Gmail Steve Mount <smmount@gmail.com>

Can we not speak of fish?
9 messages
Steve Mount <steve@stevemount.info> Thu, May 27, 2010 at 8:14 AM
To: Charles Delwiche <delwiche@umd.edu>, charles mitter <cmitter@umd.edu>
My dear friends in systematics,

I have a question about systematics that I would like your opinion on.  It seems a sufficiently central question that I suspect you have already formed an opinion.  The issue is a practical one, regarding how biologists should use terms.  It is also philosophical (but in the rigorous sense, relating to the idea that without a proper philosophical basis one cannot do science at all).

Consider a monophyletic group of organisms, G, and another phylogenetic group within it, C (for clade).  Let us suppose that C is characterized by some fundamental innovation, such that organisms within this clade have a long list of features not found in the other species within G.  Furthermore, species within G but not C share a long list of features that have been lost by all species in C.  As a result, there is a need to talk about another grouping, W (for wrong), of those species within G but not C.  There is no doubt about the phylogeny.  C and G are monophyletic but W is not.  Molecules and morphology agree.  However, all species within W share many features lacking in all species within C, and this is true both morphologically and molecularly. 

Is it ever right for a scientist to talk about W as a group?
You know the list (reptiles, fish, dicots, prokaryotes). 

Back story.
This came up last night as an argument between Jonathan Eisen and myself, on Twitter.  You can see most of it by looking at feeds for
phylogenomics, ongenetics and smount, but given the volatile and perspective-based nature of Twitter feeds I've pasted the relevant tweets into the attached word document (it reads from most recent to earliest so my might want to start at the bottom and work up).  Jonathan is at the ASM meeting.  He is a Twitter addict who has generated over 4500 tweets in the last year or so (a day with only 10 would be unusual for him).  I find it useful and interesting to follow him.  I am both ongenetics and smount (I didn't mean to switch but I changed computers and forgot to switch).

I find it useful to refer to prokaryotes (and to fish).  Jonathan says "grouping together bacteria/archaea is inappropriate; I note in my evolution textbook we use "bacteria & archaea" a lot".  Wouldn't it be simpler if he just used "prokaryote."?  I'm looking for advice here.

Thanks,

Steve


--
Stephen M. Mount
Center for Bioinformatics and Computational Biology
Dept. of Cell Biology and Molecular Genetics
H. J. Patterson Hall
University of Maryland
College Park, MD    20742-5815

Phone      301-405-6934
alt. ph.   301-405-9904
URL        www.SteveMount.org
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Steve Mount <steve@stevemount.info> Thu, May 27, 2010 at 8:18 AM
To: Charles Delwiche <delwiche@umd.edu>, charles mitter <cmitter@umd.edu>
The missing attachment is here.
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Twitter-clade.doc
100K

Charles Francis Delwiche <delwiche@umd.edu> Thu, May 27, 2010 at 5:28 PM
To: smount-contact <steve@stevemount.info>
Cc: Charles Mitter <cmitter@umd.edu>
Well, I'm basically with Jonathan on this, although I think I'm slightly more moderate.  "Fish," "prokaryotes," "reptiles," "dicots," etc. are really form-classes -- they describe the appearance of the organism, but not its evolutionary relationships.  Naming paraphyletic groups is somewhat less objectionable than naming grossly polyphyletic ones, so I don't object to naming the North American Drosophila in a way that ignores the Hawaiian species that are derived from within it (this an example of your C/G case).  But it really is confusing to refer to prokaryotes.  Although they have coupled transcription and translation, the are other aspects of DNA replication, transcription, and translation that show striking similarities between Archaea and Eukarya.  If you talk about "prokaryotes" as if the term represented a lineage rather than a morphology then it tends to obscure both diversity within them similarities between Archaea and Eukarya. 

The reason this is important is that hides the predictive value that a natural classification can provide.  Within your group G there would be some taxa that are more closely related to C than others, and they will share properties with C despite the long branch and loss of characters you describe.  If you treat "fish" as a group it is confusing that Teleosts have immune systems that more nearly resemble those of tetrapods than do those of lampreys or hagfish.  I don't know anything about lung- or lobe-finned fish immunology, but I'll bet they are even more tetrapod-like than those of Teleosts.  Much the same statements could be made for skeletal structure, tooth anatomy, ventilation mechanisms, and I don't know what all else.

