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Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event.

TLDR
It is proposed that polyploidization may have contributed to the survival and propagation of several plant lineages during or following the KT extinction event and might have been better able to adapt to the drastically changed environment 65 million years ago.
Abstract
Mostflowering plants have been shown to be ancient polyploids that have undergone one or more whole genome duplications early in their evolution. Furthermore, many different plant lineages seem to have experienced an additional, more recent genome duplication. Starting from paralogous genes lying in duplicated segments or identified in large expressed sequence tag collections, we dated these youngest duplication events through penalized likelihood phylogenetic tree inference. We show that a majority of these independent genome duplications are clustered in time and seem to coincide with the Cretaceous‐Tertiary (KT) boundary. The KT extinction event is the most recent mass extinction caused by one or more catastrophic events such as a massive asteroid impact and/or increasedvolcanicactivity.Theseeventsarebelievedtohavegenerated global wildfires and dust clouds that cut off sunlight during long periods of time resulting in the extinction of 60% of plant species, as well as a majority of animals, including dinosaurs. Recent studies suggest that polyploid species can have a higher adaptability and increased tolerance to different environmental conditions. We propose that polyploidization may have contributed to the survival and propagation of several plant lineages during or following the KT extinction event. Due to advantages such as altered gene expression leading to hybrid vigor and an increased set of genes and alleles available for selection, polyploid plants might have been better able to adapt to the drastically changed environment 65 million years ago. angiosperms eudicots Cretaceous–Tertiary boundary penalized likelihood polyploidy

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Journal ArticleDOI

Genome sequence and analysis of the tuber crop potato.

Xun Xu, +96 more
- 10 Jul 2011 - 
TL;DR: The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin.
Journal ArticleDOI

Ancestral polyploidy in seed plants and angiosperms

TL;DR: Comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages are used to elucidate two groups of ancient gene duplications, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms.
Journal ArticleDOI

The genome of the domesticated apple ( Malus × domestica Borkh.)

Riccardo Velasco, +90 more
- 01 Oct 2010 - 
TL;DR: It is shown that a relatively recent (>50 million years ago) genome-wide duplication has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae, which partly support the monophyly of the ancestral paleohexaploidy of eudicots.
Journal ArticleDOI

The evolutionary significance of polyploidy

TL;DR: How, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity is discussed.
Journal ArticleDOI

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

Andrew H. Paterson, +77 more
- 20 Dec 2012 - 
TL;DR: It is shown that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago, conferred about 30–36-fold duplication of ancestral angiosperm genes in elite cottons, genetic complexity equalled only by Brassica among sequenced angiosperms.
References
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Journal ArticleDOI

Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Journal ArticleDOI

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
Journal ArticleDOI

PAML 4: Phylogenetic Analysis by Maximum Likelihood

TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
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Relaxed Phylogenetics and Dating with Confidence

TL;DR: In this paper, the authors introduce a new approach to perform relaxed phylogenetic analysis, which can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times.
Journal ArticleDOI

PAML: a program package for phylogenetic analysis by maximum likelihood

TL;DR: The strength of PAML, in comparison with other phylogenetic packages currently available, is its implementation of a variety of evolutionary models, which include several models of variable evolutionary rates among sites, models for combined analyses of multiple gene sequence data and models for amino acid sequences.
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