Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods.

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

authors： Wiens JJ,Fetzner JW,Parkinson CL,Reeder TW

更新日期：2005-10-01 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

authors： Morard R,Escarguel G,Weiner AK,André A,Douady CJ,Wade CM,Darling KF,Ujiié Y,Seears HA,Quillévéré F,de Garidel-Thoron T,de Vargas C,Kucera M

更新日期：2016-09-01 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

authors： Pereira SL,Baker AJ,Wajntal A

更新日期：2002-12-01 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

authors： Arkhipova IR

更新日期：2006-12-01 00:00:00

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

authors： Jondelius U,Wallberg A,Hooge M,Raikova OI

更新日期：2011-12-01 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

authors： Szöllõsi GJ,Rosikiewicz W,Boussau B,Tannier E,Daubin V

更新日期：2013-11-01 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

authors： Sanderson MJ,Boss D,Chen D,Cranston KA,Wehe A

更新日期：2008-06-01 00:00:00

abstract：:Species are the starting point for most studies of ecology and evolution, but the proper circumscription of species can be extremely difficult in morphologically variable lineages, and there are still few convincing examples of molecularly informed species delimitation in plants. Here, we focus on the Viburnum nudum c...

journal_title：Systematic biology

authors： Spriggs EL,Eaton DAR,Sweeney PW,Schlutius C,Edwards EJ,Donoghue MJ

更新日期：2019-03-01 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

authors： Beiko RG,Keith JM,Harlow TJ,Ragan MA

更新日期：2006-08-01 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

authors： Steeman ME,Hebsgaard MB,Fordyce RE,Ho SY,Rabosky DL,Nielsen R,Rahbek C,Glenner H,Sørensen MV,Willerslev E

更新日期：2009-12-01 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

authors： Sang T,Zhong Y

更新日期：2000-09-01 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

authors： Huelsenbeck JP,Nielsen R

更新日期：1999-06-01 00:00:00

abstract：:Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of estimating phylogenies by using discrete morphological data, maximum parsimony remains the only option. This paper explores ...

journal_title：Systematic biology

authors： Lewis PO

更新日期：2001-11-01 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

authors： Struck TH,Purschke G,Halanych KM

更新日期：2006-02-01 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

authors： Landis M,Edwards EJ,Donoghue MJ

更新日期：2021-01-01 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

authors： Popp M,Oxelman B

更新日期：2004-12-01 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：: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：: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：:Nucleotide transitions are frequently down-weighted relative to transversions in phylogenetic analysis. This is based on the assumption that transitions, by virtue of their greater evolutionary rate, exhibit relatively more homoplasy and are therefore less reliable phylogenetic characters. Relative amounts of homoplas...

journal_title：Systematic biology

authors： Broughton RE,Stanley SE,Durrett RT

更新日期：2000-12-01 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

authors： Kim J

更新日期：1998-03-01 00:00:00

abstract：:The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of th...

journal_title：Systematic biology

authors： Kolmann MA,Hughes LC,Hernandez LP,Arcila D,Betancur-R R,Sabaj MH,López-Fernández H,Ortí G

更新日期：2020-08-12 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

authors： Leschen RA,Buckley TR

更新日期：2007-02-01 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：:It is common for studies that employ the comparative method for the study of adaptation, i.e. documentation of potentially adaptive across-species patterns of trait-environment or trait-trait correlation, to be designated as "macroevolutionary." Authors are justified in using "macroevolution" in this way by appeal to ...

journal_title：Systematic biology

authors： Olson ME

更新日期：2021-01-07 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

authors： Dowton M,Austin AD

更新日期：2002-02-01 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

authors： Streicher JW,Schulte JA 2nd,Wiens JJ

更新日期：2016-01-01 00:00:00

abstract：:The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2-dimensional plane, however the accuracy of the...

journal_title：Systematic biology

authors： Louca S

更新日期：2020-07-29 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

authors： Koch NM,Thompson JR

更新日期：2020-09-03 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