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Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales
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 systematicsExpand
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Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies.
The molecular era has fundamentally reshaped our knowledge of the evolution and diversification of angiosperms. One outstanding question is the phylogenetic placement of Amborella trichopoda Baill.,Expand
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.
In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispeciesExpand
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Estimating phylogenetic trees from genome‐scale data
The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as “species tree” methods have been proposed toExpand
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Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade
Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided theExpand
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Horizontal transfer of expressed genes in a parasitic flowering plant
BackgroundRecent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimateExpand
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Phylogeny of the clusioid clade (Malpighiales): evidence from the plastid and mitochondrial genomes.
PREMISE OF THE STUDY The clusioid clade includes five families (i.e., Bonnetiaceae, Calophyllaceae, Clusiaceae s.s., Hypericaceae, and Podostemaceae) represented by 94 genera and ≈1900 species.Expand
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The Impact of Missing Data on Species Tree Estimation.
Phylogeneticists are increasingly assembling genome-scale data sets that include hundreds of genes to resolve their focal clades. Although these data sets commonly include a moderate to high amountExpand
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Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting.
It is well known that species with elevated substitution rates can give rise to disproportionately long branches in the species tree. This combination of long and short branches can contribute toExpand
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Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region
Recent plastid phylogenomic studies have helped clarify the backbone phylogeny of angiosperms. However, the relatively limited taxon sampling in these studies has precluded strongly supportedExpand
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