Whole-genome duplication and plant macroevolution

JW Clark, PCJ Donoghue - Trends in plant science, 2018 - cell.com
Whole-genome duplication (WGD) is characteristic of almost all fundamental lineages of
land plants. Unfortunately, the timings of WGD events are loosely constrained and …

[HTML][HTML] Handling multi-mapped reads in RNA-seq

G Deschamps-Francoeur, J Simoneau… - Computational and …, 2020 - Elsevier
Many eukaryotic genomes harbour large numbers of duplicated sequences, of diverse
biotypes, resulting from several mechanisms including recombination, whole genome …

The evolution of a tropical biodiversity hotspot

MG Harvey, GA Bravo, S Claramunt, AM Cuervo… - Science, 2020 - science.org
The tropics are the source of most biodiversity yet inadequate sampling obscures answers to
fundamental questions about how this diversity evolves. We leveraged samples assembled …

Constructing a broadly inclusive seed plant phylogeny

SA Smith, JW Brown - American journal of botany, 2018 - Wiley Online Library
Premise of the Study Large phylogenies can help shed light on macroevolutionary patterns
that inform our understanding of fundamental processes that shape the tree of life. These …

Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms

GW Stull, XJ Qu, C Parins-Fukuchi, YY Yang, JB Yang… - Nature Plants, 2021 - nature.com
Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity
across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy …

[HTML][HTML] Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Y Liu, MG Johnson, CJ Cox, R Medina, N Devos… - Nature …, 2019 - nature.com
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least
400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive …

[HTML][HTML] So many genes, so little time: a practical approach to divergence-time estimation in the genomic era

SA Smith, JW Brown, JF Walker - PloS one, 2018 - journals.plos.org
Phylogenomic datasets have been successfully used to address questions involving
evolutionary relationships, patterns of genome structure, signatures of selection, and gene …

Quartet sampling distinguishes lack of support from conflicting support in the green plant tree of life

JB Pease, JW Brown, JF Walker… - American journal of …, 2018 - Wiley Online Library
Premise of the Study Phylogenetic support has been difficult to evaluate within the green
plant tree of life partly due to a lack of specificity between conflicted versus poorly informed …

Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity

LA Nikolov, P Shushkov, B Nevado, X Gan… - New …, 2019 - Wiley Online Library
The Brassicaceae family comprises c. 4000 species including economically important crops
and the model plant Arabidopsis thaliana. Despite their importance, the relationships among …

Plastid phylogenomic insights into the evolution of Caryophyllales

G Yao, JJ Jin, HT Li, JB Yang, VS Mandala… - Molecular Phylogenetics …, 2019 - Elsevier
The Caryophyllales includes 40 families and 12,500 species, representing a large and
diverse clade of angiosperms. Collectively, members of the clade grow on all continents and …