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Author
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Topic: Flagellum and the TTSS evolved from common ancestor
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Doubting Thomas
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posted 27. March 2004 13:59
From Gene 312 (2003), pp. 151-163 (available for free online):
quote:
Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events
ABSTRACT
Type III secretion systems (TTSS) are unique bactrerial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as decided from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.
The principal conclusion (that bacterial flagella and type III secretion systems evolved from a common ancestor), is given on p. 153:
quote:
3. RESULTS
3.1. Evolution of the type III secretion system from flagella is unlikely
All four protein trees are compatible with the hypothesis that both flagellar and TTSS protein subfamilies are monophyletc [i.e., derived from a single ancestor]
A comparison of different artists' renderings of the flagellum and the TTSS demonstrates the strong physical resemblance of the two systems:
Flagellum from E. coli K-12 MG1655:
http://www.genome.ad.jp/kegg/pathway/eco/eco02040.html
Type III secretion system from different strain of E. coli :
http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=ece&mapno=03070
The evidence presented in this paper strongly suggests that the bacterial flagellum that we find today did evolve from an ancient ancestor.
[ 27. March 2004, 14:31: Message edited by: Doubting Thomas ]
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Mike Gene
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posted 27. March 2004 20:53
Yeah, but their arguments are quite weak. Also, their main motivation for skepticism was outlined in their introduction and seems rather strange to me:
quote:
Second, the suggestion that a simpler system (TTSS) is derived from a more complex system (flagella) is quite odd in an evolutionary context since it runs against the progressionist grain that pervades evolutionary thought since the days of Jean-Baptiste Lamarck. As was pointed out by Aizawa (2001): “The flagellum is a beautifully designed architecture almost completed in evolution. Why should those sophisticated skills be abandoned to go back to boring soluble proteins?”
Our evolutionary context was set by Lamarck? And Aizawa’s argument is quite odd. Haven’t these guys heard of microsporidia? myxozoa? mycoplasma? Anyway, to their results……
The abstract of the paper asserts: The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted.
That’s a rather strong claim. Yet their whole argument effectively boils down to this: Branch lengths indicate that the levels of diversity are similar in the TTSS and flagella subtrees implying a similar degree of antiquity for both groups.
In other words, let’s imagine the TTSS evolved from the flagellar export system in chlamydiae (as JF Kim argues). Gophna et al. are (for example) then assuming that the TTSS machinery should thus nest with the chlamydiae flagellar export system. That doesn’t seem like a very good assumption to me.
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Doubting Thomas
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posted 28. March 2004 15:18
Here is a reduced and edited part of the most recent analysis of the flagellum arising together with the TTSS by Ian Musgrave and Peter Gegenheimer. I'm posting it in support of the thesis posted at the top of this thread and in response to some of Mike Gene's points:
quote:
Proposed evolutionary pathways:
A possible scenario for the evolution of the eubacterial flagella is as follows: a secretory system arose first, based around the SMC rod pore forming complex, which was the common ancestor of the type III secretory system, and the flagellar system.
The proto-flagellar filament arose next as part of the protein secretion structure (cf the Pseudomonas pilus, the Salmonella filamentous apendages and the E coli filamentous structures), finally (as suggested by the presence of at least two, if not three, indpendent motors) an ion pump which was doing something else [see note] became associated with this structure and motility (presumably weak) occured fortuitosly. Even today MotAB can freely dissociate and re-associate with the flagellar structure. This early, limited motility was later refined into the more compentent system we see today. Alternatively, the ion pumps became linked to the proto-flagella to provide extra "power" to pump proteins out of the complex, and flagella motion occured via fortuitous mutations in the linkers FliG,N,M later on. Regulation and switching can be added on later as there are modern eubacteria that lack these and function well in their environments.
Significantly, flagellar and other non-flagellar proteins are exported into culture medium via the flagellum, and MotA deletion slows transport through the flagellum, suggesting that the flagella still functions as a protein secretion system(5,6). Furthermore, the genes for "rivet" rod and SMC ring complex form a single transcription unit, are the orientation and order of these genes are very similar between the type III secretory systems and the flagellum(8).
