Table 1. Species delimitation methods based on multi-locus nuDNA sequences used in this study.

Method	Input	Category	Reference	Description	SD Criteria
STRUCTURE	alignment of phased alleles	PG	Pritchard et al. [26] Falush et al. [53]	Bayesian clustering method based on the estimation of allele frequencies	ΔK and plateau methods
Haplowebs	alignment of phased alleles	PG	Flot et al. [30]	Allele-sharing method, in which groups of individuals sharing a unique pool of alleles are connected by curves.	Group of individuals constituting a field for recombination [FFR]
Conspecificity matrix (CM)	Conspecificity scores	PG	Debortoli et al. [31]	The conspecificity matrix was generated by calculating for each pair of individuals a conspecificity score, i.e., the number of markers supporting conspecificity in haploweb analyses.	Number of markers supporting the hypothesis of conspecificity
BPP (Bayesian Phylogenetics and Phylogeography)	alignment of consensus sequences	MSC	Yang and Rannala [64]	Bayesian method based on the MSC model, in which a reversible-jump Markov chain Monte Carlo algorithm is used to calculate the posterior probabilities of species delimitations.	Probability ≥ 0.95
STACEY (Species Tree and Classification Estimation, Yarely)	alignment of phased alleles	MSC	Jones [24]	Bayesian method implemented in BEAST 2 [65] for the inference of a “species or minimal clusters tree” (SMC) under the birth-death-collapse tree prior and without the requirement of a guide tree.	Probability ≥ 0.95
			Individual assignment of alleles: present study
*BEAST (Species Tree Ancestral Reconstruction in BEAST)	alignment of phased alleles	MSC + P	Program: Heled and Drummond [19]; Individual assignment of alleles: present study	Bayesian method implemented in BEAST 2 [65] based on the MSC model	Probability ≥ 0.95
Bootstrap Analysis of Haplotypes	alignment of phased haplotypes	PG+ + P	Present study	Bootstrap consensus tree reconstructed with ML, MP or NJ methods	Bootstrap ≥ 90
Supermatrix MrBayes	alignment of consensus sequences	P	Ronquist et al. [46]	Bayesian inference of phylogeny	Probability ≥ 0.95
PhyML			Guindon et al. [47]	ML method for tree construction	Bootstrap ≥ 90
SuperTRI (SuperTree with Reliability Indices)	Weighted binary matrix of node support for each locus	P	Ropiquet et al. [20]	Three measures are calculated to estimate the reliability of the nodes (SBP, MPP and NRep) using the branch support values (PP) of all phylogenetic hypotheses produced during the separate Bayesian analyses of the 21 introns	(1) SBP ≥ 90 (2) MPP ≥ 0.1 (3) NRep ≥ 2

SD: Species delimitation; PG: Population Genetics; MSC: Multispecies Coalescent; P: Phylogenetic methods; SBP: Supertree Boostrap Percentage; MPP: Mean Posterior Probability

Rep: Reproducibility Index; SPR: Subtree Pruning and Re-grafting