Taxacom: Barcodes and species

[=?iso-8859-1?Q?L=FCcking=2C_Robert?=]

Dear Rich,

from a mycology perspective: barcodes are what they are, a compromise between speed and resolution. We have to move away from the idea that a single, new approach fits and resolves everything. There are much better resolved approaches, e.g. microsatellites or RADseq which in fungi have successfully resolved lineages with identical barcodes. The advantage of the barcodes is in the fact that a large number of samples can be treated with a simple approach, both in sequencing and analysis. Genomic approaches that go much deeper can only be done with much fewer samples, so there is always a catch. Notwithstanding the limits of barcodes: their consequent use has substantially improved taxonomic accuracy in organisms compared to morphology-based approaches.

Regards
Robert


-----Urspr?ngliche Nachricht-----
Von: Taxacom <taxacom-bounces at lists.ku.edu> Im Auftrag von Jared Bernard via Taxacom
Gesendet: Montag, 3. Juni 2024 10:37
An: Richard Pyle <Deepreef at bishopmuseum.org>
Cc: taxacom at lists.ku.edu
Betreff: 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
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