We present CCSconsensuser, an end-to-end pipeline that generates consensus sequences from amplicon sequencing using high-fidelity reads produced by PacBio circular consensus sequencing (CCS).
We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a ‘soft’ barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification.
We present restriction site-associated DNA sequencing (RAD-seq) genomic data for 2,292 specimens, which unequivocally supports the delimitation of two new species, here described as Bactrocera borneoensis sp. n. Doorenweerd & San Jose and B. incognita sp. n. Doorenweerd & San Jose.
Under concatenation, both datasets suggest identical species relationships with mostly high statistical support. However, multispecies coalescent and multispecies network approaches suggest markedly different hypotheses and detected significant gene flow.
As the amount of genomic data for nonmodel taxa grows, it is increasingly clear that gene flow across species barriers in insects is much more common than previously thought.
In the E. rubivora complex, ddRAD data resolved all four species, contrary to morphological and COI data, which supports a potential scenario of host plant-driven speciation where the host plant specialization provides an ecological barrier to hybridization.
Our results show that the morphological differences between B. frauenfeldi and B. albistrigata (de Meijere) are part of a continuum that cannot be phylogenetically separated into monophyletic groups.