Abstract:
:Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov chain or chains, the sampling density, the proposal mechanism, and, if Metropolis-coupled MCMC is being used, the number of heated chains and their temperatures. Although some parameter settings have been examined in detail in the literature, others are frequently chosen with more regard to computational time or personal experience with other data sets. Such choices may lead to inadequate sampling of tree space or an inefficient use of computational resources. We performed a detailed study of convergence and mixing for 70 randomly selected, putatively orthologous protein sets with different sizes and taxonomic compositions. Replicated runs from multiple random starting points permit a more rigorous assessment of convergence, and we developed two novel statistics, delta and epsilon, for this purpose. Although likelihood values invariably stabilized quickly, adequate sampling of the posterior distribution of tree topologies took considerably longer. Our results suggest that multimodality is common for data sets with 30 or more taxa and that this results in slow convergence and mixing. However, we also found that the pragmatic approach of combining data from several short, replicated runs into a "metachain" to estimate bipartition posterior probabilities provided good approximations, and that such estimates were no worse in approximating a reference posterior distribution than those obtained using a single long run of the same length as the metachain. Precision appears to be best when heated Markov chains have low temperatures, whereas chains with high temperatures appear to sample trees with high posterior probabilities only rarely.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Beiko RG,Keith JM,Harlow TJ,Ragan MAdoi
10.1080/10635150600812544subject
Has Abstractpub_date
2006-08-01 00:00:00pages
553-65issue
4eissn
1063-5157issn
1076-836Xpii
G6213Q5W084H6115journal_volume
55pub_type
杂志文章abstract::Although most often used to represent phylogenetic uncertainty, network methods are also potentially useful for describing the phylogenetic complexity expected to characterize recent species radiations. One network method with particular advantages in this context is split decomposition. However, in its standard imple...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150590906046
更新日期:2005-02-01 00:00:00
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
doi:10.1080/10635150701311370
更新日期:2007-04-01 00:00:00
abstract::Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provi...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv070
更新日期:2016-01-01 00:00:00
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
doi:10.1093/sysbio/syw082
更新日期:2017-01-01 00:00:00
abstract::Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv035
更新日期:2015-09-01 00:00:00
abstract::Penelope-like elements (PLEs) are a relatively little studied class of eukaryotic retroelements, distinguished by the presence of the GIY-YIG endonuclease domain, the ability of some representatives to retain introns, and the similarity of PLE-encoded reverse transcriptases to telomerases. Although these retrotranspos...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150601077683
更新日期:2006-12-01 00:00:00
abstract::Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet, most reconstruction methods like maximum likelihood (ML) do not explicitly maximize this accuracy. To address this problem, we propose a Bayesian solution. Given tree samples, we propose finding the tr...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr021
更新日期:2011-07-01 00:00:00
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
doi:10.1093/sysbio/syp020
更新日期:2009-04-01 00:00:00
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
doi:10.1093/sysbio/syr118
更新日期:2012-05-01 00:00:00
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
doi:10.1093/sysbio/syr052
更新日期:2011-10-01 00:00:00
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
doi:10.1080/10635150290102546
更新日期:2002-12-01 00:00:00
abstract::Stochastic birth-death models provide the foundation for studying and simulating evolutionary trees in phylodynamics. A curious feature of such models is that they exhibit fundamental symmetries when the birth and death rates are interchanged. In this article, we first provide intuitive reasons for these known transfo...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syz039
更新日期:2019-09-01 00:00:00
abstract::All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351599260319
更新日期:1999-06-01 00:00:00
abstract::The Noah's Ark Problem (NAP) is a comprehensive cost-effectiveness methodology for biodiversity conservation that was introduced by Weitzman (1998) and utilizes the phylogenetic tree containing the taxa of interest to assess biodiversity. Given a set of taxa, each of which has a particular survival probability that ca...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150600873876
更新日期:2006-08-01 00:00:00
abstract::We found that trends in the rate of description of 580,000 marine and terrestrial species, in the taxonomically authoritative World Register of Marine Species and Catalogue of Life databases, were similar until the 1950s. Since then, the relative number of marine to terrestrial species described per year has increased...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr080
更新日期:2012-10-01 00:00:00
abstract::Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level eve...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syt054
更新日期:2013-11-01 00:00:00
abstract::Comprehensive phylogenetic analyses utilize data from distinct sources, including nuclear, mitochondrial, and plastid molecular sequences and morphology. Such heterogeneous datasets are likely to require distinct models of analysis, given the different histories of mutational biases operating on these characters. The ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351502753475853
更新日期:2002-02-01 00:00:00
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
doi:10.1080/10635150290069995
更新日期:2002-08-01 00:00:00
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
doi:10.1093/sysbio/syaa069
更新日期:2020-09-03 00:00:00
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
doi:10.1093/sysbio/syz005
更新日期:2019-09-01 00:00:00
abstract::In this article, we use supermatrix data-mining methods to reconstruct a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank. We explore the properties of these trees and their utility for phylogenetic inference, and show that even the highly incomplete alignments characteristic o...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys088
更新日期:2013-03-01 00:00:00
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
doi:10.1080/10635150390132731
更新日期:2003-02-01 00:00:00
abstract::We conducted a geometric morphometric analysis of interspecific body shape variation among representatives of 31 species of darters (Pisces: Percidae) to determine whether there is evidence of a phylogenetic effect in body shape variation. Cartesian transformation grids representing relative shape differences of indiv...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150390197019
更新日期:2003-08-01 00:00:00
abstract::Horizontal gene transfer (HGT) is one of the main mechanisms driving the evolution of microorganisms. Its accurate identification is one of the major challenges posed by reticulate evolution. In this article, we describe a new polynomial-time algorithm for inferring HGT events and compare 3 existing and 1 new tree com...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp103
更新日期:2010-03-01 00:00:00
abstract::Ants (Hymenoptera: Formicidae) are conspicuous organisms in most terrestrial ecosystems, often attaining high levels of abundance and diversity. In this study, we investigate the evolutionary history of a major clade of ants, the subfamily Dolichoderinae, whose species frequently achieve ecological dominance in ant co...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq012
更新日期:2010-05-01 00:00:00
abstract::The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa045
更新日期:2021-01-01 00:00:00
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
pub_type: 杂志文章
doi:10.1093/sysbio/syw039
更新日期:2016-09-01 00:00:00
abstract::Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many group...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw031
更新日期:2016-09-01 00:00:00
abstract::Characters derived from advertisement calls, morphology, allozymes, and the sequences of the small subunit of the mitochondrial ribosomal gene (12S) and the cytochrome oxidase I (COI) mitochondrial gene were used to estimate the phylogeny of frogs of the Physalaemus pustulosus group (Leptodactylidae). The combinabilit...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351598260932
更新日期:1998-06-01 00:00:00
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
doi:10.1080/10635150490503053
更新日期:2004-10-01 00:00:00