Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models.

abstract：:We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed...

journal_title：Systematic biology

authors： Schoch CL,Sung GH,López-Giráldez F,Townsend JP,Miadlikowska J,Hofstetter V,Robbertse B,Matheny PB,Kauff F,Wang Z,Gueidan C,Andrie RM,Trippe K,Ciufetti LM,Wynns A,Fraker E,Hodkinson BP,Bonito G,Groenewald JZ,Arzanlou

更新日期：2009-04-01 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：: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

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：: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：:Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur c...

journal_title：Systematic biology

authors： Poelstra J,Salmona J,Tiley GP,Schüßler D,Blanco MB,Andriambeloson JB,Bouchez O,Campbell CR,Etter PD,Hohenlohe PA,Hunnicutt KE,Iribar A,Johnson EA,Kappeler PM,Larsen PA,Manzi S,Ralison JM,Randrianambinina B,Rasoloariso

更新日期：2020-07-08 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：: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：: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：: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：:Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, t...

journal_title：Systematic biology

authors： Yoder JB,Briskine R,Mudge J,Farmer A,Paape T,Steele K,Weiblen GD,Bharti AK,Zhou P,May GD,Young ND,Tiffin P

更新日期：2013-05-01 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：: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：:Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet, most reconstruction methods like maximum likelihood (ML) do not explicitly maximize this accuracy. To address this problem, we propose a Bayesian solution. Given tree samples, we propose finding the tr...

journal_title：Systematic biology

authors： Huggins PM,Li W,Haws D,Friedrich T,Liu J,Yoshida R

更新日期：2011-07-01 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

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：: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：: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：: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

abstract：:Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse ...

journal_title：Systematic biology

authors： Goremykin VV,Nikiforova SV,Biggs PJ,Zhong B,Delange P,Martin W,Woetzel S,Atherton RA,McLenachan PA,Lockhart PJ

更新日期：2013-01-01 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：: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：: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：: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：: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：: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：: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：: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：: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：: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