Freethought & Rationalism Archive

Nic Tamzek · 01-18-2003, 09:49 PM

Finally got around to reading the paper; I agree that the actual phylogeny published in the paper looks more impressive.

To their credit, the authors do take seriously the multiple-loss objection (bolds added thoroughout):

Quote:

Despite the presumed evolutionary advantages associated with full-sized wings (macroptery), nearly all pterygote (winged) orders have many partially winged (brachypterous) or wingless (apterous) lineages, and some entire orders are secondarily wingless (for example, fleas, lice, grylloblattids and mantophasmatids), with about 5% of extant pterygote species being flightless2, 3. Thousands of independent transitions from a winged form to winglessness have occurred during the course of insect evolution; however, an evolutionary reversal from a flightless to a volant form has never been demonstrated clearly for any pterygote lineage. Such a reversal is considered highly unlikely because complex interactions between nerves, muscles, sclerites and wing foils are required to accommodate flight4.

And they even calculate what kind of weighting it would take to make multiple-loss the most parsimonious:

Quote:

The most parsimonious reconstruction (MPR) of the states 'winged' and 'wingless' unambiguously places the ancestral state for phasmids as wingless, with wings derived on four (ACCTRAN optimization) or five (DELTRAN optimization) occasions (Fig. 3). Forcing the ancestral state as winged requires 13 steps in males and 14 steps in females, and is the MPR only when wing gain is weighted six times wing loss. Similar results are found when winged is divided into 'fully winged' and 'partially winged' and the states are treated as unordered. Wing states were also mapped by means of likelihood methods on both the bayesian and likelihood trees, to take into account branch lengths in determining probabilities of ancestral states14. When the rate of wing gain is set equal to that of wing loss, the phasmid ancestor is reconstructed as wingless (P < 0.001), with four independent wing gains in more derived stick insect lineages. When the ratio of the rate of wing loss over wing gain ranges from 1 to 1,400, there is a >95% probability that the ancestral phasmid was wingless.

In other words, p(wingless phasmid ancestor) < 0.001 if the rate of wing loss = rate of wing gain, and remains p < 0.05 if the rate of wing loss is 1400x that of wing gain.

If I read the methods right, they tried a range of wing loss rates up to 10000x that of wing gain, so presumably at some rate larger than 1400 (not right at 1400, that is still ~95% support for wingess ancestor) multiple-loss becomes more likely (how this rate relates to the weighting of characters is obscure to me).

So I guess it depends on what one thinks is more likely: a very high relative rate of wing loss occurences (e.g. >5000x that of wing gain occurences) or the re-evolution ideas proposed in the paper. Given the citation of thousands of independent wing losses among insects at the beginning of the paper I think that the former remains a possibility.

Their re-evolution idea predicts that some of those wingless lineages would somehow be able to maintain the viability of the genetic machinery for wings even while those genes are not being expressed for millions (?) of years. Perhaps the sharing of gene function could accomplish some of this, but it would still be surprising to me...

nic

PS: Also in that issue are some other great evo articles:

1) On spatial modelling of sympatric speciation:

Quote:

http://www.nature.com/cgi-taf/DynaPa...21225b_fs.html

Evolutionary biology: Splitting in space

DIETHARD TAUTZ

Diethard Tautz is in the Department of Genetics, University of Cologne, Weyertal 121, 50931 Cologne, Germany.
e-mail: tautz@uni-koeln.de

Disjunct distributions of closely related species are not necessarily the outcome of passive fragmentation of populations. Instead, they can be the consequence of speciation within a population.

Until recently, the overriding credo for explaining how new species are formed has run as follows: first, a population of organisms splits into several subpopulations; once isolated from other members of their own kind, these subpopulations become adapted to local conditions; so, over millions of years, their descendants evolve into new species. This is 'allopatric speciation', a concept in which spatial separation comes first and genetic divergence follows, and which has dominated biological thinking for many decades. The alternative, 'sympatric speciation', in which new species are created within a single population, has long been seen as a heresy � to the extent that young biologists would risk their careers if they proposed that such a mechanism could occur1.

