Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees.

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

authors： Buschbom J,Barker D

更新日期：2006-06-01 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

authors： Collin R

更新日期：2003-10-01 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

authors： Purvis A,Agapow PM

更新日期：2002-12-01 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

authors： Daniels SR,Phiri EE,Klaus S,Albrecht C,Cumberlidge N

更新日期：2015-07-01 00:00:00

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

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

更新日期：2016-03-01 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

authors： Dalquen DA,Zhu T,Yang Z

更新日期：2017-05-01 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

authors： Stone EA

更新日期：2011-05-01 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

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

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

authors： Stadler T,Steel M

更新日期：2019-09-01 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

authors： de Queiroz K

更新日期：2007-12-01 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

authors： Poulin R,Presswell B

更新日期：2016-11-01 00:00:00

abstract：:When doing a bootstrap analysis with a single tree saved per pseudoreplicate, biased search algorithms may influence support values more than actual properties of the data set. Two methods commonly used for finding phylogenetic trees consist of randomizing the input order of species in multiple addition sequences foll...

journal_title：Systematic biology

authors： Goloboff PA,Simmons MP

更新日期：2014-11-01 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

authors： Yesson C,Culham A

更新日期：2006-10-01 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

authors： Singhal S,Hoskin CJ,Couper P,Potter S,Moritz C

更新日期：2018-11-01 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

authors： Poux C,Chevret P,Huchon D,de Jong WW,Douzery EJ

更新日期：2006-04-01 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

authors： Ward PS,Brady SG,Fisher BL,Schultz TR

更新日期：2010-05-01 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

authors： Brassac J,Blattner FR

更新日期：2015-09-01 00:00:00

abstract：:Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they ...

journal_title：Systematic biology

authors： Pečnerová P,Moravec JC,Martínková N

更新日期：2015-11-01 00:00:00

abstract：:Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for th...

journal_title：Systematic biology

authors： Behdenna A,Pothier J,Abby SS,Lambert A,Achaz G

更新日期：2016-09-01 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

authors： Bergsten J,Nilsson AN,Ronquist F

更新日期：2013-09-01 00:00:00

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

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

更新日期：2004-02-01 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

authors： Allio R,Scornavacca C,Nabholz B,Clamens AL,Sperling FA,Condamine FL

更新日期：2020-01-01 00:00:00

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

authors： Cohan FM

更新日期：2001-08-01 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

authors： Townsend JP,Lopez-Giraldez F

更新日期：2010-07-01 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

authors： Cannatella DC,Hillis DM,Chippindale PT,Weigt L,Rand AS,Ryan MJ

更新日期：1998-06-01 00:00:00

abstract：:Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a h...

journal_title：Systematic biology

authors： Huelsenbeck JP,Bollback JP

更新日期：2001-06-01 00:00:00

abstract：:The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lin...

journal_title：Systematic biology

authors： Beaulieu JM,O'Meara BC,Donoghue MJ

更新日期：2013-09-01 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

authors： O'Connor A,Wills MA

更新日期：2016-09-01 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

authors： Lee JY,Joseph L,Edwards SV

更新日期：2012-03-01 00:00:00

abstract：:Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse ...

journal_title：Systematic biology

authors： Goremykin VV,Nikiforova SV,Biggs PJ,Zhong B,Delange P,Martin W,Woetzel S,Atherton RA,McLenachan PA,Lockhart PJ

更新日期：2013-01-01 00:00:00