Population genomics of the facultatively asexual duckweed Spirodela polyrhiza

• Published in: The New phytologist Vol. 224; no. 3; pp. 1361 - 1371
• Main Authors: Ho, Eddie K. H., Bartkowska, Magdalena, Wright, Stephen I., Agrawal, Aneil F.
• Format: Journal Article
• Language: English
• Published: England Wiley 01.11.2019; Wiley Subscription Services, Inc
• Subjects: Aquatic plants; Arabidopsis thaliana; asexual reproduction; Biological evolution; Decay; Duckweed; Evolution; Floating plants; Freshwater plants; Genetic diversity; Genetic variation; genome; Genomes; geographical distribution; Linkage disequilibrium; metagenomics; Plant species; Population; population size; Propagation; purifying selection; recombination; selfing; Sex; Species; Spirodela polyrhiza; Very Low Frequencies; genetic diversity; purifying selection; recombination; Spirodela polyrhiza; asexual reproduction; duckweed
• ISSN: 0028-646X; 1469-8137; 1469-8137
• DOI: 10.1111/nph.16056

• Clonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome. • We examine genome-wide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually. • We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. A potential explanation for this observation is that a very low frequency of sex renders selection ineffective. However, there is a pronounced decay in linkage disequilibrium over 40 kb, suggesting that though sex may be rare at the individual level it is not too infrequent at the population level. In addition, neutral diversity is affected by the physical proximity of selected sites, which would be unexpected if sex was exceedingly rare at the population level. • The amount of genetic mixing as assessed by the decay in linkage disequilibrium is not dissimilar from selfing species such as Arabidopsis thaliana, yet selection appears to be much less effective in duckweed. We discuss alternative explanations for the signature of weak purifying selection.