Coalescent Methods

Divergence times, demographic change, gene flow, and conservation

The multispecies coalescent (MSC) model has been important for species tree estimation where incomplete lineage sorting generates gene tree discordance among species. I am more interested in how the MSC (and coalescent methods more broadly) can be used to infer divergence times between species and populations or change in population size over time.

I am also interested in network estimation under the MSC. The goal is to take a data-inclusive approach, moving from species tree estimation followed by post-hoc tests for introgression to probabilistic inference with networks. I am currently investigating the performance of network methods for estimating speciation times and the timing of introgression or hybridization.

The MSC permeates many aspects of my research including chickens ¹, mouse lemurs ², divergence time estimation ³, and conservation genetics ⁴. The MSC is incredibly valuable for conservation genetics, as it allows robust estimation of divergence time and population sizes with few (2 or 3) individuals per population compared to allele frequency-based approaches. I still stress that sometimes simpler and less computationally demanding methods work very well though, it depends on the amount of expected ILS
. Figure 5 from Tiley et al. 2020b ⁴ Comparison of different divergence time estimation strategies.