8 Works

Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity

Jonathan L. Payne, Alison G. Boyer, James H. Brown, Seth Finnegan, Michal Kowaleski, , S. Kathleen Lyons, Craig R. McClain, Daniel W. McShea, Phillip M. Novack-Gottshall, Felisa A. Smith, Jennifer A. Stempien, Steve C. Wang, M. Kowalewski & R. A. Krause
NOTE: See also http://bodysize.nescent.org. ABSTRACT: The maximum size of organisms has increased enormously since the initial appearance of life >3.5 billion years ago (Gya), but the pattern and timing of this size increase is poorly known. Consequently, controls underlying the size spectrum of the global biota have been difficult to evaluate. Our period-level compilation of the largest known fossil organisms demonstrates that maximum size increased by 16 orders of magnitude since life first appeared in...

Data from: Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Stefanie Hartmann, André Wehe & Todd J. Vision
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony is a phylogenetic optimization criterion in which a species tree is selected that minimizes the number of gene duplications induced among a set of gene trees. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic...

Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster

Greg Gibson, Rebecca Riley-Berger, Larry Harshman, Artyom Kopp, Scott Vacha, Sergey Nuzhdin & Marta Wayne
Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least...

Data from: Phylogenetic assessment of molecular and morphological data for eutherian mammals

Fu-Guo R. Liu & Michael M. Miyamoto
The interordinal relationships of eutherian (placental) mammals were evaluated by a phylogenetic analysis of four published data sets (three sequence and one morphological). The nature and degree of support and conflict for particular groups were assessed by separate bootstrap and homogeneity tests that were followed by combined analyses of the sequence and morphological data. Between orders, strong support (i.e., >95% bootstrap scores) was found for a paraphyletic Artiodactyla (relative to Cetacea) and a monophyletic Cetartiodactyla...

Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity

Jonathan L. Payne, Alison G. Boyer, James H. Brown, Seth Finnegan, Michal Kowaleski, , S. Kathleen Lyons, Craig R. McClain, Daniel W. McShea, Phillip M. Novack-Gottshall, Felisa A. Smith, Jennifer A. Stempien, Steve C. Wang, D. W. McShea, M. Kowalewski, J. L. Payne, R. A. Krause, S. C. Wang, P. M. Novack-Gottshall, A. G. Boyer, J. H. Brown & F. A. Smith
NOTE: See also http://bodysize.nescent.org. ABSTRACT: The maximum size of organisms has increased enormously since the initial appearance of life >3.5 billion years ago (Gya), but the pattern and timing of this size increase is poorly known. Consequently, controls underlying the size spectrum of the global biota have been difficult to evaluate. Our period-level compilation of the largest known fossil organisms demonstrates that maximum size increased by 16 orders of magnitude since life first appeared in...

Data from: Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Stefanie Hartmann, André Wehe & Todd J. Vision
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony is a phylogenetic optimization criterion in which a species tree is selected that minimizes the number of gene duplications induced among a set of gene trees. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic...

Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster

Greg Gibson, Rebecca Riley-Berger, Larry Harshman, Artyom Kopp, Scott Vacha, Sergey Nuzhdin & Marta Wayne
Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least...

Data from: Phylogenetic assessment of molecular and morphological data for eutherian mammals

Fu-Guo R. Liu & Michael M. Miyamoto
The interordinal relationships of eutherian (placental) mammals were evaluated by a phylogenetic analysis of four published data sets (three sequence and one morphological). The nature and degree of support and conflict for particular groups were assessed by separate bootstrap and homogeneity tests that were followed by combined analyses of the sequence and morphological data. Between orders, strong support (i.e., >95% bootstrap scores) was found for a paraphyletic Artiodactyla (relative to Cetacea) and a monophyletic Cetartiodactyla...

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