Taxacom: Barcodes and species

Richard Pyle Deepreef at bishopmuseum.org
Mon May 27 21:46:28 CDT 2024 

Thanks, Les.

80% seems like a pretty good tool to me.  Any one tool in the toolbox isn't going to be 100% right all the time.  I think our jobs as taxonomists are to use as many tools as we have available to us, and integrate/synthesize them in the context of our experience and familiarity with our own respective groups, then make assertions about labelling things with names (species and their synonyms, hierarchical classifications, etc.) in a way that we feel will best facilitate human-human communication.

In the two examples I gave, where my conclusion was that communication was best facilitated by recognizing two distinct species in each case, the fact that the distinct species share COI haplotypes is an interesting anecdote -- analogous to them having the same number of dorsal-fin spines, lateral-line scales, gill-rakers, etc. -- but not more than an anecdote.  Additional sequencing would always be interesting, but I seriously doubt that the outcome from such analyses would persuade me (or any other taxonomist familiar with the group) to reconsider the conclusion that regarding them as distinct species best facilitates human-human communication.

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.

> -----Original Message-----
> From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Leslie Watling
> via Taxacom
> Sent: Tuesday, May 28, 2024 3:59 AM
> To: Cc: Taxacom Mailinglist <taxacom at lists.ku.edu>
> Subject: Re: Taxacom: Barcodes and species
> 
> Rich and others,
> 
> I think the fundamental issue re barcodes is that the mitochondrial genes
> might change at a pace that is different from the nuclear genes that
> determine the animal's morphology. It has always bothered me that such
> emphasis is put on mitochondrial genes when they have nothing to do with
> morphology.
> 
> With newer high throughput sequencing and looking at many, many nuclear
> gene sequences we are seeing that relationships that seemed to exist, no
> longer do. In the group I study, deep-sea bamboo corals, the relationships
> determined by a few mitochondrial genes have proven to be correct about
> 80% of the time, most probably because those lineages are deep (time) and
> well separated. But the other 20% is proving to be quite interesting.
> 
> So it is quite likely that two fishes with the same COI sequence could be
> separate species with slight differences elsewhere in the whole genome. If
> one gene says things are different, probably they are, but if one gene says
> they are not different, well, maybe they aren't or maybe they are. Your
> example, Rich, is one that should be subjected to high throughput
> sequencing.
> 
> Les
> 
> 
> Les Watling
> Professor Emeritus
> School of Life Sciences
> University of Hawaii
> 
> Professor Emeritus
> School of Marine Sciences
> University of Maine
> 
> 
> 
> On Mon, May 27, 2024 at 1:00 PM <taxacom-request at lists.ku.edu> wrote:
> 
> > Daily News from the Taxacom Mailing List
> >
> > When responding to a message, please do not copy the entire digest
> > into your reply.
> > ____________________________________
> >
> >
> > Today's Topics:
> >
> >    1. Re: Barcodes and species (David Campbell)
> >    2. Re: Barcodes and species (Richard Pyle)
> >    3. Re: Barcodes and species (Stephen Thorpe)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sun, 26 May 2024 14:14:30 -0400
> > From: David Campbell <pleuronaia at gmail.com>
> > Cc: "taxacom at lists.ku.edu" <taxacom at lists.ku.edu>
> > Subject: Re: Taxacom: Barcodes and species
> > Message-ID:
> >         <CAN1+Hk89G8=+
> > 9k1uVyDLxu8MQ9hfWhNe_1PSHpvdMJnDAL04vg at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > 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%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdoi.org%2F10.11646%2Fzootaxa.1671.1.2_&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cc01d41fb48894c168d1d08dc7ec06621%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638524612052217553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kDJbXDwNH2atkXdYrIHH0zT5b1enPJ1sGRGbqUJIrrE%3D&reserved=0
> > _;!!PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8z
> > bFxAMTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQhbOIHp$
> > > > 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
> > > > 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.
> > > >
> > > > > -----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
> > > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Taxacom Mailing List
> > > > >
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> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
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> > > 1987-2024.
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
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> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
> > > > > You can reach the person managing the list at:
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> > > > >
> > > > > Nurturing nuance while assailing ambiguity for about 37 years,
> > > 1987-2024.
> > > > >
> > > >
> > > > _______________________________________________
> > > > Taxacom Mailing List
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> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
> > > > 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.
> > > >
> > > >
> > > >
> > >
> > > --
> > >
> > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fhepialidsoftheworld.com.au%2F__%3B!!Pv&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cc01d41fb48894c168d1d08dc7ec06621%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638524612052217553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kYC74fSWt6l2f1ij%2FhvlISYFYjSyot8Z6hQlg7yXT7M%3D&reserved=0
> > DODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxAMT
> > FWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQQrGQG4$
> > (use the 'visit archived web site'
> > > link, then the 'Ghost Moth Research page' link.
> > > _______________________________________________
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> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
> > > 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.
> > >
> > >
> > >
> >
> > --
> > Dr. David Campbell
> > Professor, Geology
> > Department of Natural Sciences
> > 110 S Main St, #7270
> > Gardner-Webb University
> > Boiling Springs NC 28017
