Inferring and validating horizontal gene transfer events using bipartition dissimilarity.

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 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：: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：:Matrix representation with parsimony (MRP) supertree construction has been criticized because the supertree may specify clades that are contradicted by every source tree contributing to it. Such unsupported clades may also occur using other supertree methods; however, their incidence is largely unknown. In this study,...

journal_title：Systematic biology

authors： Bininda-Emonds OR

更新日期：2003-12-01 00:00:00

abstract：:We collected ~29 kb of sequence data using Roche 454 pyrosequencing in order to estimate the timing and pattern of diversification in the carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols for reduced representation library construction, we generated sequence data from 86 individuals across 10 po...

journal_title：Systematic biology

authors： Zellmer AJ,Hanes MM,Hird SM,Carstens BC

更新日期：2012-10-01 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：: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：: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

authors： Xia X,Xie Z,Kjer KM

更新日期：2003-06-01 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

authors： Hinchliff CE,Roalson EH

更新日期：2013-03-01 00:00:00

abstract：:The Noah's Ark Problem (NAP) is a comprehensive cost-effectiveness methodology for biodiversity conservation that was introduced by Weitzman (1998) and utilizes the phylogenetic tree containing the taxa of interest to assess biodiversity. Given a set of taxa, each of which has a particular survival probability that ca...

journal_title：Systematic biology

authors： Hartmann K,Steel M

更新日期：2006-08-01 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：: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：: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：:Whereas examples of insular speciation within the endemic-rich Macaronesian hotspot flora have been documented, the phylogeography of recently evolved plants in the region has received little attention. The Macaronesian red fescues constitute a narrow and recent radiation of four closely related diploid species distri...

journal_title：Systematic biology

authors： Díaz-Pérez A,Sequeira M,Santos-Guerra A,Catalán P

更新日期：2008-10-01 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

authors： de Queiroz K

更新日期：2007-12-01 00:00:00

abstract：:This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species....

journal_title：Systematic biology

authors： Szöllősi GJ,Tannier E,Daubin V,Boussau B

更新日期：2015-01-01 00:00:00

abstract：:Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associ...

journal_title：Systematic biology

authors： Levy Karin E,Wicke S,Pupko T,Mayrose I

更新日期：2017-11-01 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：: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：: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：:We found that trends in the rate of description of 580,000 marine and terrestrial species, in the taxonomically authoritative World Register of Marine Species and Catalogue of Life databases, were similar until the 1950s. Since then, the relative number of marine to terrestrial species described per year has increased...

journal_title：Systematic biology

authors： Costello MJ,Wilson S,Houlding B

更新日期：2012-10-01 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：: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：: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：:Understanding the origin of island endemics is a central task of historical biogeography. Recent methodological advances provide a rigorous framework to determine the relative contribution of different biogeographic processes (e.g., vicariance, land migration, long-distance dispersal) to the origin of island endemics....

journal_title：Systematic biology

authors： Salvo G,Ho SY,Rosenbaum G,Ree R,Conti E

更新日期：2010-12-01 00:00:00

abstract：:We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the fami...

journal_title：Systematic biology

authors： Kallal RJ,Dimitrov D,Arnedo MA,Giribet G,Hormiga G

更新日期：2020-03-01 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

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：: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：: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

authors： Hughes J,Kennedy M,Johnson KP,Palma RL,Page RD

更新日期：2007-04-01 00:00:00