PMC:7519301 / 22543-23837 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7519301","sourcedb":"PMC","sourceid":"7519301","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7519301","text":"Fig. 4. Limited evidence of adaptation of the viral population. (A–C) Bootstrapped global estimates of Nei’s GST and Jost’s D for population differentiation for each structural gene. (A) Estimates of Nei’s GST (closed circles) and Jost’s D (open circles) comparing sequences sampled from the Hubei province to sequences subsequently sampled globally. Estimates of (B) Nei’s GST and (C) Jost’s D comparing sequences sampled before or after a specific date. Lines connect the median estimates across datasets for each gene. (D) Ln-transformed phylogenetic η, indicative of the number of iterative events in the sampled subtree, for subtrees from each internal node (after the root) of a down-sampled SARS-CoV-2 whole-genome phylogeny (dark gray), of a phylogeny simulated under neutral parameters (gold), and of a phylogeny simulated under positive time-dependent rates (b(t) = 0.01e0.4t, green). (E) Box plot of ln-transformed phylogenetic η estimates across all down-sampled SARS-CoV-2 whole-genome phylogenies, phylogenies simulated under neutral parameters, and phylogenies simulated under different positive time dependencies, α. Asterisks indicate significant differences in mean values (Student’s t test, P \u003c 0.05) between the SARS-CoV-2 and positive time-dependent phylogenies at each α.","divisions":[{"label":"label","span":{"begin":0,"end":7}}],"tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T86","span":{"begin":167,"end":182},"obj":"Body_part"},{"id":"T87","span":{"begin":517,"end":521},"obj":"Body_part"},{"id":"T88","span":{"begin":716,"end":722},"obj":"Body_part"},{"id":"T89","span":{"begin":993,"end":999},"obj":"Body_part"}],"attributes":[{"id":"A86","pred":"fma_id","subj":"T86","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A87","pred":"fma_id","subj":"T87","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A88","pred":"fma_id","subj":"T88","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A89","pred":"fma_id","subj":"T89","obj":"http://purl.org/sig/ont/fma/fma84116"},{"subj":"T86","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T87","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T88","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T89","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T105","span":{"begin":699,"end":707},"obj":"Disease"},{"id":"T106","span":{"begin":699,"end":703},"obj":"Disease"},{"id":"T107","span":{"begin":976,"end":984},"obj":"Disease"},{"id":"T108","span":{"begin":976,"end":980},"obj":"Disease"},{"id":"T109","span":{"begin":1233,"end":1241},"obj":"Disease"},{"id":"T110","span":{"begin":1233,"end":1237},"obj":"Disease"}],"attributes":[{"id":"A105","pred":"mondo_id","subj":"T105","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A106","pred":"mondo_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A107","pred":"mondo_id","subj":"T107","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A108","pred":"mondo_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A109","pred":"mondo_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A110","pred":"mondo_id","subj":"T110","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T105","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T106","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T107","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T108","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T109","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T110","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T185","span":{"begin":66,"end":67},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T186","span":{"begin":178,"end":182},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T187","span":{"begin":185,"end":186},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T188","span":{"begin":366,"end":367},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T189","span":{"begin":440,"end":441},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T190","span":{"begin":517,"end":521},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T191","span":{"begin":684,"end":685},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T192","span":{"begin":749,"end":750},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T193","span":{"begin":811,"end":812},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T194","span":{"begin":870,"end":874},"obj":"http://purl.obolibrary.org/obo/CLO_0002040"},{"id":"T195","span":{"begin":1205,"end":1209},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"attributes":[{"subj":"T185","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T186","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T187","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T188","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T189","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T190","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T191","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T192","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T193","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T194","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T195","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T71","span":{"begin":527,"end":529},"obj":"Chemical"},{"id":"T72","span":{"begin":797,"end":801},"obj":"Chemical"}],"attributes":[{"id":"A71","pred":"chebi_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/CHEBI_33319"},{"id":"A72","pred":"chebi_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/CHEBI_29287"},{"id":"A73","pred":"chebi_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/CHEBI_30050"},{"subj":"T71","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T72","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"315","span":{"begin":699,"end":709},"obj":"Species"},{"id":"316","span":{"begin":976,"end":986},"obj":"Species"},{"id":"317","span":{"begin":1233,"end":1243},"obj":"Species"}],"attributes":[{"id":"A315","pred":"tao:has_database_id","subj":"315","obj":"Tax:2697049"},{"id":"A316","pred":"tao:has_database_id","subj":"316","obj":"Tax:2697049"},{"id":"A317","pred":"tao:has_database_id","subj":"317","obj":"Tax:2697049"},{"subj":"315","pred":"source","obj":"LitCovid-PubTator"},{"subj":"316","pred":"source","obj":"LitCovid-PubTator"},{"subj":"317","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T140","span":{"begin":0,"end":7},"obj":"Sentence"},{"id":"T141","span":{"begin":9,"end":351},"obj":"Sentence"},{"id":"T142","span":{"begin":352,"end":456},"obj":"Sentence"},{"id":"T143","span":{"begin":457,"end":1133},"obj":"Sentence"},{"id":"T144","span":{"begin":1134,"end":1294},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T140","pred":"source","obj":"LitCovid-sentences"},{"subj":"T141","pred":"source","obj":"LitCovid-sentences"},{"subj":"T142","pred":"source","obj":"LitCovid-sentences"},{"subj":"T143","pred":"source","obj":"LitCovid-sentences"},{"subj":"T144","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#ec93da","default":true},{"id":"LitCovid-PD-MONDO","color":"#93ece4"},{"id":"LitCovid-PD-CLO","color":"#ecca93"},{"id":"LitCovid-PD-CHEBI","color":"#b093ec"},{"id":"LitCovid-PubTator","color":"#93ec96"},{"id":"LitCovid-sentences","color":"#ec93aa"}]}]}}