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Full-Text Articles in Life Sciences
A Phylogeny Of Belonolaimus Populations In Florida Inferred From Dna Sequences, Byron Adams, U. Gozel, K. Nguyen, R. Inserra, R. Giblin-Davis
A Phylogeny Of Belonolaimus Populations In Florida Inferred From Dna Sequences, Byron Adams, U. Gozel, K. Nguyen, R. Inserra, R. Giblin-Davis
Byron Adams
The D2-D3 and ITS regions of rDNA from 33 Florida populations of Belonolaimus spp. were sequenced and subjected to phylogenetic analysis. Our objective was to derive a theoretical evolutionary framework for interpreting phenotypic differences as they relate to the taxonomy of the genus. The most striking aspect of the phylogenetic analysis is that none of the three nominal species (B. longicaudatus, B. euthychilus, and B. gracilis) are monophyletic. Additionally, two taxa appear to have discordant ITS and LSU sequences. Three major clades of B. longicaudatus exhibited discernible, overlapping, geographic foci from east to west across the peninsula. Morphological character states …
Another Look At The Root Of The Angiosperms Reveals A Familiar Tale, Bryan Drew, Brad Ruhfel, Stephen Smith, Michael Moore, Barbara Briggs, Matthew Gitzendanner, Pamela Soltis, Douglas Soltis
Another Look At The Root Of The Angiosperms Reveals A Familiar Tale, Bryan Drew, Brad Ruhfel, Stephen Smith, Michael Moore, Barbara Briggs, Matthew Gitzendanner, Pamela Soltis, Douglas Soltis
Brad R. Ruhfel
Since the advent of molecular phylogenetics more than 25 years ago, a major goal of plant systematists has been to discern the root of the angiosperms. Although most studies indicate that Amborella trichopoda is sister to all remaining extant flowering plants, support for this position has varied with respect to both the sequence data sets and analyses employed. Recently, Goremykin et al. (2013) questioned the “Amborella-sister hypothesis” using a “noise-reduction” approach and reported a topology with Amborella + Nymphaeales (water lilies) sister to all remaining angiosperms. Through a series of analyses of both plastid genomes and mitochondrial genes, we continue …
Combined Morphological And Molecular Phylogeny Of The Clusioid Clade (Malpighiales) And The Placement Of The Ancient Rosid Macrofossil Paleoclusia, Brad Ruhfel, Peter Stevens, Charles Davis
Combined Morphological And Molecular Phylogeny Of The Clusioid Clade (Malpighiales) And The Placement Of The Ancient Rosid Macrofossil Paleoclusia, Brad Ruhfel, Peter Stevens, Charles Davis
Brad R. Ruhfel
Premise of research. The clusioid clade is a member of the large rosid order Malpighiales and contains∼1900 species in five families: Bonnetiaceae, Calophyllaceae, Clusiaceae sensu stricto (s.s.), Hypericaceae, and Podostemaceae. Despite recent efforts to clarify their phylogenetic relationships using molecular data, no such data are available for several critical taxa, including especially Hypericum ellipticifolium (previously recognized in Lianthus), Lebrunia, Neotatea, Thysanostemon, and the second-oldest rosid fossil (∼90 Ma), Paleoclusia chevalieri. Here, we (i) assess congruence between phylogenies inferred from morphological and molecular data, (ii) analyze morphological and molecular data simultaneously to place taxa lacking molecular data, and (iii) use ancestral …
Phylogenomics And A Posteriori Data Partitioning Resolve The Cretaceous Angiosperm Radiation Malpighiales, Zhenxiang Xi, Brad Ruhfel, Hanno Schaefer, André Amorim, M. Sugumaran, Kenneth Wurdack, Peter Endress, Merran Matthews, Peter Stevens, Sarah Mathews, Charles Davis
Phylogenomics And A Posteriori Data Partitioning Resolve The Cretaceous Angiosperm Radiation Malpighiales, Zhenxiang Xi, Brad Ruhfel, Hanno Schaefer, André Amorim, M. Sugumaran, Kenneth Wurdack, Peter Endress, Merran Matthews, Peter Stevens, Sarah Mathews, Charles Davis
Brad R. Ruhfel
The angiosperm order Malpighiales includes ∼16,000 species and constitutes up to 40% of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm systematics during the last 20 y, relationships within Malpighiales remain poorly resolved, possibly owing to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 additional clades in Malpighiales and substantially increased resolution along the backbone. This greatly improved phylogeny revealed a dynamic history of shifts in net diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas …
Maximum Likelihood Estimates Of Species Trees: How Accuracy Of Phylogenetic Inference Depends Upon The Divergence History And Sampling Design, John Mccormack, Huateng Huang, L. Knowles
Maximum Likelihood Estimates Of Species Trees: How Accuracy Of Phylogenetic Inference Depends Upon The Divergence History And Sampling Design, John Mccormack, Huateng Huang, L. Knowles
John E. McCormack
The understanding that gene trees are often in discord with each other and with the species trees that contain them has led researchers to methods that incorporate the inherent stochasticity of genetic processes in the phylogenetic estimation procedure. Recently developed methods for species-tree estimation that not only consider the retention and sorting of ancestral polymorphism but also quantify the actual probabilities of incomplete lineage sorting are expected to provide an improvement over earlier summary-statistic based approaches that discard much of the information content of gene trees. However, these new methods have yet to be tested on truly challenging evolutionary histories …