Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy

Non‐random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization...

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Bibliographic Details
Published in:Molecular ecology resources 2021-07, Vol.21 (5), p.1434-1451
Main Authors: Shastry, Vivaswat, Adams, Paula E., Lindtke, Dorothea, Mandeville, Elizabeth G., Parchman, Thomas L., Gompert, Zachariah, Buerkle, C. Alex
Format: Article
Language:English
Subjects:
admixture
Admixtures
ancestry
Bayesian analysis
Chromosomes
Clustering
Data analysis
Diploids
Entropy
Gene mapping
Gene sequencing
Genetic diversity
Genetics
Genomes
genotype likelihoods
Genotypes
Hybridization
Hybrids
introgression
Mathematical models
Model accuracy
Natural populations
Parameter estimation
Ploidy
polyploids
Polyploidy
Population genetics
Populations
Sex chromosomes
Statistical analysis
Statistical models
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Summary:Non‐random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization between differentiated populations. Accounting for this mixture and structure is important when mapping the genetics of traits and learning about the formative evolutionary processes that shape genetic variation among individuals and populations. Stratified genetic relatedness among individuals is commonly quantified using estimates of ancestry that are derived from a statistical model. Development of these models for polyploid and mixed‐ploidy individuals and populations has lagged behind those for diploids. Here, we extend and test a hierarchical Bayesian model, called entropy, which can use low‐depth sequence data to estimate genotype and ancestry parameters in autopolyploid and mixed‐ploidy individuals (including sex chromosomes and autosomes within individuals). Our analysis of simulated data illustrated the trade‐off between sequencing depth and genome coverage and found lower error associated with low‐depth sequencing across a larger fraction of the genome than with high‐depth sequencing across a smaller fraction of the genome. The model has high accuracy and sensitivity as verified with simulated data and through analysis of admixture among populations of diploid and tetraploid Arabidopsis arenosa. see also the Perspective by Filip Kolář
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.13330