This re-enforces the idea that eubacterial flagella and type III transport arose from a common ancestral system, and that motility arose as the co-option of an exitsing system that was doing something else. It would not be the first time that a secretory system was co-opted into motility, as the cyanobacteria have co-opted a carbohydrate export system to produce gliding motion.
The above discussion dealt with the accquisition of the main components, the molecular details of the actual changes are less certain, given how little we know about the details of the channeling of the protons and how FliG generates rotation. A speculative idea for the evolutionary linkage of the protoFliG to motor function is as follows. FliG, the torque generator, is a Y shaped molecule, and the rotor sits on the arms of the Y. The protoFLiG was originally a support system for the transport machinary. Adding the MotAB system to the protoflagellar complex adds protons to drive the transported substrates faster up the hollow rotor. Then a mutation alters protoFliG so that proton acceptance by FliG causes one of the arms of the Y to rotate (as seen in other molecules), then this would rotate the rotor, and hence the filament, and motion commences. As I said this is speculative, and a more detailed analysis of FliG and the FliG homologs, plus other components of the system, is needed to get a clearer picture.
Conclusions:
I have presented evidence that eubacterial flagellar systems evolved from, and still function today as, secretory systems.
This is a very tentative sketch, but it does seem that a fully detailed evolutionary explanation for eubacterial flagella is not so distant. While the details of the motor/rotor/filament system assembly seem reasonably clear, the details of the evolution of the FliG,M,N torque generating sytem are lacking, as we know little about how these systems generate torque.
It would be very interesting to see if addition of MotAB to a type III secretory system produces torque without any further modifcation. Can you replace FliG with HrpQ (or other homologs) in the flagella and still get torque? Can you substitute motors between Virio and E. coli? This is a rich field for research.
The eubacterial flagellar system is also interesting as it shows how misleading "design" thinking is. In this case what is defined as IC depends on our point of view. When viewed as a motile stucture, the flagella is IC. Remove the motor, it stops functioning, remove the hook (universal joint) it stops functioning, remove the fliament it ... well, it still works sort of :-). Viewing the flagellum as a motor, and an IC motor at that, provides no insights into the origin or functioning of this structure.
But view it as a secretory structure, it is NOT IC, remove the filament and it still works, remove the hook and it still works, remove the motor and it still works, not as well as with the motor, but it still works.
Thus, if the flagella is a secretory system that has been co-opted for a motile function (while still retaining some of it's secretory function), then the ICness of the system is in the mind of the beholder, and a clear path for it's evolution is opened up.
References:
1. Asai Y, Kawagishi I, Sockett RE, and Homma M. (1999 Oct). Hybrid motor with H(+)- and Na(+)-driven components can rotate Vibrio polar flagella by using sodium ions. J Bacteriol, 181, 6332-8.
2. Berry RM, and Armitage JP. (1999). The bacterial flagella motor. Adv Microb Physiol, 41, 291-337.
3. Faugy DM and Farrel K, (1999 Feb) A twisted tale: the origin and evolution of motility and chemotaxis in prokaryotes. Microbiology, 145, 279-280.
4. Delahay RM, Knutton S, Shaw RK, Hartland EL, Pallen MJ, Frankel G. (1999 Dec 10) The coiled-coil domain of EspA is essential for the assembly of the type III secretion translocon on the surface of enteropathogenic Escherichia coli. J Biol Chem, 274(50):35969-74.
5. Komoriya K, Shibano N, Higano T, Azuma N, Yamaguchi S, Aizawa SI. (1999 Nov) Flagellar proteins and type III-exported virulence factors are the predominant proteins secreted into the culture media of Salmonella typhimurium. Mol Microbiol, 34(4):767-79.
6. Young GM, Schmiel DH, Miller VL. (1999 May 25) A new pathway for the secretion of virulence factors by bacteria: the flagellar export apparatus functions as a protein-secretion system. Proc Natl Acad Sci U S A, 96(11):6456-61.
