Phylogeny inference under time-decaying migration and varying information content

Postspeciation gene flow is widespread across the Tree of Life but is ignored as a cause of gene tree discordance under the standard multispecies coalescent. Where interspecific migration has occurred but is not modelled explicitly, effective population sizes, divergence times and topology can be seriously misestimated. Isolation-with-migration and multispecies coalescent-with-introgression models explicitly model migration but include additional parameters that limit their computational viability with even moderately sized molecular data sets. Here we simulate the evolution of sequences which vary in molecular information content under the coalescent while allowing continuous, tree-wide gene flow/migration between contemporaneous branches, the rate of which decreases with time since divergence. Using simulated sequences, we evaluate the performance of DENIM under rapidly to gradually time-decaying migration and benchmark its performance against the standard MSC method StarBeast3. DENIM..., , , # Phylogeny inference under time-decaying migration and varying information content

Input and output files for the simulated and empirical data for DENIM and StarBeast3 with supporting Figure S1 and Tables S1 and S2.

## Description of the data and file structure

Empirical data: the folder \"Empirical-data\" contains the empirical results and a Read-me.txt file explaining the file contents. The folder \"Bat-primate-sequence-data\" contains the bat and primate sequence data from Jebb et al. (2020), provided separately for licensing reasons.

Simulated data: folders beginning with \"Simdat\" include files for the simulated data with a Read-me.txt file in \"Simdat_9_Readme-and-SimulatedMigs\" explaining the file contents.

Folders \"8_Locus-length-number-combs-not-included_filepart*\" are the input and output data files for simulated locus length and number combinations that failed to reach convergence after several weeks of computation.

Figure S1 and Tables S1 and S2 are included as separate f...