Expression divergence between duplicate genes

WH Li, J Yang, X Gu - TRENDS in Genetics, 2005 - cell.com
A general picture of the role of expression divergence in the evolution of duplicate genes is
emerging, thanks to the availability of completely sequenced genomes and functional …

Evaluating the role of natural selection in the evolution of gene regulation

JC Fay, PJ Wittkopp - Heredity, 2008 - nature.com
Surveys of gene expression reveal extensive variability both within and between a wide
range of species. Compelling cases have been made for adaptive changes in gene …

Detecting signatures of selection on gene expression

PD Price, DH Palmer Droguett, JA Taylor… - Nature Ecology & …, 2022 - nature.com
A substantial amount of phenotypic diversity results from changes in gene expression levels
and patterns. Understanding how the transcriptome evolves is therefore a key priority in …

Efficient control of population structure in model organism association map**

HM Kang, NA Zaitlen, CM Wade, A Kirby… - Genetics, 2008 - academic.oup.com
Genomewide association map** in model organisms such as inbred mouse strains is a
promising approach for the identification of risk factors related to human diseases. However …

Phylogenetic signal, evolutionary process, and rate

LJ Revell, LJ Harmon, DC Collar - Systematic biology, 2008 - academic.oup.com
A recent advance in the phylogenetic comparative analysis of continuous traits has been
explicit, model-based measurement of “phylogenetic signal” in data sets composed of …

Using phylogenetic, functional and trait diversity to understand patterns of plant community productivity

MW Cadotte, J Cavender-Bares, D Tilman, TH Oakley - PloS one, 2009 - journals.plos.org
Background Two decades of research showing that increasing plant diversity results in
greater community productivity has been predicated on greater functional diversity allowing …

Modeling gene expression evolution with an extended Ornstein–Uhlenbeck process accounting for within-species variation

RV Rohlfs, P Harrigan, R Nielsen - Molecular biology and …, 2014 - academic.oup.com
Much of the phenotypic variation observed between even closely related species may be
driven by differences in gene expression levels. The current availability of reliable …

Pairwise comparisons across species are problematic when analyzing functional genomic data

CW Dunn, F Zapata, C Munro, S Siebert… - Proceedings of the …, 2018 - pnas.org
There is considerable interest in comparing functional genomic data across species. One
goal of such work is to provide an integrated understanding of genome and phenotype …

Phylogenetic ANOVA: the expression variance and evolution model for quantitative trait evolution

RV Rohlfs, R Nielsen - Systematic biology, 2015 - academic.oup.com
A number of methods have been developed for modeling the evolution of a quantitative trait
on a phylogeny. These methods have received renewed interest in the context of genome …

Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae

MA Alexandrou, BA Swartz, NJ Matzke… - Molecular phylogenetics …, 2013 - Elsevier
Multiple rounds of whole genome duplication have repeatedly marked the evolution of
vertebrates, and correlate strongly with morphological innovation. However, less is known …