COI gene analyses
To detect the COI haplotypic structure of A. alalia and A.
mantiqueira , a haplotype network was designed using PopART with the TCS
network option (Leigh & Bryant, 2015). To propose a phylogenetic
hypothesis, a Bayesian inference (BI) was carried out using MrBayes v.
3.2 (Ronquist et al., 2012) on the CIPRES portal (Miller et al., 2010),
including one individual of A. catarina as an outgroup (Table 1).
The model-jumping feature was employed to select the best nucleotide
substitution model (Ronquist & Huelsenbeck, 2003). The model with the
highest posterior probability was the GTR submodel [121131]. The
gamma parameter was also included to allow site rate variation. Four
simultaneous chains were run for 107 generations in
two runs, sampling trees every 1,000 cycles. The first 25% of trees
were discarded as “burn-in”. The convergence of the likelihood traces
of the independent runs was assessed with TRACER v1.5 (Rambaut et al.,
2018), and the ESS (effective sample size) values were verified to be
above 3,700 for all parameters, which indicates that they were
sufficiently sampled to estimate their posterior distributions (Drummond
et al., 2006).