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 …

Rates of evolutionary change in viruses: patterns and determinants

S Duffy, LA Shackelton, EC Holmes - Nature Reviews Genetics, 2008 - nature.com
Understanding the factors that determine the rate at which genomes generate and fix
mutations provides important insights into key evolutionary mechanisms. We review our …

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 …

SIFT missense predictions for genomes

R Vaser, S Adusumalli, SN Leng, M Sikic, PC Ng - Nature protocols, 2016 - nature.com
The SIFT (sorting intolerant from tolerant) algorithm helps bridge the gap between mutations
and phenotypic variations by predicting whether an amino acid substitution is deleterious …

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 …

The developmental transcriptome of Drosophila melanogaster

BR Graveley, AN Brooks, JW Carlson, MO Duff… - Nature, 2011 - nature.com
Drosophila melanogaster is one of the most well studied genetic model organisms;
nonetheless, its genome still contains unannotated coding and non-coding genes …

The Drosophila melanogaster Genetic Reference Panel

TFC Mackay, S Richards, EA Stone, A Barbadilla… - Nature, 2012 - nature.com
A major challenge of biology is understanding the relationship between molecular genetic
variation and variation in quantitative traits, including fitness. This relationship determines …

Phylosymbiosis: relationships and functional effects of microbial communities across host evolutionary history

AW Brooks, KD Kohl, RM Brucker, EJ van Opstal… - PLoS …, 2016 - journals.plos.org
Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern, whereby
the ecological relatedness of host-associated microbial communities parallels the phylogeny …

Genomic architecture and introgression shape a butterfly radiation

NB Edelman, PB Frandsen, M Miyagi, B Clavijo… - Science, 2019 - science.org
We used 20 de novo genome assemblies to probe the speciation history and architecture of
gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete …

The cytochrome p450 homepage

DR Nelson - Human genomics, 2009 - Springer
Abstract The Cytochrome P450 Homepage is a universal resource for nomenclature and
sequence information on cytochrome P450 (CYP) genes. The site has been in continuous …