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 tree estimate that is closest on average to the samples. This "median" tree is known as the Bayes estimator (BE). The BE literally maximizes posterior expected accuracy, measured in terms of closeness (distance) to the true tree. We discuss a unified framework of BE trees, focusing especially on tree distances that are expressible as squared euclidean distances. Notable examples include Robinson-Foulds (RF) distance, quartet distance, and squared path difference. Using both simulated and real data, we show that BEs can be estimated in practice by hill-climbing. In our simulation, we find that BEs tend to be closer to the true tree, compared with ML and neighbor joining. In particular, the BE under squared path difference tends to perform well in terms of both path difference and RF distances.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Huggins PM,Li W,Haws D,Friedrich T,Liu J,Yoshida Rdoi
10.1093/sysbio/syr021subject
Has Abstractpub_date
2011-07-01 00:00:00pages
528-40issue
4eissn
1063-5157issn
1076-836Xpii
syr021journal_volume
60pub_type
杂志文章abstract::Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, an...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701656378
更新日期:2007-12-01 00:00:00
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 ch...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150600812544
更新日期:2006-08-01 00:00:00
abstract::The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, rece...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490423430
更新日期:2004-04-01 00:00:00
abstract::Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclea...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syt101
更新日期:2014-03-01 00:00:00
abstract::Performance measures of phylogenetic estimation methods such as accuracy, consistency, and power are an attempt at summarizing an ensemble of a given estimator's behavior. These summaries characterize an ensemble behavior with a single number, leading to a variety of definitions. In particular, the relationships betwe...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351598261021
更新日期:1998-03-01 00:00:00
abstract::The dominance of angiosperms has played a direct role in the diversification of insects, especially Coleoptera. The shift to angiosperm feeding from other diets is likely to have increased the rate of speciation in Phytophaga. However, Phytophaga is only one of many hyperdiverse lineages of beetles and studies of host...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701211844
更新日期:2007-02-01 00:00:00
abstract::As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.arizona.edu/pb), which offers a view of GenBank tailored for molecular phylogenetics...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150802158688
更新日期:2008-06-01 00:00:00
abstract::Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here, we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance. Discordance has been found to be rampant in genome-wide da...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw018
更新日期:2016-07-01 00:00:00
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
doi:10.1080/10635150490888840
更新日期:2004-12-01 00:00:00
abstract::Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence bet...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635159950127321
更新日期:2000-09-01 00:00:00
abstract::Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syx032
更新日期:2017-11-01 00:00:00
abstract::How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids an...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500234625
更新日期:2005-10-01 00:00:00
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
doi:10.1093/sysbio/syaa085
更新日期:2021-01-07 00:00:00
abstract::In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa003
更新日期:2020-09-01 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::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::Although calyptraeid gastropods are not well understood taxonomically, in part because their simple plastic shells are the primary taxonomic character, they provide an ideal system to examine questions about evolution in the marine environment. I conducted a phylogenetic analysis of calyptraeid gastropods using DNA se...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150390235430
更新日期:2003-10-01 00:00:00
abstract::Phylogenetic reconstruction, divergence time estimations and ancestral range estimation were undertaken for 66% of the Afrotropical freshwater crab fauna (Potamonautidae) based on four partial DNA loci (12S rRNA, 16S rRNA, cytochrome oxidase one [COI], and histone 3). The present study represents the most comprehensiv...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv011
更新日期:2015-07-01 00:00:00
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
doi:10.1080/10635150701424553
更新日期:2007-06-01 00:00:00
abstract::Even though relationships within Annelida are poorly understood, Eunicida is one of only a few major annelid lineages well supported by morphology. The seven recognized eunicid families possess sclerotized jaws that include mandibles and a maxillary apparatus. The maxillary apparatuses vary in shape and number of elem...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500354910
更新日期:2006-02-01 00:00:00
abstract::We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is...
journal_title:Systematic biology
pub_type: 杂志文章,评审
doi:10.1093/sysbio/syt029
更新日期:2013-09-01 00:00:00
abstract::Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life, but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger datasets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflic...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa054
更新日期:2020-07-18 00:00:00
abstract::We explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr101
更新日期:2012-03-01 00:00:00
abstract::Previous phylogenetic analyses of tetrapod 18S ribosomal RNA (rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as "definitive ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150390196948
更新日期:2003-06-01 00:00:00
abstract::We collected ~29 kb of sequence data using Roche 454 pyrosequencing in order to estimate the timing and pattern of diversification in the carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols for reduced representation library construction, we generated sequence data from 86 individuals across 10 po...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys048
更新日期:2012-10-01 00:00:00
abstract::The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before a...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/46.3.464
更新日期:1997-09-01 00:00:00
abstract::Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the sam...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500481390
更新日期:2006-04-01 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::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::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
doi:10.1093/sysbio/syq098
更新日期:2011-05-01 00:00:00