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 26 May 2024 23:21:15 +0000
> > From: Richard Pyle <Deepreef at bishopmuseum.org>
> > To: John Grehan <calabar.john at gmail.com>
> > Cc: "taxacom at lists.ku.edu" <taxacom at lists.ku.edu>
> > Subject: Re: Taxacom: Barcodes and species
> > Message-ID:
> >         <
> >
> BYAPR01MB5352BE9E265E86EBC308B5D1B7F72 at BYAPR01MB5352.prod.exc
> hangelabs
> > .com
> > >
> >
> > Content-Type: text/plain; charset="utf-8"
> >
> > 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 s  ingle 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 Hawai?i 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%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdoi.org%2F10.11646%2Fzootaxa.1671.1.2_&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cc01d41fb48894c168d1d08dc7ec06621%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638524612052217553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kDJbXDwNH2atkXdYrIHH0zT5b1enPJ1sGRGbqUJIrrE%3D&reserved=0
> > _;!!PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8z
> > bFxAMTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQhbOIHp$
> > 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 Hawai?i 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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Flists.ku.edu%2Flistinfo%2Ftaxacom__&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cc01d41fb48894c168d1d08dc7ec06621%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638524612052217553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=K9b5XdjDC1d8jW8ZpT03q2JuZLdiwmKVQliuuNY54%2Bs%3D&reserved=0;!!
> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
> > > 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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Flists.ku.edu%2Flistinfo%2Ftaxacom__&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cc01d41fb48894c168d1d08dc7ec06621%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638524612052217553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=K9b5XdjDC1d8jW8ZpT03q2JuZLdiwmKVQliuuNY54%2Bs%3D&reserved=0;!!
> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
> > > 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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Flists.ku.edu%2Flistinfo%2Ftaxacom__&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cc01d41fb48894c168d1d08dc7ec06621%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638524612052217553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=K9b5XdjDC1d8jW8ZpT03q2JuZLdiwmKVQliuuNY54%2Bs%3D&reserved=0;!!
> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
> > 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%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fhepialidsoftheworld.com.au%2F__%3B!!Pv&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cc01d41fb48894c168d1d08dc7ec06621%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638524612052217553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kYC74fSWt6l2f1ij%2FhvlISYFYjSyot8Z6hQlg7yXT7M%3D&reserved=0
> > DODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxAMT
> > FWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQQrGQG4$
> > (use the 'visit archived web site' link, then the 'Ghost Moth Research
> > page' link.
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 27 May 2024 02:56:39 +0000 (UTC)
> > From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> > To: John Grehan <calabar.john at gmail.com>,  Richard Pyle
> >         <deepreef at bishopmuseum.org>
> > Cc: "taxacom at lists.ku.edu" <taxacom at lists.ku.edu>
> > Subject: Re: Taxacom: Barcodes and species
> > Message-ID: <1263212438.4573268.1716778599339 at mail.yahoo.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> >  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 d
> > ifferences. 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 s  ingle 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 Hawai?i 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%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdoi.org%2F10.11646%2Fzootaxa.1671.1.2_&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cc01d41fb48894c168d1d08dc7ec06621%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638524612052217553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kDJbXDwNH2atkXdYrIHH0zT5b1enPJ1sGRGbqUJIrrE%3D&reserved=0
> > _;!!PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8z
> > bFxAMTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQhbOIHp$
> > 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 Hawai?i 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
> > > >
> > >
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> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
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> 2024.
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> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
> > > You can reach the person managing the list at:
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> > >
> > > Nurturing nuance while assailing ambiguity for about 37 years, 1987-
> 2024.
> > >
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> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
> > You can reach the person managing the list at:
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> >
> >
> >
> > --
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> > DODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxAMT
> > FWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQQrGQG4$
> > (use the 'visit archived web site' link, then the 'Ghost Moth Research
> > page' link.
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> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
> > You can reach the person managing the list at:
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> > Nurturing nuance while assailing ambiguity for about 37 years, 1987-2024.
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> >
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
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> > PvDODwlR4mBZyAb0!RBv0Sv3jzvlkcDaOrAZaWoS9vZ_JNnIMGs-
> I_H5OMdS1Cod8zbFxA
> > MTFWNGfTSDn4F4QZByKUfpVQQyUmJN_Qg6GdQU6BUrl$
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> > ------------------------------
> >
> > End of Taxacom Digest, Vol 217, Issue 16
> > ****************************************
> >
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