This is why we Must Never Speak of Fish Again.

Chuck

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--
Charles F. Delwiche, Associate Professor, Cell Biology and Molecular Genetics
Mail: 2108 Biosciences Research Building
University of Maryland - College Park  Bldg.  #413
College Park, MD 20742-4407
http://www.life.umd.edu/labs/delwiche  tel: 301-405-8286 fax: 301-314-1248

They have a large barge with a radio antenna tower on it that they would charge up and discharge. - GYBE


Charles Mitter <cmitter@umd.edu> Thu, May 27, 2010 at 5:30 PM
To: Charles Francis Delwiche <delwiche@umd.edu>, smount-contact <steve@stevemount.info>
thanks chuck!
i will expand on this answer later this evening.
it's an argument that has existed in some form at least since Aristotle; i treat it in my systematics course.
________________________________________
From: Charles Francis Delwiche
Sent: Thursday, May 27, 2010 5:28 PM
To: smount-contact
Cc: Charles Mitter
Subject: Re: Can we not speak of fish?

Well, I'm basically with Jonathan on this, although I think I'm slightly more moderate.  "Fish," "prokaryotes," "reptiles," "dicots," etc. are really form-classes -- they describe the appearance of the organism, but not its evolutionary relationships.  Naming paraphyletic groups is somewhat less objectionable than naming grossly polyphyletic ones, so I don't object to naming the North American Drosophila in a way that ignores the Hawaiian species that are derived from within it (this an example of your C/G case).  But it really is confusing to refer to prokaryotes.  Although they have coupled transcription and translation, the are other aspects of DNA replication, transcription, and translation that show striking similarities between Archaea and Eukarya.  If you talk about "prokaryotes" as if the term represented a lineage rather than a morphology then it tends to obscure both diversity within them similarities between Archaea and Eukarya.

The reason this is important is that hides the predictive value that a natural classification can provide.  Within your group G there would be some taxa that are more closely related to C than others, and they will share properties with C despite the long branch and loss of characters you describe.  If you treat "fish" as a group it is confusing that Teleosts have immune systems that more nearly resemble those of tetrapods than do those of lampreys or hagfish.  I don't know anything about lung- or lobe-finned fish immunology, but I'll bet they are even more tetrapod-like than those of Teleosts.  Much the same statements could be made for skeletal structure, tooth anatomy, ventilation mechanisms, and I don't know what all else.

This is why we Must Never Speak of Fish Again.

Chuck


On May 27, 2010, at 8:14 AM, Steve Mount wrote:

My dear friends in systematics,

I have a question about systematics that I would like your opinion on.  It seems a sufficiently central question that I suspect you have already formed an opinion.  The issue is a practical one, regarding how biologists should use terms.  It is also philosophical (but in the rigorous sense, relating to the idea that without a proper philosophical basis one cannot do science at all).

Consider a monophyletic group of organisms, G, and another phylogenetic group within it, C (for clade).  Let us suppose that C is characterized by some fundamental innovation, such that organisms within this clade have a long list of features not found in the other species within G.  Furthermore, species within G but not C share a long list of features that have been lost by all species in C.  As a result, there is a need to talk about another grouping, W (for wrong), of those species within G but not C.  There is no doubt about the phylogeny.  C and G are monophyletic but W is not.  Molecules and morphology agree.  However, all species within W share many features lacking in all species within C, and this is true both morphologically and molecularly.

Is it ever right for a scientist to talk about W as a group?
You know the list (reptiles, fish, dicots, prokaryotes).

Back story.
This came up last night as an argument between Jonathan Eisen and myself, on Twitter.  You can see most of it by looking at feeds for
phylogenomics<http://twitter.com/phylogenomics>, ongenetics<http://twitter.com/ongenetics> and smount<http://twitter.com/smount>, but given the volatile and perspective-based nature of Twitter feeds I've pasted the relevant tweets into the attached word document (it reads from most recent to earliest so my might want to start at the bottom and work up).  Jonathan is at the ASM meeting.  He is a Twitter addict who has generated over 4500 tweets in the last year or so (a day with only 10 would be unusual for him).  I find it useful and interesting to follow him.  I am both ongenetics and smount (I didn't mean to switch but I changed computers and forgot to switch).

