Selection efficacy differs between lifestages in the haploid-diploid Marchantia polymorpha subsp. ruderalis DOI Creative Commons
Tianyu Shen,

Philippe Gadient,

Justin Goodrich

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 9, 2024

Abstract Ploidy has profound effects on evolution. Perhaps the most compelling effect is related to dominance: In cells with more than one genome copy, of non-dominant deleterious variants are ‘masked’ some extent, leading a reduction in efficacy selection. This, turn, leads increased levels nucleotide diversity, and it may also affect substitution rates. To test this predicted association between ploidy selection, we studied scale per-gene patterns genetic diversity divergence haploid-diploid bryophyte Marchantia. We treated lifestage gene expression bias as continuous covariate accounted for genomic autocorrelation using smoothing splines general additive regression model (GAM) framework. Consistent lower purifying found sequence Watterson’s θ , net at non-degenerate sites genes diploid-biased expression. These showed reduced codon usage bias. addition, chromosome 5 be an outlier overall decreased site-frequency spectrum skewed towards common alleles, linkage disequilibrium. study, show utility generalized models population genomics, present evidence associated difference discuss parallels evolution (diploid) sex chromosomes why observed unlikely mediated by masking.

Language: Английский

Selection efficacy differs between lifestages in the haploid-diploid Marchantia polymorpha subsp. ruderalis DOI Creative Commons
Tianyu Shen,

Philippe Gadient,

Justin Goodrich

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 9, 2024

Abstract Ploidy has profound effects on evolution. Perhaps the most compelling effect is related to dominance: In cells with more than one genome copy, of non-dominant deleterious variants are ‘masked’ some extent, leading a reduction in efficacy selection. This, turn, leads increased levels nucleotide diversity, and it may also affect substitution rates. To test this predicted association between ploidy selection, we studied scale per-gene patterns genetic diversity divergence haploid-diploid bryophyte Marchantia. We treated lifestage gene expression bias as continuous covariate accounted for genomic autocorrelation using smoothing splines general additive regression model (GAM) framework. Consistent lower purifying found sequence Watterson’s θ , net at non-degenerate sites genes diploid-biased expression. These showed reduced codon usage bias. addition, chromosome 5 be an outlier overall decreased site-frequency spectrum skewed towards common alleles, linkage disequilibrium. study, show utility generalized models population genomics, present evidence associated difference discuss parallels evolution (diploid) sex chromosomes why observed unlikely mediated by masking.

Language: Английский

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