Bayesian tests of topology hypotheses with an example from diving beetles.

abstract：:Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level eve...

journal_title：Systematic biology

authors： Szöllõsi GJ,Rosikiewicz W,Boussau B,Tannier E,Daubin V

更新日期：2013-11-01 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：: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：: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：: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：: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：:Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a h...

journal_title：Systematic biology

authors： Huelsenbeck JP,Bollback JP

更新日期：2001-06-01 00:00:00

abstract：:Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 spec...

journal_title：Systematic biology

authors： Popp M,Oxelman B

更新日期：2004-12-01 00:00:00

abstract：:The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpi...

journal_title：Systematic biology

authors： O'Connor A,Wills MA

更新日期：2016-09-01 00:00:00

abstract：:Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynami...

journal_title：Systematic biology

authors： Duchene S,Bouckaert R,Duchene DA,Stadler T,Drummond AJ

更新日期：2019-03-01 00:00:00

abstract：:The remarkable fossil record of whales and dolphins (Cetacea) has made them an exemplar of macroevolution. Although their overall adaptive transition from terrestrial to fully aquatic organisms is well known, this is not true for the radiation of modern whales. Here, we explore the diversification of extant cetaceans ...

journal_title：Systematic biology

authors： Steeman ME,Hebsgaard MB,Fordyce RE,Ho SY,Rabosky DL,Nielsen R,Rahbek C,Glenner H,Sørensen MV,Willerslev E

更新日期：2009-12-01 00:00:00

abstract：:Population structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission pat...

journal_title：Systematic biology

authors： Volz EM,Carsten W,Grad YH,Frost SDW,Dennis AM,Didelot X

更新日期：2020-09-01 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：: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：: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：: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：: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：:The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time...

journal_title：Systematic biology

authors： Landis M,Edwards EJ,Donoghue MJ

更新日期：2021-01-01 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：:Significant phylogenetic codivergence between plant or animal hosts (H) and their symbionts or parasites (P) indicates the importance of their interactions on evolutionary time scales. However, valid and realistic methods to test for codivergence are not fully developed. One of the systems where possible codivergence ...

journal_title：Systematic biology

authors： Schardl CL,Craven KD,Speakman S,Stromberg A,Lindstrom A,Yoshida R

更新日期：2008-06-01 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：: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：:Phylogenetic reconstruction, divergence time estimations and ancestral range estimation were undertaken for 66% of the Afrotropical freshwater crab fauna (Potamonautidae) based on four partial DNA loci (12S rRNA, 16S rRNA, cytochrome oxidase one [COI], and histone 3). The present study represents the most comprehensiv...

journal_title：Systematic biology

authors： Daniels SR,Phiri EE,Klaus S,Albrecht C,Cumberlidge N

更新日期：2015-07-01 00:00:00

abstract：:The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and reso...

journal_title：Systematic biology

authors： Dececchi TA,Balhoff JP,Lapp H,Mabee PM

更新日期：2015-11-01 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：: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：:Characters derived from advertisement calls, morphology, allozymes, and the sequences of the small subunit of the mitochondrial ribosomal gene (12S) and the cytochrome oxidase I (COI) mitochondrial gene were used to estimate the phylogeny of frogs of the Physalaemus pustulosus group (Leptodactylidae). The combinabilit...

journal_title：Systematic biology

authors： Cannatella DC,Hillis DM,Chippindale PT,Weigt L,Rand AS,Ryan MJ

更新日期：1998-06-01 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：: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