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. Failure to account for migration can lead to the misestimation of effective population sizes, divergence times, and topology. Isolation-with-migration and multispecies coalescent-with-introgression models accommodate migration but involve additional parameters that limit their computational viability with even moderate sized molecular datasets. Problematically, very large datasets may be required for reliable parameter estimation under these models. This study evaluates IM-based phylogeny inference using simulated and empirical datasets with a focus on incorporating gradually time-decaying migration, reflecting realistic expectations of reduced gene flow among more divergent lineages. We compare the performance of DENIM (an IM model) and StarBeast3 (an MSC model) using sequences simulated with continuous low-level migration and no ..., , , # Data from: Phylogeny inference under time-decaying migration and varying information content

[https://doi.org/10.5061/dryad.cc2fqz6d1](https://doi.org/10.5061/dryad.cc2fqz6d1)

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 \"Anopheles_data.zip\" contains all the DENIM and StarBeast3 analyses for the *Anopheles gambiae* sequence data.

Simulated data: folders beginning with \"1_\" to \"7_\" contain the simulated data results.

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.

Read-me.txt: a text file providing more detailed information about the folder structure and file contents.

**Version changes:**

20 Sept. 2024: Added DENIM and StarBeast3 analyses for the simul...