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














  • Multiple cophylogenetic analyses reveal frequent cospeciation between pelecaniform birds and Pectinopygus lice.

    abstract::Lice in the genus Pectinopygus parasitize a single order of birds (Pelecaniformes). To examine the degree of congruence between the phylogenies of 17 Pectinopygus species and their pelecaniform hosts, sequences from mitochondrial 12S rRNA, 16S rRNA, COI, and nuclear wingless and EF1-alpha genes (2290 nucleotides) and ...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Hughes J,Kennedy M,Johnson KP,Palma RL,Page RD

    更新日期:2007-04-01 00:00:00

  • Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species.

    abstract::We develop a maximum likelihood (ML) method for estimating migration rates between species using genomic sequence data. A species tree is used to accommodate the phylogenetic relationships among three species, allowing for migration between the two sister species, while the third species is used as an out-group. A Mar...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Dalquen DA,Zhu T,Yang Z

    更新日期:2017-05-01 00:00:00

  • The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?

    abstract::Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions ...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Murray GG,Weinert LA,Rhule EL,Welch JJ

    更新日期:2016-03-01 00:00:00

  • Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data.

    abstract::Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). Howe...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Blair C,Ané C

    更新日期:2020-05-01 00:00:00

  • Untangling complex histories of genome mergings in high polyploids.

    abstract::Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated netw...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Brysting AK,Oxelman B,Huber KT,Moulton V,Brochmann C

    更新日期:2007-06-01 00:00:00

  • Assessing progress in systematics with continuous jackknife function analysis.

    abstract::Systematists expect their hypotheses to be asymptotically precise. As the number of phylogenetically informative characters for a set of taxa increases, the relationships implied should stabilize on some topology. If true, this increasing stability should clearly manifest itself if an index of congruence is plotted ag...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Miller JA

    更新日期:2003-02-01 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

  • Computing Bayes factors using thermodynamic integration.

    abstract::In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent phylogenetic works, the numerical evaluation of marginal likelihoods has often been performed using the harmonic mean estimation procedure. In the ...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Lartillot N,Philippe H

    更新日期:2006-04-01 00:00:00

  • Perils of paralogy: using HSP70 genes for inferring organismal phylogenies.

    abstract::Conserved genes have found their way into the mainstream of molecular systematics. Many of these genes are members of multigene families. A difficulty with using single genes of multigene families for phylogenetic inference is that genes from one species may be paralogous to those from another taxon. We focus attentio...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Martin AP,Burg TM

    更新日期:2002-08-01 00:00:00

  • Incomplete Lineage Sorting in Mammalian Phylogenomics.

    abstract::The impact of incomplete lineage sorting (ILS) on phylogenetic conflicts among genes, and the related issue of whether to account for ILS in species tree reconstruction, are matters of intense controversy. Here, focusing on full-genome data in placental mammals, we empirically test two assumptions underlying current u...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Scornavacca C,Galtier N

    更新日期:2017-01-01 00:00:00

  • Evolution of a RNA polymerase gene family in Silene (Caryophyllaceae)-incomplete concerted evolution and topological congruence among paralogues.

    abstract::Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 spec...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Popp M,Oxelman B

    更新日期:2004-12-01 00:00:00

  • Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

    abstract::Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of ...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Near TJ,Bossu CM,Bradburd GS,Carlson RL,Harrington RC,Hollingsworth PR Jr,Keck BP,Etnier DA

    更新日期:2011-10-01 00:00:00

  • The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.

    abstract::We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Schoch CL,Sung GH,López-Giráldez F,Townsend JP,Miadlikowska J,Hofstetter V,Robbertse B,Matheny PB,Kauff F,Wang Z,Gueidan C,Andrie RM,Trippe K,Ciufetti LM,Wynns A,Fraker E,Hodkinson BP,Bonito G,Groenewald JZ,Arzanlou

    更新日期:2009-04-01 00:00:00

  • Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how dietary convergence and parallelism obfuscate traditional morphological taxonomy.

    abstract::The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of th...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Kolmann MA,Hughes LC,Hernandez LP,Arcila D,Betancur-R R,Sabaj MH,López-Fernández H,Ortí G

    更新日期:2020-08-12 00:00:00

  • Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae.

    abstract::Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete tax...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Zhang R,Wang YH,Jin JJ,Stull GW,Bruneau A,Cardoso D,De Queiroz LP,Moore MJ,Zhang SD,Chen SY,Wang J,Li DZ,Yi TS

    更新日期:2020-07-01 00:00:00

  • Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits.

    abstract::Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key proces...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Tarasov S

