How Genetic studies reveal new relationships, species

[jhyatt]

Thanks Adam.

"Smaller difference in COI". Noting the other factors- range, flight period, etc. how the heck then would one determine Sp vs SSP considering COI?

If we use 2% as a safe range for species (noting that many are now less than that), what might be the difference for a ssp? Must be less than 1/3 of 1%, considering glaucus and appalachiensis.

I expect the answer is "it depends" and "the other factors" but then still....we can argue morphology all day, argue about distant populations, etc...even combining all the factors, are there ANY guidelines for Sp vs SSP now?

To me, DNA data is just another character to use in making what is fundamentally a subjective decision. The DNA % difference is neither stronger nor weaker evidence of speciation than morphology and biology. Species are biological facts, but the rest of classification, both higher and lower levels, is a human construct. At least, that's the way I look at the situation....

jh

[Chuck]

(John) that makes me wonder what the pros have been doing for two centuries, arguing about whether something is a species or subspecies.

While CO1 gives some insight- and clears up some of these issues, I'd hope there was SOME standard being set...or at least a baseline guideline.

I see a lot of stuff in BOLD BINs that are all roughly equal off the same branch, and presumably then all manner of taxa(?) could be named as species.

[adamcotton]

COI does not really give a reliable indication of species status, only a suggestion of probability. On the other hand a combination of various mitochondrial genes and importantly also a number of nuclear genes gives a much better indication of specificity ... but even then results can be unreliable in some cases.

Adam.

PS. I agree with John's comment just above. DNA characters are just that ... another category of characters. They should be taken into consideration alongside all other 'traditional' characters.

[Chuck]

Interesting paper on genetically differing populations of African Ciclids (fish) cohabiting the same waters. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700518/

Take-aways: (1) populations are genetically isolated despite being capable of interbreeding because of mating preferences; (2) the same situation is suggested for western US stick insects of the genus Timena, Heliconius, Drosophila, Anopheles, and a slew of non-insect animals.

In the case of the African Ciclids, the authors suggest that speciation may have started only 500 - 1000 years ago.

[Chuck]

I've been uploading to BOLD.

A collaborator (who's a name-brand professional) uses GenBank. He says "which BOLD mines now and then."

Um...should I be uploading data to BOLD or genbank? What's the difference?

The one difference I can find is that I can't figure out how to search for COI sequences on Genbank.

Appreciate any insight.

[adamcotton]

One advantage of BOLD is they require(?) a photo of the sequenced specimen and locality data to be uploaded as well as the sequence. That means it is possible to confirm the identity of the specimen that the sequence came from. GenBank was adapted from medical use to a biological one, and unless things have changed they only require country of origin (useless for confirmation of taxon identity) and the scientific publication reference, so it is/was impossible to confirm the sequence identity, especially given that taxonomic hypotheses change and also sometimes the original specimen was misidentified by the geneticist who sequenced it (I have found instances of this!).

Adam.

[Chuck]

Thanks Adam! Very useful. Being a ground pounder forced into the genetics stuff, I want an image and collecting data readily available. So I'll continue with BOLD.