Tracing the decay of the historical signal in biological sequence 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：: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 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：: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：:Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topolog...

journal_title：Systematic biology

authors： Zhang C,Huelsenbeck JP,Ronquist F

更新日期：2020-09-01 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：: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：: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：: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：: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：:The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be...

journal_title：Systematic biology

authors： Mueller RL

更新日期：2006-04-01 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：:Previous phylogenetic analyses of tetrapod 18S ribosomal RNA (rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as "definitive ...

journal_title：Systematic biology

authors： Xia X,Xie Z,Kjer KM

更新日期：2003-06-01 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：: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：: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 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：: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：: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：:Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). Howe...

journal_title：Systematic biology

authors： Blair C,Ané C

更新日期：2020-05-01 00:00:00

abstract：:The impact of incomplete lineage sorting (ILS) on phylogenetic conflicts among genes, and the related issue of whether to account for ILS in species tree reconstruction, are matters of intense controversy. Here, focusing on full-genome data in placental mammals, we empirically test two assumptions underlying current u...

journal_title：Systematic biology

authors： Scornavacca C,Galtier N

更新日期：2017-01-01 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：: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：: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：:Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provi...

journal_title：Systematic biology

authors： Pérez-Escobar OA,Balbuena JA,Gottschling M

更新日期：2016-01-01 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：: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：:Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for th...

journal_title：Systematic biology

authors： Behdenna A,Pothier J,Abby SS,Lambert A,Achaz G

更新日期：2016-09-01 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：: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