10.5061/DRYAD.7KP90
Živković, Daniel
Ludwig Maximilian University of Munich
Tellier, Aurélien
Ludwig Maximilian University of Munich
Data from: Germ banks affect the inference of past demographic events
Dryad
dataset
2012
Evolutionary theory
2012-08-27T15:59:37Z
2012-08-27T15:59:37Z
en
https://doi.org/10.1111/mec.12039
835814 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Continuous progress in empirical population genetics based on whole genome
polymorphism data requires the theoretical analysis of refined models in
order to interpret the evolutionary history of populations with adequate
accuracy. Recent studies focus prevalently on the aspects of demography
and adaptation, whereas age-structure (e.g. in plants via the maintenance
of seed banks) has attracted less attention. Germ banking, i.e. seed or
egg dormancy, is a prevalent and important life-history trait in plants
and invertebrates, which buffers against environmental variability and
modulates species extinction in fragmented habitats. Within this study, we
investigate the combined effect of germ banking and time-varying
population size on the neutral coalescent, and particularly derive the
allele frequency spectrum under some simplifying assumptions. We then
perform an ABC analysis using two simple demographic scenarios - a
population expansion and an instantaneous decline. We demonstrate the
appreciable influence of seed banks on the estimation of demographic
parameters depending on the germination rate with biases scaled by the
square of the germination rate. In the more complex case of a population
bottleneck, which comprises an instantaneous decline and an expansion
phase, ignoring information on the germination rate denies reliable
estimates of the bottleneck parameters via the allelic spectrum. In
particular, when seeds remain in the bank over several generations, recent
expansions may remain invisible in the frequency spectrum, whereas ancient
declines leave signatures much longer than in the absence of seed bank.
msdirTBS_SB.tarCompress file containing the c++ code modified from
Hudson's mstbs to include coalescent simulations with seed banks.
When extracting the content of the tar file, you find 3 pdfs with
description of ms and mstbs options (msdoc, msTBSdoc), and one for the
seed bank extension (msTBS_SBdoc).seed bank - notebookMathematica notebook
to compute the main analytical results in the article (Zivkovic and
Tellier).seed bank.nb