PT  - JOURNAL ARTICLE
AU  - Breitling, Paula
AU  - Stamatakis, Alexandros
AU  - Chernomor, Olga
AU  - Bettisworth, Ben
AU  - Reszczynski, Lukasz
TI  - Empirical Analysis of Phylogenetic Quasi-Terraces
AID  - 10.1101/810309
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 810309
4099  - http://biorxiv.org/content/early/2019/10/18/810309.short
4100  - http://biorxiv.org/content/early/2019/10/18/810309.full
AB  - Terraces in phylogenetic tree space are, among other things, important for the design of tree space search strategies. While the phenomenon of phylogenetic terraces is already known for unlinked partition models on partitioned phylogenomic data sets, it has not yet been studied if an analogous structure is present under linked and scaled partition models. To this end, we analyze aspects such as the log-likelihood distributions, likelihood-based significance tests, and nearest neighborhood interchanges on the trees residing on a terrace and compare their distributions among unlinked, linked, and scaled partition models. Our study shows that there exists a terrace-like structure under linked and scaled partition models as well. We denote this phenomenon as quasi-terrace. Therefore quasi-terraces should be taken into account in the design of tree search algorithms as well as when reporting results on ‘the’ final tree topology in empirical phylogenetic studies.