Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Light sheet fluorescence microscopy

EHK Stelzer, F Strobl, BJ Chang, F Preusser… - Nature Reviews …, 2021 - nature.com
Light sheet fluorescence microscopy (LSFM) uses a thin sheet of light to excite only
fluorophores within the focal volume. Light sheet microscopes (LSMs) have a true optical …

Agricultural intensification and climate change are rapidly decreasing insect biodiversity

PH Raven, DL Wagner - Proceedings of the National …, 2021 - National Acad Sciences
Major declines in insect biomass and diversity, reviewed here, have become obvious and
well documented since the end of World War II. Here, we conclude that the spread and …

Scientists' warning to humanity on insect extinctions

P Cardoso, PS Barton, K Birkhofer, F Chichorro… - Biological …, 2020 - Elsevier
Here we build on the manifesto 'World Scientists' Warning to Humanity, issued by the
Alliance of World Scientists. As a group of conservation biologists deeply concerned about …

A species-level timeline of mammal evolution integrating phylogenomic data

S Álvarez-Carretero, AU Tamuri, M Battini… - Nature, 2022 - nature.com
High-throughput sequencing projects generate genome-scale sequence data for species-
level phylogenies,–. However, state-of-the-art Bayesian methods for inferring timetrees are …

Key innovations and the diversification of Hymenoptera

BB Blaimer, BF Santos, A Cruaud, MW Gates… - Nature …, 2023 - nature.com
The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most
diverse animal lineages, but whether specific key innovations have contributed to its …

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

AM Kozlov, D Darriba, T Flouri, B Morel… - …, 2019 - academic.oup.com
Motivation Phylogenies are important for fundamental biological research, but also have
numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree …

Origin of angiosperms and the puzzle of the Jurassic gap

HT Li, TS Yi, LM Gao, PF Ma, T Zhang, JB Yang… - Nature plants, 2019 - nature.com
Angiosperms are by far the most species-rich clade of land plants, but their origin and early
evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny …

BUSCO applications from quality assessments to gene prediction and phylogenomics

RM Waterhouse, M Seppey, FA Simão… - Molecular biology …, 2018 - academic.oup.com
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly
changing technologies and expanding data volumes make evaluation of completeness a …

New methods to calculate concordance factors for phylogenomic datasets

BQ Minh, MW Hahn, R Lanfear - Molecular biology and …, 2020 - academic.oup.com
We implement two measures for quantifying genealogical concordance in phylogenomic
data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF) …