Pitfalls and windfalls of detecting demographic declines using population genetics in long-lived species

Detecting recent demographic changes is a crucial component of species
conservation and management, as many natural populations face declines due
to anthropogenic habitat alteration and climate change. Genetic methods
allow researchers to detect changes in effective population size (Ne) from
sampling at a single timepoint. However, in species with long lifespans,
there is a lag between the start of a decline in a population and the
resulting decrease in genetic diversity. This lag slows the rate at which
diversity is lost, and therefore makes it difficult to detect recent
declines using genetic data. However, the genomes of old individuals can
provide a window into the past, and can be compared to those of younger
individuals, a contrast that may help reveal recent demographic declines.
To test whether comparing the genomes of young and old individuals can
help infer recent demographic bottlenecks, we use forward-time,
individual-based simulations with varying mean individual lifespans and
extents of generational overlap. We find that age information can be used
to aid in the detection of demographic declines when the decline has been
severe. When average lifespan is long, comparing young and old individuals
from a single timepoint has greater power to detect a recent (within the
last 50 years) bottleneck event than comparing individuals sampled at
different points in time. Our results demonstrate how longevity and
generational overlap can be both a hindrance and a boon to detecting
recent demographic declines from population genomic data.