Demographic history and isolation with migration model caveats
Estimating population sizes and timing demographic events depends on
accurate estimates of mutation rate per generation. As such, an
important caveat to the demographic and isolation with migration results
relates to assumptions about generation times and mutation rates in
these bird species. Generation times are reliable when information about
age of sexual maturity, adult survival, and offspring survival is known
in a species. In tropical bird species, little of this information is
known, and indeed none of the focal species studied here have known
generation times. Additionally, reproductive effort is known to vary
among temperate and tropical species (Hau et al., 2010), and even along
elevational gradients in tropical regions (Boyce et al., 2015).
The mutation rates we used here were calculated from time-calibrated
avian phylogenies, and implicitly rely on accurate timing of nodes from
the estimated phylogeny (Oliveros et al., 2019). These mutation rate
estimates are in numbers of mutations per year (Table 1) and are
generally consistent in magnitude with other Passeriformes mutation rate
estimates (Nam et al., 2010). As such, in the context of estimating
mutation rate per generation, we likely have more certainty in our
absolute mutation rates (per year) and less certainty in mutation rate
per generation because of unknown generation times. Regardless, we
expect that our two-year generation time assumptions are within a
reasonable amount of error from real values, e.g., we don’t expect these
values to be off by an order of magnitude.
Overall, given the uncertainties with both mutation rate and generation
times, we should expect that any population sizes and timings estimated
in demographic histories and isolation with migration models may vary.
Absolute timing events will be inaccurate proportional to error in our
absolute mutation rate estimates (mutations per year). Because our
population size estimates (i.e., 4Nμ) directly depend on mutation rates
per generation, the error in population size estimates will directly
scale with our error in estimating how the mutation rate relates to
generation times. For example, if the true generation times of our focal
species range from a year to four years (and we used an estimate of two
years), estimated effective population sizes will be doubled or halved,
respectively. Because we see a strong correlation between genomic
diversity and harmonic mean of population sizes including all
individuals across species (Fig. 3), even with potential error in
estimating generation times, we can still interpret relative differences
between species’ genomic diversities and population size trends.