Gunilla and I always talked about this possibility, but never got a clear proof for it in our group. Nonetheless, there are a few examples in other orders if I remember well. Cheers

Thanks Ximo. I am only aware of the following papers on fungi but am hoping to gather some additional references for arthropods.

O’Donnell, K. & Cigelnik, E. (1997) Two Divergent Intragenomic rDNA ITS2 Types within a Monophyletic Lineage of the Fungus Fusarium Are Nonorthologous. Molecular Phylogenetics and Evolution 7 (1): 103–116.

Hughes KW, Morris SD, Reboredo-Segovia A (2015) Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving heterozygotes between Gymnopus dichrous taxa I and II. MycoKeys 10: 45–56.

In xanthophycean algae:

Rybalka N., Wolf M., Andersen R.A.; Friedl T. 2013. Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae). BMC Evol. Biol. 13 (39):1471-2148. doi: 10.1186/1471-2148-13-39.