Over the past few years, however, modelling work2-4 has shown that spatial separation of populations is not a prerequisite for genetic splitting. Doebeli and Dieckmann (page 259 of this issue5) now go even further. They propose that spatial separation is a secondary consequence of adaptive genetic divergence under sympatric conditions. In other words, splitting of a population in space can follow genetic splitting within it.

[...]

And on lateral gene transfer, somewhat in rebuttal to Woese and Ford Doolittle and other down-with-the-tree-of-life-model types:

Quote:

http://www.nature.com/cgi-taf/DynaPa...21217a_fs.html

Nature 421, 217 (2003); doi:10.1038/421217a

Microbial phylogenomics: Branching out

ROBERT L. CHARLEBOIS1, ROBERT G. BEIKO1 & MARK A. RAGAN2

Seven years after the publication of the first microbial genome sequence � that of Haemophilus influenzae � the roster of microbial genomes has topped 100. Despite early fears that whole-genome sequencing might be economically justified only for human pathogens, this list represents a gratifyingly broad range of microbial phenotypes � soil bacteria and photosynthesizers, thermophiles and halophiles, animal and plant pathogens, and more. At least 12 prokaryotic phyla are represented, as are a few eukaryotes � enough to allow a meaningful examination of the Tree of (microbial) Life.

In the early days of molecular phylogenetics (the mid-1960s to the early 1990s), it was thought that sequencing was the path to enlightenment � more sequences of more genes could only improve the depth and resolution of our knowledge of life's history. But instead, our 100-genome world is riven by seemingly irreconcilable conflicts; ambiguities and discrepancies are the norm, rather than the exception. Some of modern biology's fundamental tenets � notably the darwinian�mendelian model of parent-to-offspring ('vertical') gene flow � have once again, at least for microbes, been thrown into doubt. Lateral (horizontal) gene flow � in which genes are transmitted across, rather than along, branches in family trees � is no longer an explanation of last resort, but a competitive model for the origin of microbial biodiversity.

[...]

Some theorists � let's call them the verticalists � remind us of the (real or supposed) inadequacies of single-gene phylogenetics. For verticalists, protein-based trees disagree because their true phylogenetic signal is too often obscured by noise and bias. Only by overcoming these obstacles � through using better models, perhaps, or cleaner data � can we understand how microbial genomes have diversified and evolved.

But others � the lateralists � point to the sophistication and power of existing methods, and argue that trees disagree because genes really do have different histories. Microbial genomes are, to a lateralist, more or less ephemeral entities that are maintained, if only fleetingly, by the vagaries of selection and chance. The apparent woesian hierarchy of taxa is only an epiphenomenon of differential barriers � whether environmental, geographical or more intrinsically biological � to lateral gene flow.

We and others have been exploring 'whole-genome trees' as a means of overcoming the noise and bias of single-protein analyses, to extract the bulk phylogenetic signals that are inherent in genomes. The input data for genome trees can be the proportions of genes or proteins that genomes hold in common, or (as we prefer) the mean pairwise similarities between shared proteins. Despite some early indications to the contrary, whole-genome trees have now largely converged on the rRNA-sequence tree.

For us � as, presumably, for the verticalists � this convergence means that lateral gene transfer has not undermined descent with modification as the default explanation for microbial biodiversity, nor (as recently suggested by Ford Doolittle) has it thrown microbial classification into disarray.Lateral transfer is not both quantitatively important and directional. One of the few widely accepted instances of lateral gene transfer � the origin of chloroplasts from relatives of cyanobacteria � is clearly visible in our whole-genome trees, and even more so in 'sub-genome trees' based on functional subsets of genomes.

