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] The evolution of aging and lifespan

S Li, JM Vazquez, PH Sudmant - Trends in Genetics, 2023 - cell.com
Aging is a nearly inescapable trait among organisms yet lifespan varies tremendously
across different species and spans several orders of magnitude in vertebrates alone. This …

Evolutionary constraint and innovation across hundreds of placental mammals

MJ Christmas, IM Kaplow, DP Genereux, MX Dong… - Science, 2023 - science.org
Zoonomia is the largest comparative genomics resource for mammals produced to date. By
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …

Origins and evolution of extreme life span in Pacific Ocean rockfishes

SRR Kolora, GL Owens, JM Vazquez, A Stubbs… - Science, 2021 - science.org
Pacific Ocean rockfishes (genus Sebastes) exhibit extreme variation in life span, with some
species being among the most long-lived extant vertebrates. We de novo assembled the …

Convergent regulatory evolution and loss of flight in paleognathous birds

TB Sackton, P Grayson, A Cloutier, Z Hu, JS Liu… - Science, 2019 - science.org
A core question in evolutionary biology is whether convergent phenotypic evolution is driven
by convergent molecular changes in proteins or regulatory regions. We combined …

The genomic basis of temporal niche evolution in a diurnal rodent

R Richardson, CY Feigin, B Bano-Otalora, MR Johnson… - Current Biology, 2023 - cell.com
Patterns of diel activity—how animals allocate their activity throughout the 24-h daily cycle—
play key roles in shaping the internal physiology of an animal and its relationship with the …

A multifunctional Wnt regulator underlies the evolution of rodent stripe patterns

MR Johnson, S Li, CF Guerrero-Juarez… - Nature ecology & …, 2023 - nature.com
Animal pigment patterns are excellent models to elucidate mechanisms of biological
organization. Although theoretical simulations, such as Turing reaction–diffusion systems …

[HTML][HTML] Pan-mammalian analysis of molecular constraints underlying extended lifespan

A Kowalczyk, R Partha, NL Clark, M Chikina - Elife, 2020 - elifesciences.org
Although lifespan in mammals varies over 100-fold, the precise evolutionary mechanisms
underlying variation in longevity remain unknown. Species-specific genetic changes have …

PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts on targeted lineages accounting for gene tree discordance

H Yan, Z Hu, GWC Thomas, SV Edwards… - Molecular Biology …, 2023 - academic.oup.com
An important goal of evolutionary genomics is to identify genomic regions whose substitution
rates differ among lineages. For example, genomic regions experiencing accelerated …

[HTML][HTML] Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence

K Fukushima, DD Pollock - Nature Ecology & Evolution, 2023 - nature.com
On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask
the signals of genotype–phenotype associations underlying convergent evolution. To …