    更新日期:2019-09-01 00:00:00

  • Phylogeny imbalance: taxonomic level matters.

    abstract::Two lines of evidence indicate that the degree of symmetry in phylogenetic topologies differs at different hierarchical levels. First, in a set of 61 phylogenies with superspecific taxa as their terminals, trees were on average more unbalanced (asymmetric) when the species richness of terminals was considered than whe...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Purvis A,Agapow PM

    更新日期:2002-12-01 00:00:00

  • A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data.

    abstract::Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approa...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Koch NM,Thompson JR

    更新日期:2020-09-03 00:00:00

  • Bacterial species and speciation.

    abstract::Bacteria are profoundly different from eukaryotes in their patterns of genetic exchange. Nevertheless, ecological diversity is organized in the same way across all of life: individual organisms fall into more less discrete clusters on the basis of their phenotypic, ecological, and DNA sequence characteristics. Each se...

    journal_title:Systematic biology

    pub_type: 杂志文章,评审


    authors: Cohan FM

    更新日期:2001-08-01 00:00:00

  • Why the phylogenetic regression appears robust to tree misspecification.

    abstract::The phylogenetic comparative method uses estimates of evolutionary relationships to explicitly model the covariance structure of interspecific data. By accounting for common ancestry, the coevolution between 2 or more traits, as a response to one another or to environmental variables, can be studied without confoundin...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Stone EA

    更新日期:2011-05-01 00:00:00

  • Tracing the decay of the historical signal in biological sequence data.

    abstract::Alignments of nucleotide or amino acid sequences may contain a variety of different signals, one of which is the historical signal that we often try to recover by phylogenetic analysis. Other signals, such as those arising due to compositional heterogeneities, among-lineage and among-site rate heterogeneities, invaria...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Ho SY,Jermiin L

    更新日期:2004-08-01 00:00:00

  • Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae).

    abstract::We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously ...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Engstrom TN,Shaffer HB,McCord WP

    更新日期:2004-10-01 00:00:00

  • Bayesian phylogenetic analysis of combined data.

    abstract::The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology....

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Nylander JA,Ronquist F,Huelsenbeck JP,Nieves-Aldrey JL

    更新日期:2004-02-01 00:00:00

  • Taxonomic Quality of Species Descriptions Varies over Time and with the Number of Authors, but Unevenly among Parasitic Taxa.

    abstract::Although concerns are being raised about a potential shortage of taxonomists and systematists, recent analyses suggest instead that the number of researchers involved in taxonomic descriptions is higher than ever and that the average number of new species described annually per taxonomist has declined in recent decade...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Poulin R,Presswell B

    更新日期:2016-11-01 00:00:00

  • BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

    abstract::Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting m...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Ayres DL,Darling A,Zwickl DJ,Beerli P,Holder MT,Lewis PO,Huelsenbeck JP,Ronquist F,Swofford DL,Cummings MP,Rambaut A,Suchard MA

    更新日期:2012-01-01 00:00:00

  • Independent contrasts and PGLS regression estimators are equivalent.

    abstract::We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs) regression under a Brownian motion model of evolution. This equivalence has seve...

    journal_title:Systematic biology

    pub_type: 杂志文章


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

    更新日期:2012-05-01 00:00:00

  • Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae).

    abstract::Species complexes undergoing rapid radiation present a challenge in molecular systematics because of the possibility that ancestral polymorphism is retained in component gene trees. Coalescent theory has demonstrated that gene trees often fail to match lineage trees when taxon divergence times are less than the ancest...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Belfiore NM,Liu L,Moritz C

    更新日期:2008-04-01 00:00:00

  • Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale).

    abstract::Lineage sorting and introgression can lead to incongruence among gene phylogenies, complicating the inference of species trees for large groups of taxa that have recently and rapidly radiated. In addition, it can be difficult to determine which of these processes is responsible for this incongruence. We explore these ...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Buckley TR,Cordeiro M,Marshall DC,Simon C

    更新日期:2006-06-01 00:00:00

  • Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias).

    abstract::Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuc...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: Sarver BAJ,Herrera ND,Sneddon D,Hunter SS,Settles ML,Kronenberg Z,Demboski JR,Good JM,Sullivan J

    更新日期:2021-01-07 00:00:00

  • Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): Combining sequence data and Exploring compositional bias solutions in Next Generation Datasets.

    abstract::The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morp...

    journal_title:Systematic biology

    pub_type: 杂志文章


    authors: de Moya RS,Yoshizawa K,Walden KKO,Sweet AD,Dietrich CH,Johnson KP

    更新日期:2020-09-26 00:00:00