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Author Topic:   Macroevolution: Its all around us...
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 136 of 306 (209932)
05-20-2005 6:43 AM
Reply to: Message 122 by mick
05-14-2005 3:23 PM


Maintaining developmental programs.
I'm not sure if any has already posted this but the Whiting lab themselves are hosting a PDF format version of the full article.
One question this paper raised for me was that of how similar the developmental program of the 're-evolved' wings were to the more primitive wingless program.
There are certainly enough conserved elements common to both wing development and the development of other systems, such as the nervous system and legs, that most of the actual genes should be maintained but I am interested in how wing specific regulatory elements would be maintained when they should be under no-selective pressure whatever.
I don't know how easy it is to observe Phasmid embryonic development or to study gene expression at different instars. But even a purely bioinformatic approach to the genomic DNA of the different species could answer a number of these questions, especially if the development of the wing in its original form is conserved in relation to a well understood model like the drosophila wing, the homology of the wing veins is a promising sign that they might be substantially conserved.
Some of these issues are also raised in a review of Whiting's work in Current Biology (Stone and French, 2003)
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 142 of 306 (210512)
05-23-2005 5:08 AM
Reply to: Message 141 by EZscience
05-22-2005 5:01 PM


Re: Maintaining developmental programs.
But do highly conserved regions automatically lose that status as soon as they are no longer transcribed ?
In terms of being themselves targets of slection? Yes, provided they are indeed wing specific and have no other function.
Are we safe in assuming that all regions of the genome experience mutation at equivalent rates?
No there are a number of factors which can locally affect mutation rates, transcriptional activation is one such, although not neccessarily such a high concern for germline mutations.
Assuning they do, perhaps this would indicate that the 'switch' is thrown somehwere post-transcription. For example, messenger RNA sometimes undergoes splicing or processing prior to translation in higher eukariotic cells, potentially yielding more than one signal protein. Preserving a 'use' for one form of the mRNA would conserve the encoding DNA sequence even though the other form (that triggers wing development) is not produced.
I think we are talking across each other to some extent.
I am quite happy to accept that all protein coding sequences neccessary for wing development are conserved, because almost all the proteins involved have developmental roles in other systems.
What I am less convinced of is the conservation of small regulatory sequences, as small as 5bp even ibp can be crucial to a sites function, which can be located kilobases up or downstream of the gene and serve to drive expression specifically in the wing.
Assuning they do, perhaps this would indicate that the 'switch' is thrown somehwere post-transcription. For example, messenger RNA sometimes undergoes splicing or processing prior to translation in higher eukariotic cells, potentially yielding more than one signal protein. Preserving a 'use' for one form of the mRNA would conserve the encoding DNA sequence even though the other form (that triggers wing development) is not produced.
Only in the functional regions, look at any multiple alignment of DNA or protein sequences from diverse species and you will often see specific regions of high conservation amid other regions of very low homology, these regions are commonly identified as those most important to the conserved function of the protein.
Alternatively, if the signal protein itself undergoes processing in the cytoplasm into more than one form, the switch could also be thrown at this level. Retention of utility of one form of the signal protein (other than the one triggering wing development) would then favor conservation of the encoding DNA sequence even in the apterous state.
Only those regions which are neccessary to the formation and function of the non-wing specific form. As long as the conformation was maintained enough for proper processing and wing specific functional residues could quite readily be lost.
Assuming you are right, and without either of these two types of mechanisms I have proposed to maintain sequence conservation, wouldn't that suggest that the longer a particular lineage remained in the apterous state, the lower the probability of its ever regaining functional wings?
It certainly would suggest that, so one key question is how long ago the various species divergences ocurred. Over tens of millions of years it would be very unlikely that all of the neccessary wing specific regions would be conserved. But not all of the regions would be neccessary for a wing to form, only for one whose development was identical to the ancestral wing.
Surely that doesn't seem to be the case.
The repeated cycle of 'gain and loss' suggests that the controlling region is well conserved even when it isn't expressed.
Not neccessarily, which is why a proper developmental genetics/ bioinformatics based approach would be needed to find out if this was true or if other developmental pathways were modified or co-opted to allow the secondary evolution of wings.
TTFN,
WK
This message has been edited by Wounded King, 05-23-2005 05:09 AM

This message is a reply to:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 144 of 306 (211490)
05-26-2005 1:14 PM
Reply to: Message 143 by EZscience
05-26-2005 10:46 AM


Re: Maintaining developmental programs.
Seemingly, this would indicate that both lineage divergence events and wing 'gain and loss' events likely occured within short periods of abrupt change, consistent with the 'punctuated equilibria' model
Would it? I would have thought that if we assume that the 're-evolved' devlopmental program is identical to the ancestral one then what it would argue is that however long the periods of change were they occurred close together in evolutionary terms, i.e within a million years or less of each other rather than tens of millions. It may be that divergence times could have been calculated from the same data that was used to construct the tree, but I didn't see any in the paper.
If the mutation leading to wing loss is only based on a single mutation, at whatever level, then it may well have arisen effectively instantaneously. As to regaining the trait, once again it depends on whether it is effectively a simple backwards mutation to the original form or an co-option of other extant systems.
Wouldn't the former be the more parsimonious explanation?
I mean, co-opting new developmental pathways to the same end seems less likely to me than reactivating old ones. If true, it would seem to imply that a tremendous degree of evolutionary flexibility exists w/r/t the assignment of function to regulatory sequences.
Once again the answer is 'not neccessarily'. It is only parsimonious unless one considers that some additional mechanism must be required to maintain sequences no longer under selective pressure for however long the gap is between the loss and regaining of flight.
Without knowing more about the specific regulatory sequences which would actually be involved it is hard to speculate on how much change would be needed. Some core binding sites for transcription factors are very small, only four base pairs, and it is not a big stretch of the imagination to think that a four base sequence may be formed quite frequently in DNA.
Regulatory regions are pretty flexible in terms of their downstream effects. Deletions of small regions can radically affect the expression pattern of a gene such as causing it to be globally expressed or lost in a specific tissue. If such a gene is near the top of a regulatory cascade then a lot of othe genes will follow.
I realise this may sound to you a lot like the scenario that you were describing, with a single master control gene for wing development regaining its function and the whole system starting up again, but in the Drosophila wing there are a number of wing specific patterns of expression which require specific regulatory elements to pattern the dorsoventral and antero-posterior axes. It is these sort of elements I think would be likely to be lost. The genes might well still be expressed, but not in exactly the patterns seen in the ancestral wing. so you might have a somewhat cruder form of the ancestral wing program, which might then be subsequently further refined. In this scenario I would expect to see quite significant differences in the wing specific upstream regulatory regions compared to normal homologous wing structures, and possibly differences in the details of gene expression during wing development.
TTFN,
WK
This message has been edited by Wounded King, 05-26-2005 01:14 PM