I find it useful to refer to prokaryotes (and to fish).  Jonathan says "grouping together bacteria/archaea is inappropriate; I note in my evolution textbook we use "bacteria & archaea" a lot".  Wouldn't it be simpler if he just used "prokaryote."?  I'm looking for advice here.

Thanks,

Steve


--
Stephen M. Mount
Center for Bioinformatics and Computational Biology
Dept. of Cell Biology and Molecular Genetics
H. J. Patterson Hall
University of Maryland
College Park, MD    20742-5815

Phone      301-405-6934
alt. ph.   301-405-9904
URL        www.SteveMount.org<http://www.SteveMount.org/>
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Steve Mount <steve@stevemount.info> Thu, May 27, 2010 at 8:41 PM
To: Charles Francis Delwiche <delwiche@umd.edu>
Cc: Charles Mitter <cmitter@umd.edu>
Chuck,

Thanks.  That's really very nice. 
Can I quote you on my blog?
Also, I like the use of strikeout in your signature.

Steve
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Delwiche Charles <delwiche@umd.edu> Thu, May 27, 2010 at 10:01 PM
To: Steve Mount <steve@stevemount.info>
Thanks, and sure.  And thanks.

The funny thing about the strikeout is that I thought it would be extremely subtle, but it is not.  People pick up on it right away.

Chuck
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Charles Francis Delwiche <delwiche@umd.edu> Fri, May 28, 2010 at 12:43 PM
To: smount-contact <steve@stevemount.info>
Cc: Charles Mitter <cmitter@umd.edu>
Hmm... thinking more about this, I looked at an ichthyology text I have and compared its phylogenies to the ones in the book we use for BSCI 207.  Although they broadly agree, the fact that the ichthyology text omits tetrapods makes the trees look distinctly different, with teleosts at the "crown".  If taxonomy were done by teleosts, tetrapods would be treated as a bizarre group of primitive fishes that couldn't hack the competition in the aquatic environment but persist in a refugium on the land.

Chuck


On May 27, 2010, at 8:41 PM, Steve Mount wrote:

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Steve Mount <steve@stevemount.info> Fri, May 28, 2010 at 1:27 PM
To: Charles Francis Delwiche <delwiche@umd.edu>
Chuck,

Is wikipedia right on this?

Osteichthyes (pronounced /ˌɒstiːˈɪkθi.iːz/), also called bony fish, are a taxonomic group of fish that have bony, as opposed to cartiligeous, skeletons. The vast majority of fish are osteichthyes, which is an extremely diverse and abundant group consisting of over 29,000 species. It is the largest class of vertebrates in existence today. Osteichthyes is divided into the ray-finned fish (Actinopterygii) and lobe-finned fish (Sarcopterygii).

In most classification systems[1] the Osteichthyes are paraphyletic with land vertebrates. That means that the nearest common ancestor of all Osteichthyes includes tetrapods amongst its descendants. Actinopterygii (ray-finned fish) are monophyletic, but the inclusion of Sarcopterygii in Osteichthyes causes Osteichthyes to be paraphyletic.

Most bony fish belong to the ray-finned fish (Actinopterygii); there are only eight living species of lobe-finned fish (Sarcopterygii), including the lungfish and coelacanths.

Traditionally, the bony fish had been treated as a class within the vertebrates, with Actinopterygii and Sarcopterygii as subclasses, but recently Osteichthyes was elevated to a superclass, with Actinopterygii and Sarcopterygii recognized as its constituent classes.[citation needed]

95% of fish and the majority of vertebrates are Actinopterygii, so I think you've got it right.  The tetrapods would be thought "not true fish."  This appears to be a common strategy by which cladists rescue paraphyletic groups.  They refer to the monophyletic "core" instead of the whole (paraphyletic) group (Clade G - Clade C), as in Jonathan's "bacteria and archaea."
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Charles Francis Delwiche <delwiche@umd.edu> Fri, May 28, 2010 at 1:43 PM
To: smount-contact <steve@stevemount.info>
Yes, I think that is correct, although there seems to be debate about whether or not the lobe-finned fish are monophyletic.

As you indicate, we could mostly sort things out by calling ray-finned fish "eufish" or something like that.  The problem, of course, is that then we would have to tell people that sharks are not true fish, etc.

Chuck
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