Combined nuclear and mitochondrial DNA sequences resolve generic relationships within the Cracidae (Galliformes, Aves).

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：: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：: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：:Alignments of nucleotide or amino acid sequences may contain a variety of different signals, one of which is the historical signal that we often try to recover by phylogenetic analysis. Other signals, such as those arising due to compositional heterogeneities, among-lineage and among-site rate heterogeneities, invaria...

journal_title：Systematic biology

authors： Ho SY,Jermiin L

更新日期：2004-08-01 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：:Two lines of evidence indicate that the degree of symmetry in phylogenetic topologies differs at different hierarchical levels. First, in a set of 61 phylogenies with superspecific taxa as their terminals, trees were on average more unbalanced (asymmetric) when the species richness of terminals was considered than whe...

journal_title：Systematic biology

authors： Purvis A,Agapow PM

更新日期：2002-12-01 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：: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：: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：: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：: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：: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：: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：: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：: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：: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：: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：:We modified the phylogenetic program MrBayes 3.1.2 to incorporate the compound Dirichlet priors for branch lengths proposed recently by Rannala, Zhu, and Yang (2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.) as a solution to the prob...

journal_title：Systematic biology

authors： Zhang C,Rannala B,Yang Z

更新日期：2012-10-01 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：: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：: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：: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：: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：: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：: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：: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 relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provi...

journal_title：Systematic biology

authors： Pérez-Escobar OA,Balbuena JA,Gottschling M

更新日期：2016-01-01 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：:Historically, comparisons of host and parasite phylogenies have concentrated on cospeciation. However, many of these comparisons have demonstrated that the phylogenies of hosts and parasites are seldom completely congruent, suggesting that phenomena other than cospeciation play an important role in the evolution of ho...

journal_title：Systematic biology

authors： Weckstein JD

更新日期：2004-02-01 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