Taxacom: Barcodes and species

Sun May 26 21:56:39 CDT 2024

 I don't see the BSC and DNA barcodes are being separate things, at least not necessarily. Basically, the BSC says that two individuals are distinct species if they are different enough to prevent free interbreeding. DNA is just one way of judging "different enough". I don't think that it makes any sense to reject the BSC entirely, simply because it makes no sense to have free interbreeding between two distinct species, because they would quickly become one species! One can also try to judge "different enough" morphologically. Sometimes morphological differences are slight, but genetic differences are high. Then we have so-called "cryptic species". More rarely, genetic differences can be slight while morphological differences are high. I don't see any particular problem with a small genetic change resulting in a relatively big morphological change that prevents free interbreeding. More of a problem is with allopatric populations with large genetic differences, but low morphological differences. Would the genetic differences block free interbreeding if the allopatric populations were to come together in the wild? Pretty hard to know how big a genetic difference is required and it may not be constant across all taxa. For me, there is really no "objective science" involved, it is simply a matter of making subjective choices where to draw the line, just as we do on morphological grounds. What annoys me is this "urban myth" that judging it on DNA is somehow more objective and therefore more scientific. It isn't!
Stephen
    On Monday, 27 May 2024 at 11:21:37 am NZST, Richard Pyle via Taxacom <taxacom at lists.ku.edu> wrote:  

 I have always seen DNA barcodes as a useful tool in the toolbox of any good taxonomist, for helping to (for example) link larval phases to adult phases of certain species, roughly approximate/identify organisms represented in eDNA samples, and in some cases, it may even function as a useful diagnostic basis for deciding whether organisms from two different populations should be labelled with the same species epithet, or if treating them as separate species makes more sense (in terms of facilitating effective communication among humans).  But since their inception, I have always pushed back against using them as “the” definitive diagnostic indicator for determining where to draw species lines.

Another example in fishes involves the species Centropyge sherpardi and C. ferrugata.  These two species are fairly similar in color, and were both described by my PhD advisor, Jack Randall as a co-author. Back when DNA barcodes were a new thing, a graduate student discovered that samples from both species had identical haplotypes for COI. She wrote me and asked me how to break the news to Jack that one of his species names is a synonym.  I explained to the student that, when I was working on a study of hybridization in that genus (there are many examples of hybrids within the genus), I had the opportunity to dive in an area where both species (ferrugata and shepardi) co-occur (Ogasawara Islands), and I very intentionally looked for hybrids on every dive I made there.  I saw many, many, many individuals of both species, living in exactly the same habitats, with harems of each species overlapping each other.  And despite seeing thousands of individuals of both species, I never saw a single individual that appeared to be a hybrid. Given how often one finds hybrids among closely-related species in this genus in areas of distributional overlap, I was surprised that these two very similar species seemed to produce no hybrids at all, even given ample opportunity to do so.

My point to the student was: forget about breaking the news to Jack that one of his species names is a synonym:  how are you going to break the news to the fishes themselves that they are the same species, when they clearly don’t know that because they don’t interbreed when given the opportunity to do so?

The Biological Species Concept is not a perfect framework as a definition for what a species is; but like DNA barcodes, it is still a very useful “rule of thumb” for making decisions on drawing lines between what we call species. All rules of thumb in taxonomy have exceptions, and therefore should not be used as the only metric for defining the taxonomic/nomenclatural landscape in nature. But I think both the BSC, and DNA barcodes, can help guide us in making sound taxonomic decisions, even if there are exceptions to both rules.

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 Hawaiʻi and the Pacific.

From: John Grehan <calabar.john at gmail.com>
Sent: Sunday, May 26, 2024 11:58 PM
To: Richard Pyle <Deepreef at bishopmuseum.org>
Cc: taxacom at lists.ku.edu
Subject: Re: Taxacom: Barcodes and species

Apologies for late response to various inputs on the COI question. Much appreciated! It seems a rather interesting conundrum - if 100% match is not necessarily corrected with con-specificity, then I wonder if a more divergent value (such as I have seen in various papers to justify species distinction) may also be misleading in this respect. But then this matter of DNA molecular similarity and phylogenetic correlation still seems like magic to me, at least at times (as I found out with the human-orangutan conundrum). Anyway, it looks as though one must take certain findings with a bit of caution. In a taxonomic catalogue of Hepialidae I did include COI input from a co-author to synonymise some names, but always with the caveat in my mind that such decisions are always contingent upon future verification, if that is even possible

Cheers, John

On Sun, May 26, 2024 at 9:30 AM Richard Pyle via Taxacom <taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>> wrote:
Two of the species we described in this paper:
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.11646%2Fzootaxa.1671.1.2&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C15001b8135dd44442a4608dc7df8a2f0%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638523754048160818%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=oaYi%2BsIzu8DP6%2F2Hzhb8dfcKK7mwclgTo1ujScYSV%2F0%3D&reserved=0
have multiple instances of identical barcodes (COI) across the type specimens of both species.

They are Chromis abyssus and Chromis circumaurea. You can Google them or look in the paper linked above to see what they look like.  They both have relatively broad (and partially overlapping) distributions. They are not dimorphic (either sexually or over the course of their lifestages) -- their color patterns are consistent throughout their respective ranges.  There has never been a hybrid seen. They differ consistently in morphology as well as color.  Even the lumpiest of lumpers would never consider them as conspecific. And yet... multiple instances of identical DNA barcodes across multiple specimens.

