Page:A taxonomic revision of the Archipini of the Caribbean (Lepidoptera, Tortricidae, Tortricinae).pdf/8

40 BOLD sample IDs. USNM specimens each have accession numbers listed in Suppl. material 1; only barcoded USNM specimens have their accession numbers listed in the material examined sections, as they are the same as the BOLD sample IDs in these instances.

Drawn-to-scale Neighbor-joining (NJ, Fig. ​Fig. 3) and Maximum Likelihood (ML, Fig. ​Fig. 4) trees of Caribbean Archipini were generated using MEGA X (Kumar et al. 2018). The ML tree was inferred using a Kimura 2-parameter model (Kimura 1980). Initial trees for the heuristic search were obtained automatically by applying Neighbor-Joining and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. The NJ tree was generated using the Neighbor-Joining method (Saitou and Nei 1987). Distances were computed using the Maximum Composite Likelihood (MCL) method (Tamura et al. 2004) and are in the units of the number of base substitutions per site. Both analyses were run with 1000 bootstrap replicates for sequences for which > 500 bp were recovered (n = 84, representing 27 different species). Mictopsichia and Mictocommosis were used as outgroups for both analyses as neither genus likely belongs to Archipini (see introduction). A pairwise distance matrix of all sequenced specimens is available in Tab 2 of Suppl. material 1 and was also computed using MEGA X (Kumar et al. 2018).

Because of the extremely limited taxon coverage, the trees were used to delineate species boundaries and examine terminal clades in the Caribbean, not as an attempt to accurately reconstruct a phylogeny. That said, these trees may help to understand basic relationships among Caribbean taxa, recognizing that future sampling is necessary.

Specimens from the following collections were examined: