Testing Multispecies Coalescent Simulators Using Summary Statistics

As genomic-scale datasets motivate research on species tree inference, simulators of the multispecies coalescent (MSC) process have become essential for the testing and evaluation of new inference methods. However, the simulators themselves must be tested to ensure that they give valid samples. This work develops methods for checking whether a collection of gene trees is in accord with the MSC model on a given species tree. When applied to well-known simulators, we find that several give flawed samples. The tests presented are capable of validating both topological and metric properties of gene tree samples, and are implemented in a freely available R package MSCsimtester so that developers and users may easily apply them.

Automated summary

As more genomic-scale datasets are being used for species tree inference, simulators of the multispecies coalescent (MSC) process are necessary to test and evaluate new inference methods. However, the simulators themselves need to be tested to ensure their validity. This study develops methods to check if a collection of gene trees aligns with the MSC model on a given species tree. The tests conducted on well-known simulators reveal flaws in some of the samples, and are implemented in the freely available R package MSCsimtester for easy application by developers and users.