7. DeRosier DJ. (1998 Apr 3). The turn of the screw: the bacterial flagellar motor. Cell, 93, 17-20.
8. Hueck CJ (1998 Jun) Type III Protein Secretion Systems in Bacterial Pathogens of Animals and Plants. Microbiol Mol Biol Rev, 62, 379-433.
9. Asai Y, Kojima S, Kato H, Nishioka N, Kawagishi I, and Homma M. (1997Aug). Putative channel components for the fast-rotating sodium-driven flagellar motor of a marine bacterium. J Bacteriol, 179, 5104-10.
10. He SY. (1997 Dec) Hrp-controlled interkingdom protein transport: learning from flagellar assembly. Trends Micro, 5, 489-495.
11. Harshey RM and Toguchi A (1996 Jun) Spining Tails: homologies amongst bacterial flagellar systems. Trends Micro, 4, 226-231.
12. Jarrel KF, Bayley DP and Kostyukova AS (1996 Sep) The Archael Flagellum: a unique motility structure. J Bacteriol, 178, 5057-5064.
13. Shah DS, and Sockett RE. (1995 Sep). Analysis of the motA flagellar motor gene from Rhodobacter sphaeroides, a bacterium with a unidirectional, stop-start flagellum. Mol Microbiol, 17, 961-9.
14. Behe, MJ. Darwin's Black Box: The Biochemical Challenge to Evolution (New York: The Free Press, 1996)
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Last updated: 2:34pm on 11/25/00 by pgegen@ku.edu
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This page is provided by Ian Musgrave and is © copyright 2000 Ian Musgrave
This page can be used freely for any non-commercial purpose but please attribute it correctly. Standard disclaimers apply.
Email reynella@werple.mira.net.au e-mail Ian with any suggestions
Created: Friday, 17 March 2000, 16:01:19
Last Updated: Friday, 17 March 2000, 16:01:19
Regarding the motility proteins MotA & MotB, examination of the genome of the familiar lab microbe E. coli shows their genes to be clustered together in a single operon, making their horizontal transfer and co-option straightforward.
[ 28. March 2004, 15:38: Message edited by: Doubting Thomas ]
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Doubting Thomas
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posted 28. March 2004 16:13
Mike Gene wrote:
quote:
Yeah, but their arguments are quite weak. Also, their main motivation for skepticism was outlined in their introduction and seems rather strange to me:
quote:
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Second, the suggestion that a simpler system (TTSS) is derived from a more complex system (flagella) is quite odd in an evolutionary context since it runs against the progressionist grain that pervades evolutionary thought since the days of Jean-Baptiste Lamarck. As was pointed out by Aizawa (2001): “The flagellum is a beautifully designed architecture almost completed in evolution. Why should those sophisticated skills be abandoned to go back to boring soluble proteins?”
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Our evolutionary context was set by Lamarck? And Aizawa’s argument is quite odd. Haven’t these guys heard of microsporidia? myxozoa? mycoplasma? Anyway, to their results……
I don't necessarily agree with their introductory comments. And as far as their comment about Lamarck, I read it as 'since Lamarck was discredited' rather than as you do.
quote:
The abstract of the paper asserts: The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted.
That’s a rather strong claim. Yet their whole argument effectively boils down to this: Branch lengths indicate that the levels of diversity are similar in the TTSS and flagella subtrees implying a similar degree of antiquity for both groups.
In other words, let’s imagine the TTSS evolved from the flagellar export system in chlamydiae (as JF Kim argues). Gophna et al. are (for example) then assuming that the TTSS machinery should thus nest with the chlamydiae flagellar export system. That doesn’t seem like a very good assumption to me.
I haven't seen Kim's paper, just the abstract from PubMed. It talks about 'chlamydialiae or related proteins'. He may be describing a more general scenario. Until I can read the full paper I will have to disreagard your criticism above.
