ArticlePLoS computational biology2019
GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity.
Article in PLoS computational biology, 2019. 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.
- On the Causes of Correlated Genomic Ancestry Across Contrasting Hybridization Histories in a Monkeyflower Species Pair.Molecular ecology · 2026Article
- Maintenance of phenotypic divergence in two sympatric monkeyflowers with weak reproductive isolation.bioRxiv : the preprint server for biology · 2026Article
- Comparative Analyses of Four Reference Genomes Reveal Exceptional Diversity and Weak Linked Selection in the Yellow Monkeyflower (Mimulus guttatus) Complex.Molecular ecology resources · 2025Article
- The Evolution of Locally Adaptive Chromosome Inversions in Mimulus guttatus.Molecular ecology · 2025Article
- Unique genetic bases of repeated life-history divergence associated with high altitude adaptation inbioRxiv : the preprint server for biology · 2025Article
- Genomic structural variation in Barramundi Perch Lates calcarifer and potential roles in speciation and adaptation.G3 (Bethesda, Md.) · 2024Article
- Characterization and distribution of a 14-Mb chromosomal inversion in native populations of rainbow trout (Oncorhynchus mykiss).G3 (Bethesda, Md.) · 2024Article
- The quantitative genetics of gene expression in Mimulus guttatus.PLoS genetics · 2024Article
- Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species.Molecular ecology · 2024Article
- The genomic scale of fluctuating selection in a natural plant population.Evolution letters · 2022Article
- Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability.Evolution; international journal of organic evolution · 2022Article
- Supergene potential of a selfish centromere.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- The genetic architecture and evolution of life-history divergence among perennials in theProceedings. Biological sciences · 2021Article
- Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers.PLoS genetics · 2021Article
- Ancestral Reconstruction of Karyotypes Reveals an Exceptional Rate of Nonrandom Chromosomal Evolution in Sunflower.Genetics · 2020Article
- Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants.Frontiers in plant science · 2020Review
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6 authors.
Funding
Abstract
Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics. We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data. The procedure, called Genome Order Optimization by Genetic Algorithm (GOOGA), couples a Hidden Markov Model with a Genetic Algorithm to analyze data from genetic mapping populations. We demonstrate the method using both simulated data (calibrated from experiments on Drosophila melanogaster) and real data from five distinct crosses within the flowering plant genus Mimulus. Application of GOOGA to the Mimulus data corrects numerous errors (misplaced sequences) in the M. guttatus reference genome and confirms or detects eight large inversions polymorphic within the species complex. Finally, we show how this method can be applied in genomic scans to improve the accuracy and resolution of Quantitative Trait Locus (QTL) mapping.
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