Taxacom: Barcodes and species

Sun May 26 13:14:30 CDT 2024

There are certain taxa for which anomalously divergent COI sequences are
found within a species (such as many pleurocerid and
semisulcospirid gastropods).

On Sun, May 26, 2024 at 11:58 AM John Grehan via Taxacom <
taxacom at lists.ku.edu> wrote:

> 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> 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%7C954b92d4896d40ee0d1b08dc7dafb7b3%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638523441315480577%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C40000%7C%7C%7C&sdata=jkYEwV%2FUlDH8fKnSZI8MOHTVrVWHU1W9WwTgzhpwTsg%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
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> > BishopMuseum.org
> > Our Mission: Bishop Museum inspires our community and visitors through
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> > environment of Hawaiʻi and the Pacific.
> >
> > > -----Original Message-----
> > > From: Taxacom <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
> > > 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> On Behalf Of Marko Prous
> > > via Taxacom
> > > Sent: Sunday, May 19, 2024 4:30 PM
> > > To: 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
> > > >
> > >
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-- 
Dr. David Campbell
Professor, Geology
Department of Natural Sciences
110 S Main St, #7270
Gardner-Webb University
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