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 …

The origin and evolution of cell types

D Arendt, JM Musser, CVH Baker, A Bergman… - Nature Reviews …, 2016 - nature.com
Cell types are the basic building blocks of multicellular organisms and are extensively
diversified in animals. Despite recent advances in characterizing cell types, classification …

[HTML][HTML] Ancient gene linkages support ctenophores as sister to other animals

DT Schultz, SHD Haddock, JV Bredeson, RE Green… - Nature, 2023 - nature.com
A central question in evolutionary biology is whether sponges or ctenophores (comb jellies)
are the sister group to all other animals. These alternative phylogenetic hypotheses imply …

[HTML][HTML] AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

TC Terwilliger, D Liebschner, TI Croll, CJ Williams… - Nature …, 2024 - nature.com
Artificial intelligence-based protein structure prediction methods such as AlphaFold have
revolutionized structural biology. The accuracies of these predictions vary, however, and …

Deeply conserved synteny and the evolution of metazoan chromosomes

O Simakov, J Bredeson, K Berkoff, F Marletaz… - Science …, 2022 - science.org
Animal genomes show networks of deeply conserved gene linkages whose phylogenetic
scope and chromosomal context remain unclear. Here, we report chromosome-scale …

[图书][B] The evolution of the sensitive soul: Learning and the origins of consciousness

S Ginsburg, E Jablonka - 2019 - books.google.com
A new theory about the origins of consciousness that finds learning to be the driving force in
the evolutionary transition to basic consciousness. What marked the evolutionary transition …

[HTML][HTML] Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Q Zhu, U Mai, W Pfeiffer, S Janssen, F Asnicar… - Nature …, 2019 - nature.com
Rapid growth of genome data provides opportunities for updating microbial evolutionary
relationships, but this is challenged by the discordant evolution of individual genes. Here we …

Revisiting metazoan phylogeny with genomic sampling of all phyla

CE Laumer, R Fernández, S Lemer… - … of the royal …, 2019 - royalsocietypublishing.org
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of
key taxa—or fail when such key taxa are not sampled. In this light, we here present the first …

[HTML][HTML] Phylum Nematoda: a classification, catalogue and index of valid genera, with a census of valid species

M Hodda - Zootaxa, 2022 - biotaxa.org
A classification of the entire Phylum Nematoda is presented, based on current molecular,
developmental and morphological evidence. The classification reflects the evolutionary …

[HTML][HTML] Comparative genomics of the major parasitic worms

Nature genetics, 2019 - nature.com
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating
chronic infections of humans and animals, decimate crop production and are a major …