Wells would not be pleased with this last one...

charlie d · 01-19-2003, 09:27 AM

Personally, assuming that the "wing re-evolution" article is correct in its interpretation of the data, what I see as its major implication is the fact that even complex and highly specific developmental pathways can be largely shared for multiple pleiotropic functions (thereby prohibiting widespread degeneration of components upon loss of a single genetic element of the pathway). This is in fact a very significant argument against "IC"-type objections, which point to the improbability of all the complex genetic components necessary from wing development evolving from scratch.

If most of the genetic network necessary for wing development is shared with and actively involved in other functions unrelated to wings, the initial appearance of wings by co-option and modification of existing pathways becomes much less problematic in probabilistic terms. Indeed, the authors do make a similar point in the article.

I think a full understanding of the evolutionary implications will require identification of the relevant genetic pathway components and their mutations. Off the top of my head, I would say the predictions according to current theory would be the following:
1. the wing development pathway will be found to be largely shared with and involved in other developmental pathways (not just duplicated and diverged from them),
2. the original wingless mutation (and all subsequent wingless mutations that allowed wing re-evolution) will be found to affect only one or a few components of the pathway,
3. such mutated components will be found to function (almost) exclusively in wing development, unlike most other elements of the pathway
4. many of the wing re-evolution mutations will be found to be direct revertants, or more likely the result of de-novo co-option of external functional genetic elements to substitute for the mutated ones.

Of course, it may also be found that the wing development pathway is entirely functionally isolated, and that wing re-evolution is the result of its mutation and degeneration, and subsequent reappearance as a whole in different lineages. This would be hard to reconcile with current theories, I think.

Now, there is a real project an enthusiastic young IDist may undertake. Alas, I am afraid it won't appear in the next revision of the official "ID research program": far from them to run the risk to be proven wrong!

RufusAtticus · 01-30-2003, 10:28 PM

Well AiG has its version up

Albion · 01-30-2003, 11:19 PM

Quote:

Well AiG has its version up

:banghead: Why do these creationist sites always try and claim that suggested explanations (like shared developmental pathways) for unusual findings have been dreamed up out of thin air in total panic with nothing behind them? Why am I even asking?:banghead:

Nic Tamzek · 01-31-2003, 01:26 AM

Quote:

Originally posted by charlie d
I think a full understanding of the evolutionary implications will require identification of the relevant genetic pathway components and their mutations. Off the top of my head, I would say the predictions according to current theory would be the following:
1. the wing development pathway will be found to be largely shared with and involved in other developmental pathways (not just duplicated and diverged from them),
2. the original wingless mutation (and all subsequent wingless mutations that allowed wing re-evolution) will be found to affect only one or a few components of the pathway,
3. such mutated components will be found to function (almost) exclusively in wing development, unlike most other elements of the pathway
4. many of the wing re-evolution mutations will be found to be direct revertants, or more likely the result of de-novo co-option of external functional genetic elements to substitute for the mutated ones.

I agree that if re-evolution happened this is how it would probably work.

However, if this is so then I think the implications that some of the press (and the article authors IIRC) made regarding a "violation" of "Dollo's Law" were overblown -- highly similar wings were not being re-evolved from scratch but simply re-expressed.

Oolon Colluphid · 01-31-2003, 03:46 AM

Quote:

Originally posted by Nic Tamzek

Their re-evolution idea predicts that some of those wingless lineages would somehow be able to maintain the viability of the genetic machinery for wings even while those genes are not being expressed for millions (?) of years. Perhaps the sharing of gene function could accomplish some of this, but it would still be surprising to me...

and

Quote:

However, if this is so then I think the implications that some of the press (and the article authors IIRC) made regarding a "violation" of "Dollo's Law" were overblown -- highly similar wings were not being re-evolved from scratch but simply re-expressed.

