A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data.

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：: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：: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：: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：: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：: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：:The obligate mutualism between pollinating fig wasps in the family Agaonidae (Hymenoptera: Chalcidoidea) and Ficus species (Moraceae) is often regarded as an example of co-evolution but little is known about the history of the interaction, and understanding the origin of functionally dioecious fig pollination has been...

journal_title：Systematic biology

authors： Weiblen GD

更新日期：2001-04-01 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：: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：: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：: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：: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：: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：: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：: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：:We conducted a geometric morphometric analysis of interspecific body shape variation among representatives of 31 species of darters (Pisces: Percidae) to determine whether there is evidence of a phylogenetic effect in body shape variation. Cartesian transformation grids representing relative shape differences of indiv...

journal_title：Systematic biology

authors： Guill JM,Heins DC,Hood CS

更新日期：2003-08-01 00:00:00

abstract：:Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence bet...

journal_title：Systematic biology

authors： Sang T,Zhong Y

更新日期：2000-09-01 00:00:00

abstract：:The evolutionary history of gains and losses of vegetative reproductive propagules (soredia) in Porpidia s.l., a group of lichen-forming ascomycetes, was clarified using Bayesian Markov chain Monte Carlo (MCMC) approaches to monophyly tests and a combined MCMC and maximum likelihood approach to ancestral character sta...

journal_title：Systematic biology

authors： Buschbom J,Barker D

更新日期：2006-06-01 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：: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：: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：: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：:A controversial topic that underlies much of phylogenetic experimental design is the relative utility of increased taxonomic versus character sampling. Conclusions about the relative utility of adding characters or taxa to a current phylogenetic study have subtly hinged upon the appropriateness of the rate of evolutio...

journal_title：Systematic biology

authors： Townsend JP,Lopez-Giraldez F

更新日期：2010-07-01 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：: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：: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 complexes undergoing rapid radiation present a challenge in molecular systematics because of the possibility that ancestral polymorphism is retained in component gene trees. Coalescent theory has demonstrated that gene trees often fail to match lineage trees when taxon divergence times are less than the ancest...

journal_title：Systematic biology

authors： Belfiore NM,Liu L,Moritz C

更新日期：2008-04-01 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：: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：: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