Gophna et al chose four highly conserved and homologous elements out of the nine found in both systems and established phylogenetic trees using standard methods. These are as follows, with their respective TTSS/flagellar designators:
1. SctN/FliI
2. SctV/FlhA
3. SctR/FliP
4. SctS/FliQ
The key points in the Gophna et al paper can be summarized in the following quotes:
From p. 159 (caption to Fig. 1):
quote:
...it is possible to position the roots so that all trees are compatible with the monophyly of the flagellar export subfamily as well as with the monophyly of its paralogous TTSS subfamily. (p. 159)
quote:
All four trees are compatible with the hypothesis that both flagellar and TTSS subfamilies are monophyletic (Fig. 2a)(p. 154)
In other words, they evolved from a common ancestor.
quote:
Thus, the suggestion that TTSS evolved from flagella {e.g. Galan and Collmer, 1999; Macnab, 1999;Nguyen et al 2000), by what can only be called 'reductive evolution,' receives no support from the phylogenetic trees. (p. 155)
quote:
Thus, the phylogenetic reconstruction does not support the claim that type III secretion systems elements originated from components of the flagellar export apparatus. (pp. 155-6)
The Gophna et al paper lends support to the work by Ian Musgrave and Peter Gegenheimer that I posted above. If the flagellum evolved, it can't be IC , by definition. But here we see that it likely did evolve. It is certainly easier to see how it might have evolved rather than how it might have been designed.
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RBH
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posted 29. March 2004 02:09
Doubting Thomas wrote quote:
Here is a reduced and edited part of the most recent analysis of the flagellum arising together with the TTSS by Ian Musgrave and Peter Gegenheimer.
I checked with Musgrave: His brief review on the Web is not "published" - it has not appeared in the peer reviewed literature. Gegenheimer was not involved in writing it, and as far as Musgrave is aware Gegenheimer has done no work in this area. I suggest that DT recheck his reference, maybe provide a URL for it, and clear this up.
Musgrave will have a chapter on the flagellum in the forthcoming "Where Intelligent Design Fails." It's due out mid-summer, last he heard.
RBH
[ 29. March 2004, 02:11: Message edited by: RBH ]
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Doubting Thomas
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posted 29. March 2004 10:47
RBH wrote:
quote:
Doubting Thomas wrote
quote:
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Here is a reduced and edited part of the most recent analysis of the flagellum arising together with the TTSS by Ian Musgrave and Peter Gegenheimer.
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I checked with Musgrave: His brief review on the Web is not "published" - it has not appeared in the peer reviewed literature. Gegenheimer was not involved in writing it, and as far as Musgrave is aware Gegenheimer has done no work in this area. I suggest that DT recheck his reference, maybe provide a URL for it, and clear this up.
Musgrave will have a chapter on the flagellum in the forthcoming "Where Intelligent Design Fails." It's due out mid-summer, last he heard.
RBH
Musgrave has long maintained this review on the web and as you can see from the tag line, grants permission for its republication with attribution. I grant you that it is not 'peer reviewed,' but neither was Darwin's Black Box. It hypothesizes exactly the same mechanism of flagellar evolution that I discussed in the peer reviewed paper by Gophna et al. You will also note where Peter Gegenheimer states that he had a hand in editing it.
As far as the URL is concerned, you have already supplied it (above).
Please note that Dr. Gegenheimer also hosts this paper on his 'RNA World' server at the University of Kansas-Lawrence. http://rnaworld.bio.ku.edu/ribozone/resource/transport/Ian%20Musgrave_flagella.htm#Evolve Musgrave could have at least acknowledged Dr. Gegenheimer's interest and support.
And thanks for the information on Musgrave's upcoming book. I'm looking forward to it.
[ 29. March 2004, 10:55: Message edited by: Doubting Thomas ]
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RBH
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posted 29. March 2004 14:29
DT wrote quote:
You will also note where Peter Gegenheimer states that he had a hand in editing it.
