The effect of phylogeny on interspecific body shape variation in darters (Pisces: Percidae).

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：:Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur c...

journal_title：Systematic biology

authors： Poelstra J,Salmona J,Tiley GP,Schüßler D,Blanco MB,Andriambeloson JB,Bouchez O,Campbell CR,Etter PD,Hohenlohe PA,Hunnicutt KE,Iribar A,Johnson EA,Kappeler PM,Larsen PA,Manzi S,Ralison JM,Randrianambinina B,Rasoloariso

更新日期：2020-07-08 00:00:00

abstract：:Following (1) the large-scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80:528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84:1-49), we present a phylo...

journal_title：Systematic biology

authors： Savolainen V,Chase MW,Hoot SB,Morton CM,Soltis DE,Bayer C,Fay MF,de Bruijn AY,Sullivan S,Qiu YL

更新日期：2000-06-01 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

authors： Near TJ,Bossu CM,Bradburd GS,Carlson RL,Harrington RC,Hollingsworth PR Jr,Keck BP,Etnier DA

更新日期：2011-10-01 00:00:00

abstract：:Phylogenomic analyses of large sets of genes or proteins have the potential to revolutionize our understanding of the tree of life. However, problems arise because estimated phylogenies from individual loci often differ because of different histories, systematic bias, or stochastic error. We have developed Concaterpil...

journal_title：Systematic biology

authors： Leigh JW,Susko E,Baumgartner M,Roger AJ

更新日期：2008-02-01 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：: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

authors： Cunningham CW

更新日期：1997-09-01 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：: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

authors： Brysting AK,Oxelman B,Huber KT,Moulton V,Brochmann C

更新日期：2007-06-01 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：: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：: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：: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：: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

authors： Ayres DL,Darling A,Zwickl DJ,Beerli P,Holder MT,Lewis PO,Huelsenbeck JP,Ronquist F,Swofford DL,Cummings MP,Rambaut A,Suchard MA

更新日期：2012-01-01 00:00:00

abstract：:Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. While simple population models produce predic...

journal_title：Systematic biology

authors： Funk ER,Spellman GM,Winker K,Withrow JJ,Ruegg KC,Zavaleta E,Taylor SA

更新日期：2020-09-17 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：: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

authors： Lartillot N,Philippe H

更新日期：2006-04-01 00:00:00

abstract：:Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topolog...

journal_title：Systematic biology

authors： Zhang C,Huelsenbeck JP,Ronquist F

更新日期：2020-09-01 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：:Systematists expect their hypotheses to be asymptotically precise. As the number of phylogenetically informative characters for a set of taxa increases, the relationships implied should stabilize on some topology. If true, this increasing stability should clearly manifest itself if an index of congruence is plotted ag...

journal_title：Systematic biology

authors： Miller JA

更新日期：2003-02-01 00:00:00

abstract：:Population structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission pat...

journal_title：Systematic biology

authors： Volz EM,Carsten W,Grad YH,Frost SDW,Dennis AM,Didelot X

更新日期：2020-09-01 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：: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：: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

authors： Varón-González C,Whelan S,Klingenberg CP

更新日期：2020-09-01 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：: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

authors： Martin AP,Burg TM

更新日期：2002-08-01 00:00:00

abstract：:Understanding the evolutionary history of species is at the core of molecular evolution and is done using several inference methods. The critical issue is to quantify the uncertainty of the inference. The posterior probabilities in Bayesian phylogenetic inference and the bootstrap values in frequentist approaches meas...

journal_title：Systematic biology

authors： Mariadassou M,Bar-Hen A,Kishino H

更新日期：2012-03-01 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

authors： Leschen RA,Buckley TR

更新日期：2007-02-01 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

authors： Singhal S,Colston TJ,Grundler MR,Smith SA,Costa GC,Colli GR,Moritz C,Pyron RA,Rabosky DL

更新日期：2020-07-18 00:00:00

abstract：:We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs) regression under a Brownian motion model of evolution. This equivalence has seve...

journal_title：Systematic biology

authors： Blomberg SP,Lefevre JG,Wells JA,Waterhouse M

更新日期：2012-05-01 00:00:00