Identification of Hidden Population Structure in Time-Scaled Phylogenies.


:Population structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealized genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome Neisseria gonorrhoeae sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance. [Antimicrobial resistance; coalescent; HIV; population structure.].


Syst Biol


Systematic biology


Volz EM,Carsten W,Grad YH,Frost SDW,Dennis AM,Didelot X




Has Abstract


2020-09-01 00:00:00














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    journal_title:Systematic biology

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    journal_title:Systematic biology

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    journal_title:Systematic biology

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    authors: Behdenna A,Pothier J,Abby SS,Lambert A,Achaz G

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    authors: Huelsenbeck JP,Bollback JP

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    authors: Blomberg SP,Lefevre JG,Wells JA,Waterhouse M

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    authors: Duchene S,Bouckaert R,Duchene DA,Stadler T,Drummond AJ

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    journal_title:Systematic biology

    pub_type: 杂志文章


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    abstract::The genomics revolution offers great promise for resolving the phylogeny of living taxa, but does it offer any benefits for reconstructing relationships among extinct (fossil) taxa? Superficially, the answer would seem to be "no," given that molecular data cannot be obtained for most fossil taxa. However, because foss...

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    authors: Stone EA

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    authors: Pfeil BE,Schlueter JA,Shoemaker RC,Doyle JJ

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    journal_title:Systematic biology

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  • Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time.

    abstract::The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpi...

    journal_title:Systematic biology

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    authors: O'Connor A,Wills MA

    更新日期:2016-09-01 00:00:00

  • Molecular and morphological phylogenetics of weevils (coleoptera, curculionoidea): do niche shifts accompany diversification?

    abstract::The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil di...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Marvaldi AE,Sequeira AS,O'Brien CW,Farrell BD

    更新日期:2002-10-01 00:00:00

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    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Ward PS,Brady SG,Fisher BL,Schultz TR

    更新日期:2010-05-01 00:00:00

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    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Díaz-Pérez A,Sequeira M,Santos-Guerra A,Catalán P

    更新日期:2008-10-01 00:00:00

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    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Weiblen GD

    更新日期:2001-04-01 00:00:00

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    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Renner SS,Won H

    更新日期:2001-09-01 00:00:00