Not to be pedantic, but no, I don't see that statement. I see a notation that Gegenheimer updated the page on which he has reproduced Musgrave's essay, but nothing about editing. That Gegenheimer's notice of "Last updated ... on 11/25/00" is inserted before the last lines of Musgrave's page (it's not in the original hosted on Musgrave's institutional site) is perhaps a little confusing, but Gegenheimer was neither a co-author nor an editor of Musgrave's piece unless he changed it without notifying Musgrave. I haven't done a line-by-line comparison to see if that's the case.
I'm being a little picky about this because Musgrave, with whom I've been acquainted for some time, was surprised to hear that he had a collaborator on the piece and asked that I clarify the point.
DT further wrote quote:
Musgrave could have at least acknowledged Dr. Gegenheimer's interest and support.
I repeat, Gegenheimer did not collaborate with Musgrave on the piece as coauthor or editor. Gegenheimer, acting independently, reproduced Musgrave's piece on his (Gegenheimer's) site some months after it was written, in a manner consistent with the requirements Musgrave has embedded in the piece, but the two have not been in communication about that essay or (from what I infer from Ian's email to me) about anything else.
RBH
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Doubting Thomas
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posted 29. March 2004 15:17
RBH wrote:
quote:
DT wrote
quote:
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You will also note where Peter Gegenheimer states that he had a hand in editing it.
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Not to be pedantic, but no, I don't see that statement. I see a notation that Gegenheimer updated the page on which he has reproduced Musgrave's essay, but nothing about editing. That Gegenheimer's notice of "Last updated ... on 11/25/00" is inserted before the last lines of Musgrave's page (it's not in the original hosted on Musgrave's institutional site) is perhaps a little confusing, but Gegenheimer was neither a co-author nor an editor of Musgrave's piece unless he changed it without notifying Musgrave. I haven't done a line-by-line comparison to see if that's the case.
I'm being a little picky about this because Musgrave, with whom I've been acquainted for some time, was surprised to hear that he had a collaborator on the piece and asked that I clarify the point.
DT further wrote
quote:
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Musgrave could have at least acknowledged Dr. Gegenheimer's interest and support.
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I repeat, Gegenheimer did not collaborate with Musgrave on the piece as coauthor or editor. Gegenheimer, acting independently, reproduced Musgrave's piece on his (Gegenheimer's) site some months after it was written, in a manner consistent with the requirements Musgrave has embedded in the piece, but the two have not been in communication about that essay or (from what I infer from Ian's email to me) about anything else.
RBH
I am not personally familiar with either Musgrave or Gegenheimer. When I saw a) that Musgrave's review was on Gegenheimer's server, and that b) Gegenheimer stated that he had updated the document, I tried to be politically correct and acknowledge both individuals, irrespective of whatever their relative contributions may have been. This was to avoid exactly the type of 'pedantic' misunderstanding that resulted in your post above. But 'updated' means to me 'put in some effort', whatever that was. And providing hosting space on a university server is by no means something that should be dismissed with only a 'So what?'
As a general rule, I do not email Bill Dembski or Mike Behe or other sources and ask either their permission or comments before posting brief excerpts of their work as inclusions in posts. If I did, I would include the note "Personal communication.' I certainly didn't think that emailing Musgrave or Gegenheimer before posting that piece was necessary either, as I was, if anything, being only over-generous with my attribution.
I hope you choose in the future to contribute more constructive content to this and other threads that I have started. Thank you for your interest.
[ 29. March 2004, 15:23: Message edited by: Doubting Thomas ]
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RBH
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posted 29. March 2004 16:36
DT wrote quote:
As a general rule, I do not email Bill Dembski or Mike Behe or other sources and ask either their permission or comments before posting brief excerpts of their work as inclusions in posts. If I did, I would include the note "Personal communication.' I certainly didn't think that emailing Musgrave or Gegenheimer before posting that piece was necessary either, as I was, if anything, being only over-generous with my attribution.
I hope you choose in the future to contribute more constructive content to this and other threads that I have started. Thank you for your interest.
