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Noah A Rosenberg - One of the best experts on this subject based on the ideXlab platform.
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the probability of reciprocal Monophyly of gene lineages in three and four species
Theoretical Population Biology, 2019Co-Authors: Rohan S Mehta, Noah A RosenbergAbstract:Abstract Reciprocal Monophyly, a feature of a genealogy in which multiple groups of descendant lineages each consist of all of the descendants of their respective most recent common ancestors, has been an important concept in studies of species delimitation, phylogeography, population history reconstruction, systematics, and conservation. Computations involving the probability that reciprocal Monophyly is observed in a genealogy have played a key role in criteria for defining taxonomic groups and inferring divergence times. The probability of reciprocal Monophyly under a coalescent model of population divergence has been studied in detail for groups of gene lineages for pairs of species. Here, we extend this computation to generate corresponding probabilities for sets of gene lineages from three and four species. We study the effects of model parameters on the probability of reciprocal Monophyly, finding that it is driven primarily by species tree height, with lesser but still substantial influences of internal branch lengths and sample sizes. We also provide an example application of our results to data from maize and teosinte.
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the probability of Monophyly of a sample of gene lineages on a species tree
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Rohan S Mehta, David Bryant, Noah A RosenbergAbstract:Monophyletic groups—groups that consist of all of the descendants of a most recent common ancestor—arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of Monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of Monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species tree model that contains arbitrarily many species. We study the effects of species tree topology and branch lengths on the Monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial Monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte.
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statistical tests for taxonomic distinctiveness from observations of Monophyly
Evolution, 2007Co-Authors: Noah A RosenbergAbstract:The observation of Monophyly for a specified set of genealogical lineages is often used to place the lineages into a distinctive taxonomic entity. However, it is sometimes possible that Monophyly of the lineages can occur by chance as an outcome of the random branching of lineages within a single taxon. Thus, especially for small samples, an observation of Monophyly for a set of lineages—even if strongly supported statistically—does not necessarily indicate that the lineages are from a distinctive group. Here I develop a test of the null hypothesis that Monophyly is a chance outcome of random branching. I also compute the sample size required so that the probability of chance occurrence of Monophyly of a specified set of lineages lies below a prescribed tolerance. Under the null model of random branching, the probability that Monophyly of the lineages in an index group occurs by chance is substantial if the sample is highly asymmetric, that is, if only a few of the sampled lineages are from the index group, or if only a few lineages are external to the group. If sample sizes are similar inside and outside the group of interest, however, chance occurrence of Monophyly can be rejected at stringent significance levels (P < 10−5) even for quite small samples (≈ 20 total lineages). For a fixed total sample size, rejection of the null hypothesis of random branching in a single taxon occurs at the most stringent level if samples of nearly equal size inside and outside the index group—with a slightly greater size within the index group—are used. Similar results apply, with smaller sample sizes needed, when reciprocal Monophyly of two groups, rather than Monophyly of a single group, is of interest. The results suggest minimal sample sizes required for inferences to be made about taxonomic distinctiveness from observations of Monophyly.
Bruce A Mcpheron - One of the best experts on this subject based on the ideXlab platform.
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molecular phylogenetic study of tephritidae insecta diptera using partial sequences of the mitochondrial 16s ribosomal dna
Molecular Phylogenetics and Evolution, 1997Co-Authors: Bruce A McpheronAbstract:Abstract We analyzed sequence data from 925 base pairs within the mitochondrial 16S ribosomal DNA from 34 tephritid species and two outgroup taxa. DNA sequences were amplified by the polymerase chain reaction and sequenced by the dideoxy chain-termination method. Patterns of nucleotide composition and substitution were assessed based on sequence comparison. Phylogenetic relationships among the included taxa were inferred using neighbor-joining and maximum parsimony methods. The trees were congruent with the morphological classification and suggested the following phylogenetic relationships: (1) Monophyly of the tribe Trypetini, s. str., excludingParastenopa;(2) a possible sister group relationship betweenPlatypareaand the subfamily Tephritinae; (3) a sister group relationship betweenHexachaetaand the tribe Toxotrypanini; (4) Monophyly of the Dacinae and possible relationship ofOedicarenato this subfamily; (5) Monophyly of the tribe Adramini; and (6) the nonmonophyletic nature of the genusRhagoletis.We propose that the 16S rDNA shows great promise for helping to create a phylogenetically based higher classification of the Tephritidae.
Elena Alvarezbuylla - One of the best experts on this subject based on the ideXlab platform.
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phylogenetics ofpinus pinaceae based on nuclear ribosomal dna internal transcribed spacer region sequences
Molecular Phylogenetics and Evolution, 1999Co-Authors: Aaron Liston, William A Robinson, Daniel Pinero, Elena AlvarezbuyllaAbstract:Abstract A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species ofPinus,representing all recognized subsections of the genus, and 2 species ofPiceaandCathayaas outgroups. Parsimony analyses of these length variable sequences were conducted using a manual alignment, 13 different automated alignments, elision of the automated alignments, and exclusion of all alignment ambiguous sites. High and moderately supported clades were consistently resolved across the different analyses, while poorly supported clades were inconsistently recovered. Comparison of the topologies highlights taxa of particularly problematic placement includingPinus nelsoniiandP. aristata.Within subgenusPinus,there is moderate support for the Monophyly of a narrowly circumscribed subsect.Pinus(=subsect.Sylvestres) and strong support for a clade of North and Central American hard pines. The HimalayanP. roxburghiimay be sister species to these “New World hard pines,” which have two well-supported subgroups, subsect.Ponderosaeand a clade of the remaining five subsections. The position of subsect.Contortaeconflicts with its placement in a chloroplast DNA restriction site study. Within subgenusStrobusthere is consistent support for the Monophyly of a broadly circumscribed subsect.Strobi(includingP. krempfiiand a polyphyletic subsect.Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects.Gerardianae, Cembroides,andBalfourianaeare poorly resolved. Support for the Monophyly of subgenusPinusand subgenusStrobusis not consistently obtained.
