ArticleBioinformatics (Oxford, England)2009
Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 42 citations in OpenAlex.
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance.Molecular biology and evolution · 2023Article
- NGS allele counts versus called genotypes for testing genetic association.Computational and structural biotechnology journal · 2022Article
- Noncoding regions underpin avian bill shape diversification at macroevolutionary scales.Genome research · 2020Article
- Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis.Molecular biology and evolution · 2018Article
- Stochastic developmental variation, an epigenetic source of phenotypic diversity with far-reaching biological consequences.Journal of biosciences · 2015Review
- Scombroid fishes provide novel insights into the trait/rate associations of molecular evolution.Journal of molecular evolution · 2014Article
- ASPM and mammalian brain evolution: a case study in the difficulty in making macroevolutionary inferences about gene-phenotype associations.Proceedings. Biological sciences · 2014Article
- Comparative genomics of brain size evolution.Frontiers in human neuroscience · 2014Article
- Evolutionary Modeling of Genotype-Phenotype Associations, and Application to Primate Coding and Non-coding mtDNA Rate Variation.Evolutionary bioinformatics online · 2013Article
- Functional primate genomics--leveraging the medical potential.Journal of molecular medicine (Berlin, Germany) · 2012Review
- Positive Selection and the Evolution of izumo Genes in Mammals.International journal of evolutionary biology · 2012Article
- Mining for genotype-phenotype relations in Saccharomyces using partial least squares.BMC bioinformatics · 2011Article
- The molecular evolution of animal reproductive tract proteins: what have we learned from mating-system comparisons?International journal of evolutionary biology · 2011Article
- Article
- Sexual selection and the molecular evolution of ADAM proteins.Journal of molecular evolution · 2010Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationMapping between genotype and phenotype is one of the primary goals of evolutionary genetics but one that has received little attention at the interspecies level. Recent developments in phylogenetics and statistical modelling have typically been used to examine molecular and phenotypic evolution separately. We have used this background to develop phylogenetic substitution models to test for associations between evolutionary rate of genotype and phenotype. We do this by creating hybrid rate matrices between genotype and phenotype.
resultsSimulation results show our models to be accurate in detecting genotype-phenotype associations and robust for various factors that typically affect maximum likelihood methods, such as number of taxa, level of relevant signal, proportion of sites affected and length of evolutionary divergence. Further, simulations show that our method is robust to homogeneity assumptions. We apply the models to datasets of male reproductive system genes in relation to mating systems of primates. We show that evolution of semenogelin II is significantly associated with mating systems whereas two negative control genes (cytochrome b and peptidase inhibitor 3) show no significant association. This provides the first hybrid substitution model of which we are aware to directly test the association between genotype and phenotype using a phylogenetic framework. AVAILABILITY: Perl and HYPHY scripts are available upon request from the authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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