Simulations of life history variation for demographic inference from
population genomic data
Abstract
Ecological differences among species influence population response to
historical environmental changes, and genetic simulations now allow us
to directly incorporate this variation into inferential models. However,
the impact of life history strategies in demographic inference has been
far less explored relative to the impact of other ecological
differences, such as dispersal capacity and habitat preference. Here, we
utilize individual-based simulations of a non-Wright-Fisher population
to ask whether differences in the average age of first reproduction of
individuals, the average adult mortality and the average number of mates
per reproductive season lead to consistent and predictable differences
in summary statistics of genetic diversity commonly used for
simulation-based parameter estimation and demographic inference. Using a
Random Forest model, we estimate three population parameters (variance
in reproductive success, generation time, and effective population size)
from genome-wide SNP variation for two bird species with distinct life
history strategies that are directly built into the simulation
machinery. Our results show that life history variation leads to
predictable differences in patterns of genetic diversity. While
prediction accuracy is low, parameter estimates from empirical datasets
agree with the expectation that species with extreme polygamy, long
adult longevity and later onset of reproduction will exhibit higher
variance in reproductive success, longer generation time and smaller
effective population sizes. Since the signal of life history differences
is observed in the genetic summary statistics, we suggest that
simulation- and model-based multi-species demographic inference should
incorporate life history parameters.