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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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Fundamentals of molecular evolution

TL;DR: Fundamentals of Molecular Evolution Dan Graur, Wen ...
Journal ArticleDOI

Constructing a broadly inclusive seed plant phylogeny.

TL;DR: This study demonstrates a means for combining available resources to construct a dated phylogeny for plants by combining genetic data from public repositories with phylogenetic data from Open Tree of Life, resulting in a seed plant phylogeny.
Journal ArticleDOI

The pineapple genome and the evolution of CAM photosynthesis

Ray Ming, +74 more
- 01 Dec 2015 - 
TL;DR: The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues, providing the first cis-regulatory link between CAM and circadian clock regulation.
Journal ArticleDOI

Evolutionary history of Coleoptera revealed by extensive sampling of genes and species.

TL;DR: A time-calibrated phylogeny for Coleoptera is infer based on 95 protein-coding genes in 373 beetle species and an association between the hyperdiversification of beetles and the rise of angiosperms is suggested.
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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