Introgressed variants obscure phylogenetic relationships but are not subject to positive selection in Australasian long-tailed parrots

Gene flow often obscures phylogenetic relationships, but the evolutionary significance of introgressed variants is unclear. Here, we examine the Australasian long-tailed parrots (Psittaculinae: Polytelini), in which an unexpected sister relationship between Polytelis alexandrae and the genus Aprosmictus, and not the other Polytelis species, has been observed. We tested whether this relationship was due to ancient introgression in whole genomes and found that the majority of gene trees had Ap. erythropterus and P. alexandrae as sister taxa, whereas network analysis indicated monophyly of Polytelis, and 48% of gene trees were in phylogenetic conflict due to introgression from Ap. erythropterus into P. alexandrae. Some 4–8% of the genome of P. alexandrae was introgressed from Ap. erythropterus, with signals of gene flow occurring throughout the genome. These findings indicate that topologies with P. alexandrae and the genus Ap. erythropterus as sister taxa were biased by gene flow and affi..., The data was generated using the methods described herein and in the manuscript Smith et al. \"Introgressed variants obscure phylogenetic relationships but are not subject to positive selection in Australasian long-tailed parrots.\"
, , README.md file was updated on Oct 24, 2024 (edited May 1, 2025; Oct 29 2025) by Brian T. Smith & Agusto Luzuriaga-Neira.\
Contacts: [[e-mail]](mailto:[e-mail]), [[e-mail]](mailto:[e-mail]).

Scripts, lists of commands, and complementary files used in data analyses related to:

# **“Introgressed variants obscure phylogenetic relationships but are not subject to positive selection in Australasian long-tailed parrots.”**

---

# Authors:

```
Brian Tilston Smith
Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA

Agusto Luzuriaga-Neira
Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA

David Alvarez-Ponce
Biology Department, University of Nevada, Reno, Reno, NV 89557, USA

Kaiya L. Provost
Biology Department, Adelphi University, Garden City, NY 11530, USA

Gregory Thom
Museum of Natural Science and Depa...,