However, the strength of the model decreases with divergence estimates older than 14 Mya under both approaches, indicating preference for the most recent estimate.
For a serial founder model with a divergence time of τD = 16000, at a putative time of the Neanderthal divergence, differences in values among populations for each of the three summary statistics are small.
One exception was seen in the estimates of parameters associated with population size changes during divergence (s, η 1, and η 2 ) in datasets simulated under the ISO model with recent divergence.
Biodiversity indices explained significantly, albeit weakly, cotton decomposition (R2 = 0.34 0.42) but only functional aspects of community structure were retained in the minimal adequate model, with functional divergence having the main effect (positive) over the two years.
For example, the interquartile range (25th – 75th percentile) of Akaike weights for the ISO model with recent divergence included values less than 0.5 with n = 10 per population.
An exception to this trend was seen for the ISO model with recent divergence, which had median Akaike weights > 0.75 across all sample sizes considered.
For instance, fitting the IM model to data simulated under the ISO model with ancient divergence required, on average, more than 14 iterations for samples of 10 diploid individuals per population.
As further validation, we constructed a linear model with expression divergence as the dependent variable, and the 11 tested factors and d N as explanatory variables; d N remained highly significant in this analysis (P < 10−).
In the IM model with recent divergence (B parameterization), we included asymmetric migration between populations, which is known to result in bias when employing approaches that assume symmetry in migration rates [ 24- 26].
