Clarify the biological process represented by alternate-topology tests for echolocation genes

Determine what biological process, if any, is represented by fitting echolocation-related gene alignments to an alternate phylogeny that groups echolocating bats and toothed whales into a clade sister to other mammals, as used in topology-based convergence tests.

Background

Some studies test for convergence by preferring an alternate gene-tree topology that clusters echolocating lineages, rather than modeling site-specific or rate-based evolutionary changes associated with the trait.

The authors argue this more likely reflects a distinct gene-tree history than convergent evolution per se and emphasize that the biological process such a topology would represent is not presently understood.

References

While \citet{Parker2013} intend for this model to represent the biological process of echo-locating lineages independently evolving similar genetic changes, it is instead more likely to represent an alternative hypothesis of the echolocation related genes having a distinct evolutionary history to that of the species tree. It is unclear what biological process this would represent, and as such it is difficult to interpret the evolutionary significance of any genes which are identified with this method.

— From trees to traits: A review of advances in PhyloG2P methods and future directions  (2501.07043 - Macdonald et al., 13 Jan 2025) in Subsection 'Caveats and strengths of different approaches to modeling replication' (Additional considerations)