Tree- based approach
A large number of tests show that PTP is superior to GMYC on simulated
data and its results are comparable to GMYC on real data sets meanwhile
PTP requires less for data sets and requires only a simple phylogenetic
tree (Zhang, Kapli, Pavlidis, &
Stamatakis, 2013 ). Therefore, in this study, we chose PTP analysis to
assist in species definition. PTP can delimit species based on the
Phylogenetic Species Concept. So the entities output by PTP are in
theory species. Bayesian Poisson tree process (bPTP) analyses were run
on the web server (https://species.h-its.org/ptp) with 100,000 MCMC
generations, a burn- in of 0.1 and other parameters as default. The ML
tree generated by RAXML is selected as the input
data(Stamatakis, 2006 ).