of proteins, s(<i>i</i>,<i>j</i>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 01:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1146798"], "description"=>"<p>The ancestral alignment score (s(<i>a<sub>X</sub></i>,<i>a<sub>Y</sub></i>)) is indicated by a small circle on each plot. There are 1056 comparisons (24 monocots×44 eudicots) for each protein. The y-axis is the same for each gene, but the x-axis is strongly dependent on the length of the protein (see also <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069924#pone-0069924-g004\" target=\"_blank\">Figure 4</a>).</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Molecular genetics", "Sequence analysis", "systems biology", "Evolutionary biology", "Forms of evolution", "Convergent evolution", "macroevolution", "Evolutionary genetics", "evolutionary theory", "Plant science", "Plant evolution", "between-groups", "alignment", "scores", "50", "51", "chloroplast", "proteins", "monocots", "eudicots", "psbf"], "article_id"=>767382, "categories"=>["Biological Sciences"], "users"=>["W. Timothy J. White", "Bojian Zhong", "David Penny"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069924.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cumulative_distribution_plots_of_the_between_groups_alignment_scores_for_50_of_the_51_chloroplast_proteins_of_monocots_and_eudicots_the_plot_for_psbF_is_Fig_2A_/767382", "title"=>"Cumulative distribution plots of the between-groups alignment scores for 50 of the 51 chloroplast proteins of monocots and eudicots (the plot for psbF is Fig 2A).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 01:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1146799"], "description"=>"<p>Because of the possibility of slightly different gene lengths just one of the two datasets is used for illustration. As expected, longer proteins show convergence more strongly. Chloroplast results (4A and 4B) are for 51 chloroplast genes for divergences of monocots and for angiosperms (flowering plants). There are 7 nuclear proteins for 4C and 12 for the mitochondrial data in 4D.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Molecular genetics", "Sequence analysis", "systems biology", "Evolutionary biology", "Forms of evolution", "Convergent evolution", "macroevolution", "Evolutionary genetics", "evolutionary theory", "Plant science", "Plant evolution", "pairwise", "alignment", "scores", "higher", "ancestral"], "article_id"=>767383, "categories"=>["Biological Sciences"], "users"=>["W. Timothy J. White", "Bojian Zhong", "David Penny"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069924.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_length_versus_proportion_of_pairwise_alignment_scores_higher_than_the_ancestral_score_for_4_datasets_/767383", "title"=>"Protein length versus proportion of pairwise alignment scores higher than the ancestral score, for 4 datasets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 01:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1146800"], "description"=>"<p>The numbers of genes for the subgroups are indicated after the data type, and the number of taxa are indicated in parentheses ‘()’following the group name. The divergence times are minimum estimates from fossils and molecular data. Columns 5–7 relate to the probability that convergence could have arisen by chance, the last two columns are from controls where convergence is <u>not</u> expected. The penultimate row gives the combined values for the 8 datasets. The final row gives the results for the first example where combined information from both subsets (eudicots and monocots) is used for estimating the ancestral sequence of both subgroups; this again indicates that our test is very conservative.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Molecular genetics", "Sequence analysis", "systems biology", "Evolutionary biology", "Forms of evolution", "Convergent evolution", "macroevolution", "Evolutionary genetics", "evolutionary theory", "Plant science", "Plant evolution"], "article_id"=>767384, "categories"=>["Biological Sciences"], "users"=>["W. Timothy J. White", "Bojian Zhong", "David Penny"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069924.t002", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_X_2_and_p_values_for_the_different_datasets_/767384", "title"=>"Summary of X<sup>2</sup> and p values for the different datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-08 01:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1146801"], "description"=>"<p>Results for the 51 genes for the monocot/eudicot chloroplast dataset, and with the ancestral sequences (a<sub>x</sub> and a<sub>y</sub>) inferred independently.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Molecular genetics", "Sequence analysis", "systems biology", "Evolutionary biology", "Forms of evolution", "Convergent evolution", "macroevolution", "Evolutionary genetics", "evolutionary theory", "Plant science", "Plant evolution", "51", "genes", "chloroplast", "ancestral", "sequences", "inferred"], "article_id"=>767385, "categories"=>["Biological Sciences"], "users"=>["W. Timothy J. White", "Bojian Zhong", "David Penny"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069924.t003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_for_the_51_genes_for_the_monocot_eudicot_chloroplast_dataset_and_with_the_ancestral_sequences_a_x_and_a_y_inferred_independently_/767385", "title"=>"Results for the 51 genes for the monocot/eudicot chloroplast dataset, and with the ancestral sequences (a<sub>x</sub> and a<sub>y</sub>) inferred independently.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-08 01:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1146803"], "description"=>"<p>The ancestral sequences for the monocots, and the eudicots, are inferred independently, and then the alignment scores calculated in the program MUSCLE. The individual column scores depend on the frequencies and properties of the two amino acids; higher scores are given for pairs that are similar (readily substitutable) or specific (more readily substitutable for each other than for other amino acids). The column scores are summed to produce the alignment score.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Molecular genetics", "Sequence analysis", "systems biology", "Evolutionary biology", "Forms of evolution", "Convergent evolution", "macroevolution", "Evolutionary genetics", "evolutionary theory", "Plant science", "Plant evolution", "alignment", "inferred", "ancestral", "monocot", "eudicot", "sequences", "psbk"], "article_id"=>767386, "categories"=>["Biological Sciences"], "users"=>["W. Timothy J. White", "Bojian Zhong", "David Penny"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069924.t001", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Calculation_of_alignment_score_for_the_inferred_ancestral_monocot_and_eudicot_sequences_of_the_psbK_gene_/767386", "title"=>"Calculation of alignment score for the inferred ancestral monocot and eudicot sequences of the psbK gene.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-08 01:38:32"}

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Relative Metric

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