Mutation rates in seeds and seed-banking influence substitution rates across the angiosperm phylogeny

Dann, Marcel; Bellot, Sidonie; Schepella, Sylwia; Schaefer, Hanno; Tellier, Aurélien

doi:10.1101/156398

Cited by 17 publications

(29 citation statements)

References 107 publications

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“…For example we assume that mutations occur in the seed/egg-bank (a consequence of DNA damage) at the same rate as in the active population. While there is support in plants for this hypothesis [54,55], we have no knowledge of supporting data in Daphnia. If mutations occur in seeds/eggs at a slower rate, we predict the estimation of dormancy to be a conservative lower bound, meaning that the seed/egg-bank is actually longer lived (e.g.…”

Section: Plos Geneticsmentioning

confidence: 72%

Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

et al. 2020

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Several methods based on the Sequential Markovian coalescence (SMC) have been developed that make use of genome sequence data to uncover population demographic history, which is of interest in its own right and is a key requirement to generate a null model for selection tests. While these methods can be applied to all possible kind of species, the underlying assumptions are sexual reproduction in each generation and nonoverlapping generations. However, in many plants, invertebrates, fungi and other taxa, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates/parameters of dormancy and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0.87 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. In conclusion, we here present a novel method to infer accurate demographies and life-history traits for species with selfing and/or seed/egg-banks. Finally, we provide recommendations for the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation.

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Section: Plos Geneticsmentioning

confidence: 72%

Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

et al. 2020

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“…This is particularly evident across the plant 492 kingdom, in which groups exhibiting very different life histories (e.g. holoparasitism, 493 epiphytism) are linked to having disparate rates of molecular evolution and thus 494 random, local molecular clocks explain better their mode of diversification (Bellot and 495 Renner 2014; Wicke et al 2016;Dann et al 2017). This calls for additional work to 496 account for differences in substitution rates when comparing gene trees.…”

Section: Results 344mentioning

confidence: 99%

Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot

Balbuena

Pérez‐Escobar

Llopis‐Belenguer

et al. 2018

Preprint

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AbstractSymbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals and nodes that maximize phylogenetic congruence. By means of simulations, we show that the output value produced is inversely proportional to the number and proportion of cospeciation events employed to build simulated tanglegrams. In addition, with time-calibrated trees, Random TaPas is also efficient at distinguishing cospeciation from pseudocospeciation. Random TaPas can handle large tanglegrams in affordable computational time and incorporates phylogenetic uncertainty in the analyses. We demonstrate its application with two real examples: Passerine birds and their feather mites, and orchids and bee pollinators. In both systems, Random TaPas revealed low cophylogenetic signal, but mapping its variation onto the tanglegram pointed to two different coevolutionary processes. We suggest that the recursive partitioning of the tanglegram buffers the effect of phylogenetic nonindependence occurring in current global-fit methods and therefore Random TaPas is more reliable than regular global-fit methods to identify host-symbiont associations that contribute most to cophylogenetic signal. Random TaPas can be implemented in the public-domain statistical software R with scripts provided herein. A User’s Guide is also available at GitHub.

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“…Phylogenetic approaches can be used to compare the substitution rates of seed banking and nonseed banking sister species (at this evolutionary scale it may be more practical to assess the qualitative aspect of seed banking). A very limited number of studies has shown, using few conserved loci (Whittle, ) or full plastome data (Dann et al ., ), that these rates do not differ significantly from one another, so that the mutation rate in seeds might be assumed to be similar to the mutation rate in plants above ground. As mutation in seeds, hidden to census size estimates, contributes to enhance the discrepancy between N cs and N e (Fig.…”

Section: Seed Banks Affect the Mutation Ratementioning

confidence: 99%

Persistent seed banking as eco‐evolutionary determinant of plant nucleotide diversity: novel population genetics insights

Tellier

2018

New Phytologist

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Contents Summary725I.Introduction725II.Seed banks decrease the population extinction rate726III.Seed banks define the effective population size727IV.Seed banks affect the mutation rate728V.Seed banks affect the effective recombination rate728VI.Seed banks influence the rate and signatures of natural selection729VII.Conclusion729Acknowledgements729References729 Summary Long‐term persistent seed banking is a common temporal bet‐hedging strategy in plants to adapt to unpredictable environments. The population genomics perspective developed in this article suggests that seed banking determines plant nucleotide diversity by decreasing the rate of genetic drift and the effect of linked selection while increasing mutational input. As a result, persistent seed banks are important factors determining the magnitude of the discrepancy between the census size of the above‐ground plant population and its genetic diversity, an effect known as the Lewontin paradox. The theoretical population genetics predictions presented here can be tested by combining genome‐wide polymorphism data with ecological studies of dormancy.

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Mutation rates in seeds and seed-banking influence substitution rates across the angiosperm phylogeny

Cited by 17 publications

References 107 publications

Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot

Persistent seed banking as eco‐evolutionary determinant of plant nucleotide diversity: novel population genetics insights

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