Had DT not added that last little needle I'd have let this lay. However, "over-generous with my attribution" and "mis-attribution of authorship" are not synonyms. So let me be very clear: Musgrave is the sole author of the piece; Gegenheimer merely reproduced it on his university's server some time later without Musgrave's knowledge.
RBH
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Doubting Thomas
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posted 29. March 2004 17:15
RBH wrote:
quote:
DT wrote
quote:
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As a general rule, I do not email Bill Dembski or Mike Behe or other sources and ask either their permission or comments before posting brief excerpts of their work as inclusions in posts. If I did, I would include the note "Personal communication.' I certainly didn't think that emailing Musgrave or Gegenheimer before posting that piece was necessary either, as I was, if anything, being only over-generous with my attribution.
I hope you choose in the future to contribute more constructive content to this and other threads that I have started. Thank you for your interest.
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Had DT not added that last little needle I'd have let this lay. However, "over-generous with my attribution" and "mis-attribution of authorship" are not synonyms. So let me be very clear: Musgrave is the sole author of the piece; Gegenheimer merely reproduced it on his university's server some time later without Musgrave's knowledge.
RBH
In no way did I 'mis-attribute authorship.' And I'm sincere in my wish that you contribute constructively to my threads.
I will not respond to any further posts on this authorship question. I consider the matter settled.
[ 29. March 2004, 17:16: Message edited by: Doubting Thomas ]
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RBH
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posted 29. March 2004 20:41
Here is Dr. Musgrave's response to DT's posting. Italics are verbatim comments from Ian referenced to the specific quotations from DT's posting.
DT wrote quote:
Musgrave has long maintained this review on the web and as you can see from the tag line, grants permission for its republication with attribution.
Na Und? Not relevant to the issue, which is accurately representing the material.
DT: quote:
I grant you that it is not 'peer reviewed,' but neither was Darwin's Black Box.
The point is that it is being discussed as if it were a published, peer reviewed paper, without making the distinction clear. It's a matter of clarity, accuracy and correct representation.
DT: quote:
It hypothesizes exactly the same mechanism of flagellar evolution that I discussed in the peer reviewed paper by Gophna et al. You will also note where Peter Gegenheimer states that he had a hand in editing it.
Where? there is a "last updated" tag on the page at Peter's site (Last updated: 2:34pm on 11/25/00 by pgegen@ku.edu), that doesn't tell you anything about editing. I can find no page where Peter says he edited it, and if he edited it, it was very minor, as I can see no readily apparent difference between the copy on Peters site and the copy on my site. On my site I don't mention Peter as he had no role in creating or editing that page.
Furthermore, light editing does not a co-author make. I have done copy editing for quite a few people but I don't get co-authorship.
DT: quote:
As far as the URL is concerned, you have already supplied it (above).
No, the web page excerpt was from Peters site, not my site. My version doesn't have the "Last updated: 2:34pm on 11/25/00 by pgegen@ku.edu" or any indication that Peter was involved (because he wasn't).
DT: quote:
Please note that Dr. Gegenheimer also hosts this paper on his 'RNA World' server at the University of Kansas-Lawrence. (http://rnaworld.bio.ku.edu/ribozone/resource/transport/Ian%20Musgrave_flagella.htm#Evolve)
This was the one referenced in the article, not the one on my server.
DT: quote:
Musgrave could have at least acknowledged Dr. Gegenheimer's interest and support.
I would have if I had known about it. Also, you can't actually get to the flagella page from http://rnaworld.bio.ku.edu/, there are no links to it, and you have to do some serious digging to find it.
This may sound all a bit precious, but it is about accurately representing the material. If getting something as simple as attributing a web page correctly is not done right, then what about the representations and interpretations of the other material?
DT: quote:
And thanks for the information on Musgrave's upcoming book.
Book CHAPTER, not book, get it right.
DT: quote:
I'm looking forward to it.
I hope you find it interesting.
Cheers,
Ian
I'm not sure if the last bit was directed to DT or me, but I'll include it here for good will.
