Paleontology, genomics, and combined-data phylogenetics: can molecular data improve phylogeny estimation for fossil taxa?

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：: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：: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：: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：: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：: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：: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：: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：:Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many group...

journal_title：Systematic biology

authors： Morard R,Escarguel G,Weiner AK,André A,Douady CJ,Wade CM,Darling KF,Ujiié Y,Seears HA,Quillévéré F,de Garidel-Thoron T,de Vargas C,Kucera M

更新日期：2016-09-01 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：:Young polyploid events are easily diagnosed by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes, pseudogenization or locus loss, and interlocus intera...

journal_title：Systematic biology

authors： Pfeil BE,Schlueter JA,Shoemaker RC,Doyle JJ

更新日期：2005-06-01 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：:Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, an...

journal_title：Systematic biology

authors： de Queiroz K

更新日期：2007-12-01 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：:Even though relationships within Annelida are poorly understood, Eunicida is one of only a few major annelid lineages well supported by morphology. The seven recognized eunicid families possess sclerotized jaws that include mandibles and a maxillary apparatus. The maxillary apparatuses vary in shape and number of elem...

journal_title：Systematic biology

authors： Struck TH,Purschke G,Halanych KM

更新日期：2006-02-01 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：: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：: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：: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：: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：:All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption...

journal_title：Systematic biology

authors： Huelsenbeck JP,Nielsen R

更新日期：1999-06-01 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：: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：: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：: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：: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：: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：: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：: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