Mikael Thollesson - One of the best experts on this subject based on the ideXlab platform.
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Bilaterian Phylogeny Based on Analyses of a Region of the Sodium–Potassium ATPase β-Subunit Gene
Journal of Molecular Evolution, 2004Co-Authors: Frank E. Anderson, Alonso J. Córdoba, Mikael ThollessonAbstract:Molecular investigations of deep-level relationships within and among the animal phyla have been hampered by a lack of slowly evolving genes that are amenable to study by molecular systematists. To provide new data for use in deep-level metazoan phylogenetic studies, primers were developed to amplify a 1.3-kb region of the α subunit of the nuclear-encoded sodium–potassium ATPase gene from 31 bilaterians representing several phyla. Maximum parsimony, maximum likelihood, and Bayesian analyses of these sequences (combined with ATPase sequences for 23 taxa downloaded from GenBank) yield congruent trees that corroborate recent findings based on analyses of other data sets (e.g., the 18S ribosomal RNA gene). The ATPase-based trees support Monophyly for several clades (including Lophotrochozoa, a form of Ecdysozoa, Vertebrata, Mollusca, Bivalvia, Gastropoda, Arachnida, Hexapoda, Coleoptera, and Diptera) but do not support Monophyly for Deuterostomia, Arthropoda, or Nemertea. Parametric bootstrapping tests reject Monophyly for Arthropoda and Nemertea but are unable to reject deuterostome Monophyly. Overall, the sodium–potassium ATPase α-subunit gene appears to be useful for deep-level studies of metazoan phylogeny.
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Bilaterian phylogeny based on analyses of a region of the sodium-potassium ATPase beta-subunit gene.
Journal of Molecular Evolution, 2004Co-Authors: Frank E. Anderson, Alonso J. Córdoba, Mikael ThollessonAbstract:Molecular investigations of deep-level relationships within and among the animal phyla have been hampered by a lack of slowly evolving genes that are amenable to study by molecular systematists. To provide new data for use in deep-level metazoan phylogenetic studies, primers were developed to amplify a 1.3-kb region of the α subunit of the nuclear-encoded sodium–potassium ATPase gene from 31 bilaterians representing several phyla. Maximum parsimony, maximum likelihood, and Bayesian analyses of these sequences (combined with ATPase sequences for 23 taxa downloaded from GenBank) yield congruent trees that corroborate recent findings based on analyses of other data sets (e.g., the 18S ribosomal RNA gene). The ATPase-based trees support Monophyly for several clades (including Lophotrochozoa, a form of Ecdysozoa, Vertebrata, Mollusca, Bivalvia, Gastropoda, Arachnida, Hexapoda, Coleoptera, and Diptera) but do not support Monophyly for Deuterostomia, Arthropoda, or Nemertea. Parametric bootstrapping tests reject Monophyly for Arthropoda and Nemertea but are unable to reject deuterostome Monophyly. Overall, the sodium–potassium ATPase α-subunit gene appears to be useful for deep-level studies of metazoan phylogeny.
Aaron Liston - One of the best experts on this subject based on the ideXlab platform.
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phylogenetics ofpinus pinaceae based on nuclear ribosomal dna internal transcribed spacer region sequences
Molecular Phylogenetics and Evolution, 1999Co-Authors: Aaron Liston, William A Robinson, Daniel Pinero, Elena AlvarezbuyllaAbstract:Abstract A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species ofPinus,representing all recognized subsections of the genus, and 2 species ofPiceaandCathayaas outgroups. Parsimony analyses of these length variable sequences were conducted using a manual alignment, 13 different automated alignments, elision of the automated alignments, and exclusion of all alignment ambiguous sites. High and moderately supported clades were consistently resolved across the different analyses, while poorly supported clades were inconsistently recovered. Comparison of the topologies highlights taxa of particularly problematic placement includingPinus nelsoniiandP. aristata.Within subgenusPinus,there is moderate support for the Monophyly of a narrowly circumscribed subsect.Pinus(=subsect.Sylvestres) and strong support for a clade of North and Central American hard pines. The HimalayanP. roxburghiimay be sister species to these “New World hard pines,” which have two well-supported subgroups, subsect.Ponderosaeand a clade of the remaining five subsections. The position of subsect.Contortaeconflicts with its placement in a chloroplast DNA restriction site study. Within subgenusStrobusthere is consistent support for the Monophyly of a broadly circumscribed subsect.Strobi(includingP. krempfiiand a polyphyletic subsect.Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects.Gerardianae, Cembroides,andBalfourianaeare poorly resolved. Support for the Monophyly of subgenusPinusand subgenusStrobusis not consistently obtained.
