Taxacom: Barcodes and species

[Richard Pyle]

Hi Jared,

I don?t think they?d be immune to pop-gen studies.  I think we?re still figuring out how to correlate patterns based on only COI, vs. other more comprehensive/sensitive DNA analysis techniques.  And yes, I think it would be fascinating to run those more advanced analysis on these Chromis (and also the Centropyge example I gave).  Tissue samples are few and far-between, but it?s certainly possible we can get more.

I?ve always believed that anything that is phylogenetically informative about morphology is *somewhere* in the genome (sensu lato).  The problem, I think, is that we (humans) are not quite ready to accurately interpret those data in a way that meaningfully correlates with ?true? phylogeny.  I think our current understanding/techniques are probably ?close enough? for most taxonomic/phylogenetic purposes, but I think the amount we don?t understand still exceeds the amount we do understand, in terms of interpreting genetic data in a phylogenetically meaningful way.

Aloha,
Rich

Richard L. Pyle, PhD
Director of Natural Sciences | Director of EXCORE
Senior Curator of Ichthyology | Database Coordinator of Natural Sciences
Administrator of ZooBank | Mother of Dragons
Bernice Pauahi Bishop Museum
1525 Bernice Street, Honolulu, HI 96817-2704
Office: (808) 848-4115;  Fax: (808) 847-8252
eMail: deepreef at bishopmuseum.org
BishopMuseum.org
Our Mission: Bishop Museum inspires our community and visitors through the exploration and celebration of the extraordinary history, culture, and environment of Hawai?i and the Pacific.

From: Jared Bernard <bernardj at hawaii.edu>
Sent: Monday, June 3, 2024 11:37 PM
To: Richard Pyle <Deepreef at bishopmuseum.org>
Cc: taxacom at lists.ku.edu
Subject: Re: Taxacom: Barcodes and species

Rich, do you think the Chromis species who share barcodes would be "immune" to population genetics studies? My own hesitations about barcodes (which are the same hesitations about morphological holotypes) notwithstanding, I would've thought that at least the barcodes within an interbreeding population would be closer related to each other than with those in another population, even within the same species. So, your case of two species having identical barcodes makes me think you wouldn't even be able to see any population structure within each species, let alone species delineations. If you can't see any genetic distinction between species, how could you tell if sisters are closer related to each other than cousins, who are more related than a neighboring family?

But it seems most phylogenetic and even popgen studies have moved away from single barcodes toward using thousands of genes or SNPs -- I think usually both nuclear and mtDNA to avoid the polar bear fiasco ;^) (doi: 10.1093/molbev/msy018). Do you think a method like that would help analyze populations of Chromis? I guess my ultimate question is whether genetic distinction could ultimately be found between the Chromis species; if there is a way to say which populations are closer related than others, then there ought to be some genetic cohesion within a species and a way to distinguish it from another species. But maybe barcodes don't do the trick in this case, even though they're supposed to be informative.
Jared
[https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4zR2vjDtBEcYJOIENtARBJAGn1lLVbt2x9SWdSbJDEC-5QhWiihq5JdvMoq39vQ_EjMhs6TkIcPwEee&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C719efd3d8e4a407c1e4b08dc841e988c%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638530515266647804%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C40000%7C%7C%7C&sdata=mdehV4zcntF4M4WJgioSL8VPWGPDKPpReMwCu3OnKgA%3D&reserved=0]