Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.

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

authors： Pfeil BE,Schlueter JA,Shoemaker RC,Doyle JJ

更新日期：2005-06-01 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：: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：: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：: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：: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：: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

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：: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：:Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally use...

journal_title：Systematic biology

authors： McFadden CS,Quattrini AM,Brugler MR,Cowman PF,Dueñas LF,Kitahara MV,Paz-García DA,Reimer JD,Rodríguez E

更新日期：2021-01-28 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

authors： Hinchliff CE,Roalson EH

更新日期：2013-03-01 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：: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：:The genomics revolution offers great promise for resolving the phylogeny of living taxa, but does it offer any benefits for reconstructing relationships among extinct (fossil) taxa? Superficially, the answer would seem to be "no," given that molecular data cannot be obtained for most fossil taxa. However, because foss...

journal_title：Systematic biology

authors： Wiens JJ

更新日期：2009-02-01 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

authors： Engstrom TN,Shaffer HB,McCord WP

更新日期：2004-10-01 00:00:00

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...

journal_title：Systematic biology

authors： 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,Arzanlou

更新日期：2009-04-01 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：: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：: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：: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：: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：:Horizontal gene transfer (HGT) is one of the main mechanisms driving the evolution of microorganisms. Its accurate identification is one of the major challenges posed by reticulate evolution. In this article, we describe a new polynomial-time algorithm for inferring HGT events and compare 3 existing and 1 new tree com...

journal_title：Systematic biology

authors： Boc A,Philippe H,Makarenkov V

更新日期：2010-03-01 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

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

更新日期：2008-06-01 00:00:00

abstract：:Siparunaceae comprise Glossocalyx with one species in West Africa and Siparuna with 65 species in the neotropics; all have unisexual flowers, and 15 species are monoecious, 50 dioecious. Parsimony and maximum likelihood analyses of combined nuclear ribosomal ITS and chloroplast trnL-trnF intergenic spacer sequences yi...

journal_title：Systematic biology

authors： Renner SS,Won H

更新日期：2001-09-01 00:00:00

abstract：:Among models of nucleotide evolution, the Barry and Hartigan (BH) model (also known as the General Markov Model) is very flexible as it allows separate arbitrary substitution matrices along edges. For a given tree, the estimates of the BH model are a set of joint probability matrices, each giving the pairwise frequenc...

journal_title：Systematic biology

authors： Zou L,Susko E,Field C,Roger AJ

更新日期：2012-12-01 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：: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：: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：: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：:Issues concerning transformational and taxic comparisons are central to understanding the impact of the recent proliferation of molecular developmental data on evolutionary biology. More importantly, an understanding of taxism and transformationalism in comparative biology is critical to assessing the impact of the re...

journal_title：Systematic biology

authors： Bang R,DeSalle R,Wheeler W

更新日期：2000-03-01 00:00:00