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 in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
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,Arzanloudoi
10.1093/sysbio/syp020subject
Has Abstractpub_date
2009-04-01 00:00:00pages
224-39issue
2eissn
1063-5157issn
1076-836Xpii
syp020journal_volume
58pub_type
杂志文章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::The obligate mutualism between pollinating fig wasps in the family Agaonidae (Hymenoptera: Chalcidoidea) and Ficus species (Moraceae) is often regarded as an example of co-evolution but little is known about the history of the interaction, and understanding the origin of functionally dioecious fig pollination has been...
journal_title:Systematic biology
pub_type: 杂志文章
doi:
更新日期:2001-04-01 00:00:00
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
doi:10.1093/sysbio/syw053
更新日期:2016-11-01 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::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::We investigate the impact of past climates on plant diversification by tracking the "footprint" of climate change on a phylogenetic tree. Diversity within the cosmopolitan carnivorous plant genus Drosera (Droseraceae) is focused within Mediterranean climate regions. We explore whether this diversity is temporally link...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/1063515060081570
更新日期:2006-10-01 00:00:00
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::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::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::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::Young polyploid events are easily diagnosed by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes, pseudogenization or locus loss, and interlocus intera...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150590945359
更新日期:2005-06-01 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::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 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
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
doi:10.1093/sysbio/syaa075
更新日期:2020-09-26 00:00:00
abstract::Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolve...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv058
更新日期:2016-01-01 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::The evolutionary history of gains and losses of vegetative reproductive propagules (soredia) in Porpidia s.l., a group of lichen-forming ascomycetes, was clarified using Bayesian Markov chain Monte Carlo (MCMC) approaches to monophyly tests and a combined MCMC and maximum likelihood approach to ancestral character sta...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150600697465
更新日期:2006-06-01 00:00:00
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
doi:10.1093/sysbio/syr100
更新日期:2012-01-01 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::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::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::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::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::The remarkable fossil record of whales and dolphins (Cetacea) has made them an exemplar of macroevolution. Although their overall adaptive transition from terrestrial to fully aquatic organisms is well known, this is not true for the radiation of modern whales. Here, we explore the diversification of extant cetaceans ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp060
更新日期:2009-12-01 00:00:00
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
doi:10.1093/sysbio/syz056
更新日期:2020-05-01 00:00:00
abstract::A controversial topic that underlies much of phylogenetic experimental design is the relative utility of increased taxonomic versus character sampling. Conclusions about the relative utility of adding characters or taxa to a current phylogenetic study have subtly hinged upon the appropriateness of the rate of evolutio...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq025
更新日期:2010-07-01 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::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
doi:10.1080/10635150600697283
更新日期:2006-06-01 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