Flexible use of conserved motifs constrains genome access in cell type evolution.

Terminal selector and subtype selector function across 200 million years of nematode evolution

The evolution of brains is subject to investigation in many different animal groups, each offering unique advantages to advance our understanding of the cellular, molecular and regulatory substrates of evolutionary change. Here, we use two nematode species, C. elegans and P. pacificus, separated by more than 200 millio...

The origin of taxonomically restricted genes in yeast

Coevolutionary mining of prokaryotic non-coding elements with a genome language model

Microbial genomes encode non-coding RNAs (ncRNAs) and nucleic-acid-interacting proteins essential to biology and biotechnology. However, discovery of these systems remains protein-centric and based on similarity to known sequences. Here, we introduce Minerva, a framework for coevolutionary mining that uses genome langu...

Concentrating cell-type-specific transcriptional signatures in bone marrow from interspecies comparisons.

Cell-type definition is commonly achieved using marker genes. Because cell types are broadly conserved across evolution, marker genes are identifiable via interspecies comparisons. We generated single-cell RNA sequencing datasets of bone marrow niche and hematopoietic progenitor compartments from four mouse species. Us...

Rates of Evolution Differ Between Cell Types Identified by Single‐Cell RNAseq in Threespine Stickleback

ABSTRACT Rates of evolutionary change vary by gene. While some broad gene categories are highly conserved with little divergence over time, others undergo continuous selection pressure and are highly divergent among populations or species. But such comparative evolutionary studies rely on gene ontology categories that...

Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans.

Humans exhibit significant phenotypic differences from other great apes, yet pinpointing the underlying genetic changes has been limited by incomplete reference genomes and a reliance on single assemblies to represent a species. We aligned 20 telomere-to-telomere (T2T) assemblies spanning great ape divergence and varia...