RBH
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Mike Gene
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posted 29. March 2004 22:34
DT,
You quote from the Gophna paper as follows:
quote:
All four trees are compatible with the hypothesis that both flagellar and TTSS subfamilies are monophyletic (Fig. 2a)(p. 154)
And then add:
quote:
In other words, they evolved from a common ancestor.
You are pushing the argument further than they did. That the trees are compatible with the hypothesis does not necessarily mean they evolved from a common ancestor.
I read the Gophna paper. As I said above, that’s their whole argument. But the argument is built on very questionable assumptions. For example, why would you expect SctS and FliQ, for example, to evolve at the same rate?
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Doubting Thomas
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posted 30. March 2004 13:44
Mike Gene wrote:
quote:
DT,
You quote from the Gophna paper as follows:
quote:
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All four trees are compatible with the hypothesis that both flagellar and TTSS subfamilies are monophyletic (Fig. 2a)(p. 154)
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And then add:
quote:
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In other words, they evolved from a common ancestor.
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You are pushing the argument further than they did. That the trees are compatible with the hypothesis does not necessarily mean they evolved from a common ancestor.
Mike, the last taxonomy text I read stated that monophyletic means 'single root,' or common ancestor. Even my well-used Webster's New World Dictionary (2nd college edition) defines it as
quote:
1. of a single stock 2. developed from a single ancestral type
And Gophna et al state on page 160:
quote:
Our analysis of the most conserved paralogs between TTSS and flagella indicates that the divergence (italics mine) between [them] may have been very ancient. Based on an estimate of 120-160 million years for the divergence between E. coli and Salmonella (Ochman and Wilson, 1987), and assuming molecular-clock regularity, the divergence (italics mine) between TTSS and flagella may have occurred hundreds of millions of years ago, much earlier than the appearance of the first multicellular eukaryotes on the evolutionary stage.
And Figure 2a shows common descent of the TTSS and flagella from a common ancestor. I don't know how much more evidence you need me to retype from this paper to show that they are claiming common ancestry and, therefore, Darwinian evolution of the bacterial flagellum.
This conclusion is hardly surprising. The flagellum we see today with its multiple functions produced by 40+ genes encoded by 10+ operons did not pop fully formed out of the primordial soup. The flagellum we see today, if only from the points of view of both parsimony and common sense, is the result of billions of years of evolution, just as is concluded by Gophna et al from analysis of gene homology data.
quote:
I read the Gophna paper. As I said above, that’s their whole argument. But the argument is built on very questionable assumptions. For example, why would you expect SctS and FliQ, for example, to evolve at the same rate?
Looking at the Figure 1d, I'd say the average length of the branches, which reflects both evolutionary time as well as the number of changes separating the proteins, is close enough to make this conclusion if you take into account their statement on page 152:
quote:
The trees constructed from the amino acid sequences will be regarded as gene trees that may or may not be congruent with the species trees due to stochastic errors and horizontal gene transfers distorting the vertical evolutionary history.
And that homologous genes would evolve at a similar average rate over the 40+ species studied does not surprise me at all.
DT
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Mike Gene
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posted 25. April 2004 18:28
DT quotes the Gophna paper as follows:
quote:
All four protein trees are compatible with the hypothesis that both flagellar and TTSS protein subfamilies are monophyletc [i.e., derived from a single ancestor]
Indeed. The trees are compatible with the hypothesis that both flagellar and TTSS protein subfamilies are monophyletic. This does not mean we have established the hypothesis. What we have is a data analysis that is simply consistent with the hypothesis. Yet as I explained before:
quote:
If TTSS sequences nested within flagellar sequence, that would not merely be an important point. Seen in the context of all the other arguments, such a finding would establish the flagella--> TTSS hypothesis. The problem is that the hypothesis of flagella --> TTSS doesn’t really predict such nesting (if you think about it). And the Gophna argument is built entirely around this questionable expectation.
So let’s put it another way. I would also say that all four protein trees are compatible with the hypothesis that the TTSS evolved from the flagellum. Do you disagree, DT? If so, explain your reasoning.
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