The evolutionary root of flowering plants.

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 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：: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 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 explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that...

journal_title：Systematic biology

authors： Lee JY,Joseph L,Edwards SV

更新日期：2012-03-01 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 insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morp...

journal_title：Systematic biology

authors： de Moya RS,Yoshizawa K,Walden KKO,Sweet AD,Dietrich CH,Johnson KP

更新日期：2020-09-26 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：: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：:Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolve...

journal_title：Systematic biology

authors： Streicher JW,Schulte JA 2nd,Wiens JJ

更新日期：2016-01-01 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：:Species delimitation and species tree inference are difficult problems in cases of recent divergence, especially when different loci have different histories. This paper quantifies the difficulty of jointly finding the division of samples to species and estimating a species tree without constraining the possible assig...

journal_title：Systematic biology

authors： O'Meara BC

更新日期：2010-01-01 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：:The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, rece...

journal_title：Systematic biology

authors： Sanmartín I,Ronquist F

更新日期：2004-04-01 00:00:00

abstract：:Randomization tests allow the formulation and statistical testing of null hypotheses about the quality of entire data sets or the quality of fit between the data and particular phylogenetic hypotheses. Randomization tests of phylogenetic hypotheses based on the concepts of split support and split conflict are describe...

journal_title：Systematic biology

authors： Wilkinson M

更新日期：1998-12-01 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

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：: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：: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：: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：: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：: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：:We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we implement two efficient MCMC proposals: the first is based on the Subtree Pruni...

journal_title：Systematic biology

authors： Rannala B,Yang Z

更新日期：2017-09-01 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：: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：: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：:In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent phylogenetic works, the numerical evaluation of marginal likelihoods has often been performed using the harmonic mean estimation procedure. In the ...

journal_title：Systematic biology

authors： Lartillot N,Philippe H

更新日期：2006-04-01 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：: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：: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