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 …

[HTML][HTML] Metazoan micrornas

DP Bartel - Cell, 2018 - cell.com
MicroRNAs (miRNAs) are∼ 22 nt RNAs that direct posttranscriptional repression of mRNA
targets in diverse eukaryotic lineages. In humans and other mammals, these small RNAs …

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 …

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 …

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

C Hoencamp, O Dudchenko, AMO Elbatsh… - Science, 2021 - science.org
We investigated genome folding across the eukaryotic tree of life. We find two types of three-
dimensional (3D) genome architectures at the chromosome scale. Each type appears and …

[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 …

Evolution by gene loss

R Albalat, C Cañestro - Nature Reviews Genetics, 2016 - nature.com
The recent increase in genomic data is revealing an unexpected perspective of gene loss as
a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This …

A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals

P Simion, H Philippe, D Baurain, M Jager, DJ Richter… - Current biology, 2017 - cell.com
Resolving the early diversification of animal lineages has proven difficult, even using
genome-scale datasets. Several phylogenomic studies have supported the classical …

Contentious relationships in phylogenomic studies can be driven by a handful of genes

XX Shen, CT Hittinger, A Rokas - Nature ecology & evolution, 2017 - nature.com
Phylogenomic studies have resolved countless branches of the tree of life, but remain
strongly contradictory on certain, contentious relationships. Here, we use a maximum …