From my limited understanding, this doesn�t look much different from birds retaining the potentially functional genes for making teeth and complete fibulas and separate tarsals (Hamp� and Kollar & Fisher). The only problem I see is that such things would be phenotypically macro-mutations, kind of all-or-nothing, which the Dawkinsian in me doesn�t like the sound of. Organisms are highly tuned to their environment; wingless ones must have been making a good living being like that. So suddenly acquiring wings again -- even nicely working ones -- sounds like too big a jump in �animal space� to work as a whole organism.

But... <shrugs> well, if that�s what seems to have happened... losing the wings in the first place, if it amounts to throwing an on/off switch (ie if the recipe for complete, useful wings is intact anyway), must have been quite a jump too.

Anyone know about bird teeth? A stepwise reduction in fibulas I can understand, since the tissue formation is reliant on what�s around it, and the fibula is still present, just reduced. But I can�t quite imagine (argument from incredulity coming right up!

) teeth being gradually reduced yet leaving the entire set-up just under the surface, just waiting for the right genetic-hormonal trigger.

Actually, I�m talking bollocks: if fibulas can, then teeth should be able to. But anyone got any thoughts? How phenotypically �digital� is all this, or to what extent �analogue�?

Just ramblin...

Cheers, DT

MrDarwin · 01-31-2003, 08:31 AM

Quote:

Originally posted by RufusAtticus
Exactly what I was thinking! How much you want to bet that there is already a paper in the works?

Since this thread has come up again, I was prompted to look up a recent paper on fossil phasmids: Tilgner 2001, "Fossil record of Phasmida," Insect Syst. Evol. 31: 473-480. This paper surveys the known fossils of Phasmida (and fossils attributed to the group) but unfortunately, fossils of this group are very rare, and the oldest fossils are either fragmentary, or are ambiguously assigned to Phasmida. Some of the best fossils are of nymphs preserved in amber, which are quite valuable but do not provide information as to whether the adults were winged or not.

01-30-2003, 10:28 PM	#13
RufusAtticus Veteran Member Join Date: Nov 2001 Location: NCSU Posts: 5,853	Spin Spin Spin... Well AiG has its version up

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01-19-2003, 09:27 AM	#12
charlie d Junior Member Join Date: Dec 2002 Location: here and there Posts: 56	Personally, assuming that the "wing re-evolution" article is correct in its interpretation of the data, what I see as its major implication is the fact that even complex and highly specific developmental pathways can be largely shared for multiple pleiotropic functions (thereby prohibiting widespread degeneration of components upon loss of a single genetic element of the pathway). This is in fact a very significant argument against "IC"-type objections, which point to the improbability of all the complex genetic components necessary from wing development evolving from scratch. If most of the genetic network necessary for wing development is shared with and actively involved in other functions unrelated to wings, the initial appearance of wings by co-option and modification of existing pathways becomes much less problematic in probabilistic terms. Indeed, the authors do make a similar point in the article. I think a full understanding of the evolutionary implications will require identification of the relevant genetic pathway components and their mutations. Off the top of my head, I would say the predictions according to current theory would be the following: 1. the wing development pathway will be found to be largely shared with and involved in other developmental pathways (not just duplicated and diverged from them), 2. the original wingless mutation (and all subsequent wingless mutations that allowed wing re-evolution) will be found to affect only one or a few components of the pathway, 3. such mutated components will be found to function (almost) exclusively in wing development, unlike most other elements of the pathway 4. many of the wing re-evolution mutations will be found to be direct revertants, or more likely the result of de-novo co-option of external functional genetic elements to substitute for the mutated ones. Of course, it may also be found that the wing development pathway is entirely functionally isolated, and that wing re-evolution is the result of its mutation and degeneration, and subsequent reappearance as a whole in different lineages. This would be hard to reconcile with current theories, I think. Now, there is a real project an enthusiastic young IDist may undertake. Alas, I am afraid it won't appear in the next revision of the official "ID research program": far from them to run the risk to be proven wrong!

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