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Journal ArticleDOI

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

TLDR
This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous.
Abstract
The establishment of modern terrestrial life is indissociable from angiosperm evolution. While available molecular clock estimates of angiosperm age range from the Paleozoic to the Late Cretaceous, the fossil record is consistent with angiosperm diversification in the Early Cretaceous. The time-frame of angiosperm evolution is here estimated using a sample representing 87% of families and sequences of five plastid and nuclear markers, implementing penalized likelihood and Bayesian relaxed clocks. A literature-based review of the palaeontological record yielded calibrations for 137 phylogenetic nodes. The angiosperm crown age was bound within a confidence interval calculated with a method that considers the fossil record of the group. An Early Cretaceous crown angiosperm age was estimated with high confidence. Magnoliidae, Monocotyledoneae and Eudicotyledoneae diversified synchronously 135-130 million yr ago (Ma); Pentapetalae is 126-121 Ma; and Rosidae (123-115 Ma) preceded Asteridae (119-110 Ma). Family stem ages are continuously distributed between c. 140 and 20 Ma. This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous. While substantial amounts of angiosperm morphological and functional diversity have deep evolutionary roots, extant species richness was probably acquired later.

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Andean uplift, drainage basin formation, and the evolution of plants living in fast-flowing aquatic ecosystems in northern South America

TL;DR: In this article, the role of landscape change on the evolution of plants living strictly in rivers across drainage basins in northern South America by conducting population structure, phylogenetic inference, and divergence-dating analyses for two species in the genus Marathrum (Podostemaceae).
Posted ContentDOI

The dynamics of stem and crown groups

TL;DR: This work model the diversity of “stem” and “crown” members of groups as seen in the fossil record, using a “birth-death model”, finding that under background conditions, the stem group members must diversify rapidly until the modern crown group emerges, at which point their diversity rapidly collapses, followed shortly by their extinction.
Journal ArticleDOI

Fossil papilionoids of the Bowdichia clade (Leguminosae) from the Paleogene of North America

TL;DR: These fossils demonstrate that the tropical American Bowdichia clade was present in North America during a period when tropical or subtropical conditions prevailed in the northern Rocky Mountains during the late Paleocene and the Mississippi Embayment during the middle Eocene.
Journal ArticleDOI

Single-cell transcriptomics unveils xylem cell development and evolution

TL;DR: In this article , the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms were determined through both single-cell and laser capture microdissection transcriptomic profiling.
References
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Journal ArticleDOI

MUSCLE: multiple sequence alignment with high accuracy and high throughput

TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space

TL;DR: The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly, and provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates.
Journal ArticleDOI

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Proceedings ArticleDOI

Creating the CIPRES Science Gateway for inference of large phylogenetic trees

TL;DR: Development of the CIPRES Science Gateway is described, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources.
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