As a side note:  another species described in the same paper -- Chromis degruyi -- has a different juvenile coloration that is part of a convergent color pattern (mimicry?) among juveniles of several species in this genus.  So similar are the colors, that one of the juvenile Paratypes of C. degruyi is, in fact, a juvenile C. alpha.  We didn't realize this until we saw the barcodes.

So... score one point for traditional morphological taxonomy (in the case of C. abyssus and C. circumaurea), and one point for the diagnostic value of DNA barcodes (C. alpha mistaken as C. degruyi) -- all within a single paper!

Aloha,
Rich

P.S. This is also the paper that launched ZooBank, in case anyone is interested...

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<mailto: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 Hawaiʻi and the Pacific.

> -----Original Message-----
> From: Taxacom <taxacom-bounces at lists.ku.edu<mailto:taxacom-bounces at lists.ku.edu>> On Behalf Of Mark Costello
> via Taxacom
> Sent: Monday, May 20, 2024 4:09 AM
> To: taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>
> Subject: Re: Taxacom: Barcodes and species
>
> Dear John,
> I recall but do not have the paper of some Drosophila species in Hawaii that
> were unmistakably morphologically different species but had the same COI
> gene. Outside insects, I have been reliably told that some other animals taxa
> (Cnidarians?) have little variation in this gene. Some genes vary more and
> some less between species and higher taxa.
> Best regards
> Mark
>
> -----Original Message-----
> From: Taxacom <taxacom-bounces at lists.ku.edu<mailto:taxacom-bounces at lists.ku.edu>> On Behalf Of Marko Prous
> via Taxacom
> Sent: Sunday, May 19, 2024 4:30 PM
> To: taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>
> Subject: Re: Taxacom: Barcodes and species
>
> Dear John,
>
> It's possible to have identical barcodes (mitochondrial COI fragment)
> between species, which can be quite common in some groups (sawflies), rare
> in Lepidoptera. You should check also few nuclear genes (or maybe even just
> one might be enough). If these correlate with morphological differences,
> good chance that these are different species despite of identical
> mitochondrial barcodes.
>
> Occasional hybridization or incomplete lineage sorting can explain this, but if
> nuclear genes clearly separate the species, mitochondrial introgression would
> be more likely explanation (mitochondrial DNA evolves faster than nuclear
> DNA).
>
> cheers,
> Marko
>
> On 5/19/24 09:07, John Grehan via Taxacom wrote:
> > As I am pretty ignorant of technical details of species designation
> > and barcode identity, I would be grateful for any feedback on whether
> > it is possible for two 'species' to have identical 'barcodes' (never
> > liked that label with its essentialist connotations).
> >
> > I have a colleague who has collected some ghost moths from the same
> > date and location. There are two morphs - for simplicity 'white spot'
> > and 'plain'. Dissections of genitalia also show differences, with the
> > white spot and plain each showing consistent differences, although
> > only 2 specimens for white spot and 3 for plain. Even with this small
> > sample I am kind of intrigued that the external difference matches the
> > internal difference.
> >
> > The genitalic differences are prominent enough that I would normally
> > view them as indicative of species difference. Perhaps there is a
> > single polymorphic species, but correlated external and internal
> > differences were a bit of a surprise. Any comments or enlightenment
> > would
> be very welcome.
> >
> > Cheers, John
> >
>
> _______________________________________________
> Taxacom Mailing List
>
> Send Taxacom mailing list submissions to: taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu> For list
> information; to subscribe or unsubscribe, visit:
> https://lists.ku.edu/listinfo/taxacom
> You can reach the person managing the list at: taxacom-owner at lists.ku.edu<mailto:taxacom-owner at lists.ku.edu>
>
> Nurturing nuance while assailing ambiguity for about 37 years, 1987-2024.
>
>
>
> _______________________________________________
> Taxacom Mailing List
>
> Send Taxacom mailing list submissions to: taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu> For list
> information; to subscribe or unsubscribe, visit:
> https://lists.ku.edu/listinfo/taxacom
> You can reach the person managing the list at: taxacom-owner at lists.ku.edu<mailto:taxacom-owner at lists.ku.edu>
>
> Nurturing nuance while assailing ambiguity for about 37 years, 1987-2024.
>

_______________________________________________
Taxacom Mailing List

Send Taxacom mailing list submissions to: taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>
For list information; to subscribe or unsubscribe, visit: https://lists.ku.edu/listinfo/taxacom
You can reach the person managing the list at: taxacom-owner at lists.ku.edu<mailto:taxacom-owner at lists.ku.edu>

Nurturing nuance while assailing ambiguity for about 37 years, 1987-2024.

--
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhepialidsoftheworld.com.au%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C15001b8135dd44442a4608dc7df8a2f0%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638523754048160818%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=IuT0arRP8aqMEBmjZX9Gw%2B%2F%2Fgh3ltLimQPStoZoBffY%3D&reserved=0 (use the 'visit archived web site' link, then the 'Ghost Moth Research page' link.
_______________________________________________
Taxacom Mailing List

Send Taxacom mailing list submissions to: taxacom at lists.ku.edu
For list information; to subscribe or unsubscribe, visit: https://lists.ku.edu/listinfo/taxacom
You can reach the person managing the list at: taxacom-owner at lists.ku.edu

Nurturing nuance while assailing ambiguity for about 37 years, 1987-2024.