How the worm got its pharynx: phylogeny, classification and Bayesian assessment of character evolution in Acoela.

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：:Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclea...

journal_title：Systematic biology

authors： Galián JA,Rosato M,Rosselló JA

更新日期：2014-03-01 00:00:00

abstract：:Lineage sorting and introgression can lead to incongruence among gene phylogenies, complicating the inference of species trees for large groups of taxa that have recently and rapidly radiated. In addition, it can be difficult to determine which of these processes is responsible for this incongruence. We explore these ...

journal_title：Systematic biology

authors： Buckley TR,Cordeiro M,Marshall DC,Simon C

更新日期：2006-06-01 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：: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：: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：:Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key proces...

journal_title：Systematic biology

authors： Tarasov S

更新日期：2019-09-01 00:00:00

abstract：:Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete tax...

journal_title：Systematic biology

authors： Zhang R,Wang YH,Jin JJ,Stull GW,Bruneau A,Cardoso D,De Queiroz LP,Moore MJ,Zhang SD,Chen SY,Wang J,Li DZ,Yi TS

更新日期：2020-07-01 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：: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：: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：: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：:The treehopper subfamily Membracinae (Insecta: Hemiptera: Membracidae) comprises the majority of genera and species diversity in the New World tropics. These treehoppers exhibit a wide range of social behaviors, making them an excellent group for studying patterns of social evolution in insects. However, to date the t...

journal_title：Systematic biology

authors： Lin CP,Danforth BN,Wood TK

更新日期：2004-06-01 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：: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：: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：: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

abstract：:Sequence divergence for segments of three mitochondrial DNA (mtDNA) genes encoding the 12S and 16S ribosomal RNA and cytochrome b was examined in newts belonging to the genus Euproctus (E. asper, E. montanus, E. platycephalus) and in three other species belonging to the same family (Salamandridae), Triturus carnifex, ...

journal_title：Systematic biology

authors： Caccone A,Milinkovitch MC,Sbordoni V,Powell JR

更新日期：1997-03-01 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：:Although most often used to represent phylogenetic uncertainty, network methods are also potentially useful for describing the phylogenetic complexity expected to characterize recent species radiations. One network method with particular advantages in this context is split decomposition. However, in its standard imple...

journal_title：Systematic biology

authors： Winkworth R,Bryant D,Lockhart P,Havell D,Moulton V

更新日期：2005-02-01 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：:There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like...

journal_title：Systematic biology

authors： Podani J

更新日期：2017-09-01 00:00:00

abstract：:The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be...

journal_title：Systematic biology

authors： Mueller RL

更新日期：2006-04-01 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：: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：: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：: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：: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：: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：: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