> > > At least in > vertebrates this gene and the mitochondria in general is affected by > introgression. Species boundaries are unfortunately not as clean as we > would hope. I would imagine the same may be true of many invertebrate taxa > and even plants. Noting some additional problems: A few vertebrates, lots of plants, and certain invertebrates are allopolyploids, requiring use of nuclear markers. Some taxa have anomalous sequences (e.g., https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2F10.1111%2Fzsc.12139&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Ccf760da7c0104c3a112608da225f02c1%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637860088866157555%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=8WH14g89TeubanlyhtUJtihFUg%2BpDpgeNld5bf%2F2Pmg%3D&reserved=0). Symbionts can be a problem (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Facademic.oup.com%2Fsysbio%2Farticle%2F58%2F4%2F445%2F1681303&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Ccf760da7c0104c3a112608da225f02c1%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637860088866157555%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=8aVrCAcV1g%2B9qFsu565aYftxhxQbxDYDKVeAcEwfd7w%3D&reserved=0), as are misidentifications of reference sequences.