Abstract:
:There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like visualization of phylogeny may also be done via other types of graphics, especially botanical (or literal) tree drawings. As a consequence, the meaning of such diagrams is not always clear: a given picture may have multiple interpretations in its different parts and two figures that look similar may actually carry quite different information. I show that these are not merely metaphors of phylogeny and may be defined mathematically as geometric shapes called branching silhouette diagrams, the name referring to their most apparent features. They have four basic forms depending on whether the time factor is considered in their construction and the relationships portrayed are of the ancestor-descendant or sister group type. By revitalizing Darwin's early suggestions on the illustration of change in the living world, I propose the term coral for the most common forms of branching silhouette which consider time and show ancestry. The others appear rarely in present-day practice and are mostly of historical value-these are cacti (named after one of Bessey's diagrams) and two types of oaks (with reference to several of Haeckel's motifs used in depicting phylogeny in the nineteenth century). The use of these terms in phylogenetic systematics facilitates better understanding of how organization of biodiversity has been visualized in science [Bessey; cladograms; coral-thinking; Darwin; graph theory; Haeckel; phylogeny; tree thinking.].
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Podani Jdoi
10.1093/sysbio/syx039subject
Has Abstractpub_date
2017-09-01 00:00:00pages
737-753issue
5eissn
1063-5157issn
1076-836Xpii
3066298journal_volume
66pub_type
杂志文章abstract::Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensi...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr073
更新日期:2011-12-01 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::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
doi:10.1080/10635150500433722
更新日期:2006-04-01 00:00:00
abstract::As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic diversity. Delimiting this cryptic diversity is challenging, both because the divergences span a continuum and because the lack of overt morphological differentiation suggests divergence has proceede...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syy026
更新日期:2018-11-01 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::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::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::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::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
doi:10.1080/10635150490503035
更新日期:2004-08-01 00:00:00
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
doi:10.1093/sysbio/syw063
更新日期:2017-05-01 00:00:00
abstract::Understanding the origin of island endemics is a central task of historical biogeography. Recent methodological advances provide a rigorous framework to determine the relative contribution of different biogeographic processes (e.g., vicariance, land migration, long-distance dispersal) to the origin of island endemics....
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq046
更新日期:2010-12-01 00:00:00
abstract::We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we implement two efficient MCMC proposals: the first is based on the Subtree Pruni...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw119
更新日期:2017-09-01 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::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::Using different data sets mainly from the plant family Rubiaceae, but in parts also from the Apocynaceae, Asteraceae, Lardizabalaceae, Saxifragaceae, and Solanaceae, we have investigated the effect of number of characters, number of taxa, and kind of data on bootstrap values within phylogenetic trees. The percentage o...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351599260085
更新日期:1999-09-01 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::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::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::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::We modified the phylogenetic program MrBayes 3.1.2 to incorporate the compound Dirichlet priors for branch lengths proposed recently by Rannala, Zhu, and Yang (2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.) as a solution to the prob...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys030
更新日期:2012-10-01 00:00:00
abstract::Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recent...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syz030
更新日期:2020-01-01 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::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::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::We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the fami...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syz043
更新日期:2020-03-01 00:00:00
abstract::The Cracidae is one of the most endangered and distinctive bird families in the Neotropics, yet the higher relationships among taxa remain uncertain. The molecular phylogeny of its 11 genera was inferred using 10,678 analyzable sites (5,412 from seven different mitochondrial segments and 5,266 sites from four nuclear ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150290102519
更新日期:2002-12-01 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::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::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::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