Phylogenetic tree reconstruction
For the mitochondrial COI dataset, the alignment of 323 sequences was
used to construct a Bayesian phylogenetic tree using the software Beast2
(Bouckaert et al, 2014), with out-group sequences of N.
purpurata , N. meanyi , N. vandykei , N. praedicta ,
and N. metallica downloaded from GenBank (accession numbers:
MN346054, KU641246, KU641248, JQ711382, KU875540). The model HKY+G was
selected as the best substitution model based on model tests conducted
with the software MEGA v7 (Kumar, Stecher, & Tamura, 2016). A clock
rate for the COI gene was set to 0.0113 per site per million years based
on the best available COI mutation rate estimate for beetles, in this
case related carabid beetles (Andújar, Serrano, & Gómez-Zurita, 2012).
Ten million steps of a Markov chain Monte Carlo (MCMC) were run to
estimate model parameters and trees, with samples drawn every 1000
steps. Two separate runs were conducted. The posterior samples were
assessed for convergence using TRACER v1.7 (Rambaut, Drummond, Xie,
Baele, & Suchard, 2018) and each parameter value was assessed to ensure
a high effective sample size (>200). Additionally, a
statistical parsimony cladistic analysis, or TCS network, was
reconstructed using Popart-1.7 (Clement, Snell, Walker, Posada, &
Crandall, 2002; Leigh & Bryant, 2015). Based on the divisions in the
TCS network, haplotypes were assigned to northern or southern
haplogroups.
A population tree based on genome-wide SNP data (12,498 SNPs,fully-filtered dataset ) was constructed using maximum
likelihood in the program IQtree version 1.6.12 (Nguyen, Schmidt, Von
Haeseler, & Minh, 2015). The substitution model GTR+ASC was selected
and the branch support was estimated based on 1,000 bootstrap
replicates. The output tree was then visualized and colored using
FigTree v1.4.1 (Rambaut, 2012). Additionally, we inferred the species
tree using the program SNAPP (Bryant, Bouckaert, Felsenstein, Rosenberg,
& RoyChoudhury, 2012), implemented in BEAST2 version 2.6.2. Thefully-filtered dataset was used, but due to computational
constraints, one random individual was selected from each of eight
populations. Individuals were chosen from populations with relatively
pure ancestry coefficients to avoid violating assumptions in the species
tree approach, namely the effect of gene flow from other populations
(see the result of sNMF analysis; Bryant et al., 2012, Stoltz et al.,
2019). SNAPP was run for 30 million Markov chain Monte Carlo (MCMC)
generations, with the custom program SNAPPER employed to run SNAPP at
faster speed (Stoltz et al., 2019). Two independent runs were conducted
and the output trees were visualized after 10% burnin using DensiTree
version 2.01 (Bouckaert 2010).