Low genetic variation is associated with low mutation rate in the giant duckweed

Abstract

One Sentence Summary: The low-down on a tiny plant: extremely low genetic diversity in an 34 aquatic plant is associated with its exceptionally low mutation rate. 35 36 Main Text 37Explaining within-species genetic diversity-measured as the level of intraspecific DNA 38 sequence variation-is a major goal in evolutionary and conservation biology, as this diversity 39 can influence how species cope with changing environments (1, 2). While intraspecific genetic 40 diversity is known to vary widely among species, the underlying causes remain controversial (3, 41 4). According to population genetic theory, the population mutation parameter (q ) is determined 42 by the product of the spontaneous neutral mutation rate (µ) and effective population size (Ne), 43 and in diploid species q = 4 ´ Ne ´ µ (5). In practice, the parameter q is often estimated by the 44 average pairwise nucleotide diversity (p) at putatively neutral sites (6). While the role of Ne in 45 explaining variation in genetic diversity among taxa has received much theoretical and empirical 46 attention (3, 4, 7), the influence of variation in mutation rate and the interaction between Ne and 47

Population genomics of the facultatively asexual duckweedSpirodela polyrhiza

“…First, the very low level of neutral diversity may reflect a very low mutation rate, potentially due to the low numbers of cell divisions per generation compared to other vascular plants. Recent estimates of mutation rate in this species are consistent with this possibility (Xu et al , 2018; Sandler et al in prep). Second, in partially asexual species, mitotic gene conversion and mitotic crossing over play a major role in reducing linkage disequilibrium in facultatively sexual organisms, but would not do so in selfers (Hartfield et al , 2018).…”

“…They suggest that the low diversity in S. polyrhiza may be due to its lower frequency of seed production compared to the other two Spirodela species. A new population genomic study parallel to ours reports very low levels of polymorphism within S. polyrhiza (Xu et al, 2018).…”

“…The observation of low diversity could be explained by either low mutation rate or a low N e . Direct estimates of the mutation rate indicate that the mutation rate is very low (i.e., one to two orders of magnitude lower than Arabidopsis ; Xu et al , 2018, Sandler et al in prep ). Based on this low estimate, Xu et al (2018) inferred that N e is quite large (∼10 6 ); our own estimate of the mutation rate (Sandler et al in prep) and diversity is broadly consistent with a large N e .…”

Low spontaneous mutation rate and Pleistocene radiation of pea aphids

“…This may cause increased selection for high fidelity of DNA polymerase in order to alleviate the mutation load resulting from accumulation of deleterious mutations during the parthenogenetic phase. A similar argument has recently been made to explain the low mutation rate observed in giant duckweed Spirodela polyrhiza (Xu et al 2019), a species that reproduces mostly by asexual budding and exhibits the lowest mutation rate of any plant (2.4x10 -10 ). On the other hand, water flea Daphnia pulex -whose life cycle includes up to 5 apomictic parthenogenetic generations between each sexual reproduction event -exhibits a mutation rate 10x higher than our estimate in pea aphids (Flynn et al 2017).…”

A newSpirodela polyrhizagenome and proteome reveal a conserved chromosomal structure with high abundances of proteins favoring energy production

“…A second hypothesis is related to how S. polyrhiza plants are clonal, and reproduce exponentially, although rarely (if ever) do they flower in nature or in culture. In the presumed absence of meiotic recombination that normally occurs during sexual reproduction, S. polyrhiza plants across their global range exhibit low genetic variation, and intriguingly also low spontaneous mutation rates (Xu et al , 2019) . The estimation of Xu et al of the S. polyrhiza mutation rate is similar to that of eubacteria and unicellular eukaryotes.…”