A Skull Might Lie: Modeling Ancestral Ranges and Diet from Genes and Shape of Tree Squirrels.

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：: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：: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：:The dominance of angiosperms has played a direct role in the diversification of insects, especially Coleoptera. The shift to angiosperm feeding from other diets is likely to have increased the rate of speciation in Phytophaga. However, Phytophaga is only one of many hyperdiverse lineages of beetles and studies of host...

journal_title：Systematic biology

authors： Leschen RA,Buckley TR

更新日期：2007-02-01 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：: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：:Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recent...

journal_title：Systematic biology

authors： Allio R,Scornavacca C,Nabholz B,Clamens AL,Sperling FA,Condamine FL

更新日期：2020-01-01 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：: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：:Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associ...

journal_title：Systematic biology

authors： Levy Karin E,Wicke S,Pupko T,Mayrose I

更新日期：2017-11-01 00:00:00

abstract：:We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the fami...

journal_title：Systematic biology

authors： Kallal RJ,Dimitrov D,Arnedo MA,Giribet G,Hormiga G

更新日期：2020-03-01 00:00:00

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 analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2-dimensional plane, however the accuracy of the...

journal_title：Systematic biology

authors： Louca S

更新日期：2020-07-29 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：:Phylogenomic analyses of large sets of genes or proteins have the potential to revolutionize our understanding of the tree of life. However, problems arise because estimated phylogenies from individual loci often differ because of different histories, systematic bias, or stochastic error. We have developed Concaterpil...

journal_title：Systematic biology

authors： Leigh JW,Susko E,Baumgartner M,Roger AJ

更新日期：2008-02-01 00:00:00

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：: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：:When doing a bootstrap analysis with a single tree saved per pseudoreplicate, biased search algorithms may influence support values more than actual properties of the data set. Two methods commonly used for finding phylogenetic trees consist of randomizing the input order of species in multiple addition sequences foll...

journal_title：Systematic biology

authors： Goloboff PA,Simmons MP

更新日期：2014-11-01 00:00:00

abstract：:All methods proposed to date for mapping landmark configurations on a phylogenetic tree start from an alignment generated by methods that make no use of phylogenetic information, usually by superimposing all configurations against a consensus configuration. In order to properly interpret differences between landmark c...

journal_title：Systematic biology

authors： Catalano SA,Goloboff PA

更新日期：2012-05-01 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：: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：: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：: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：: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：:We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously ...

journal_title：Systematic biology

authors： Engstrom TN,Shaffer HB,McCord WP

更新日期：2004-10-01 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：: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：: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：: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：:Lice in the genus Pectinopygus parasitize a single order of birds (Pelecaniformes). To examine the degree of congruence between the phylogenies of 17 Pectinopygus species and their pelecaniform hosts, sequences from mitochondrial 12S rRNA, 16S rRNA, COI, and nuclear wingless and EF1-alpha genes (2290 nucleotides) and ...

journal_title：Systematic biology

authors： Hughes J,Kennedy M,Johnson KP,Palma RL,Page RD

更新日期：2007-04-01 00:00:00