Phylogenetic analyses were required to reveal historical relationships among taxa and to test the validity of the prevailing species hypotheses. Maximum likelihood (ML) trees for ddRADseq datasets were inferred with the IQ-Tree program94 with 5000 ultrafast bootstrap support for branches95. Haplotype networks for COI were computed with a modified script in RStudio (originally from https://johnbhorne.wordpress.com/2016/09/15/still-making-haplotype-networks-the-old-way-how-to-do-it-in-r/) using packages ape/5.396 and pegas/0.1197 and PopArt/1.7 using the TCS method98,99. Maximum likelihood trees for COI datasets were constructed using MEGA7100 with bootstrap support estimated from 500 replicates and the GTR + G substitution model.

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