This message is a reply to:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 146 of 306 (211740)
05-27-2005 7:51 AM
Reply to: Message 145 by MickD
05-27-2005 7:38 AM


So you are in the dogs giving birth to cats camp then?
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 161 of 306 (212568)
05-30-2005 4:39 AM
Reply to: Message 160 by EZscience
05-28-2005 9:25 PM


Re: Maintaining developmental programs.
Definitely! In fact a detailed comparative is exactly what I was initially suggesting although I was more interested in genetic rather than morphological comparison. Whiting states that the homology already observed between phasmid wings and those of other insects, given that the ancestral phasmid state is thought to be wingless, shows conservation of wing morphology over a wingless period of evolution.
I suspect the limits of what can be gleaned from purely morphological data have been reached and only an analysis of the actual developmental program could tell us how conserved the wing is to the previous form. The variations on a theme don't have to be apparent in the final developed wing morphology.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 224 of 306 (218315)
06-21-2005 4:42 AM
Reply to: Message 223 by TimChase
06-21-2005 12:37 AM


Re: "Convergent DNA"
but to neighboring (or at least relatively close) parts of the genome of the same organism.
I'm not sure how you are measuring 'close' here. The microsatellites studied were taken from throughout the human genome, so they were only close in as much as they were part of the same genome.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 229 of 306 (218610)
06-22-2005 6:29 AM
Reply to: Message 225 by TimChase
06-21-2005 10:36 AM


Re: "Convergent DNA"
Well personally I did go to the original paper. That is what I was basing my statement, that they compared microsatellite regions from throughout the genome, on.
(Vowles and Amos, 2004) writes:
From the human genomic sequence, maximum sample size was set at 5,000 randomly selected loci for length classes (AC)2 to (AC)5. For longer microsatellites, of which fewer than 5,000 could be found, all sequences encountered were included.
So they looked at 5000 randomly selected short microsatellite regions and all the available longer microsatellites from throughout the genome.
The effect certainly is local in that a microsatellite predisposes nearby regions to certain mutations. Since many similar microsatellites are found throughout the genome they will predispose many sites throughout the genome to similar patterns of mutation. Similarly if such microsatellites are found in another species there is no reason to suppose they they will not also predipose the local DNA sequence to similar patterns of mutation.
So while the effect of the microsatellites is local the similarities are seen around microsatellites throughout the genome. So the 'convergent' sequences are not necessarily near to each other.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 239 of 306 (218899)
06-23-2005 7:32 AM
Reply to: Message 238 by crashfrog
06-23-2005 7:03 AM


The principle is still sound. If specific sequences can predispose neighouring regions of sequence to specifc patterns of mutation throughout the human genome there is no reason to believe that similar sequences will not lead to similar patterns in other species.
Of course there is a possibility that some specific mechanism is in operation in the human genome and that these patterns would not occur in species lacking the neccessary elements of that mechanism. But in the absence of any such mechanism and assuming it is the composition of the sequence itself that is leading to the effect then there is no reason to doubt that they could lead to convergence in sequences across species.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 241 of 306 (218960)
06-23-2005 12:00 PM
Reply to: Message 240 by EZscience
06-23-2005 11:41 AM


Re: Relevance?
Well they would be relevant as a confounding factor to phylogenies based on genetic data, in the same way that morphological convergence can be a confounding factor in constructing phylogenies based on morphological data.
At the moment there is no evidence that there is any convergence above the amounts expected, let alone a significant amount, in the majority of sequences used to construct phylogenies.
Randman's initial contention was, as I understood it, that morphological convergence in aparticular trait might be tied to convergence of the genetic sequences underlying that trait. Which, if it were the case, might produce problematic data for phylogenetic analyses and undercut the evidence, in favour of common descent, from the congruence of morphological and genetic phylogenies.
This relies on a lot of very unlikely factors, such as ignoring the fact that no-one is likely to start relying solely on the HOX genes or any other key developmental genes likely to affect morphology as their source of data for constructing phylogenies.
But in theory it could produce confounding data.
TTFN,
WK

This message is a reply to:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 244 of 306 (218978)
06-23-2005 12:40 PM
Reply to: Message 243 by PaulK
06-23-2005 12:16 PM


Re: Relevance?
1) The location of the microsatellites - if the locations in 2 species were not very close they would affect different regions of DNA
From the Vowles and Amos paper
If homologous loci are identified through comparisons among their immediate flanking sequences, an element of circularity will be introduced, since loci with lower rates of evolution will be identified preferentially. To circumvent this problem, we used a region 300 bases in length and 220 bases downstream of the microsatellite to conduct each Megablast search.
A total of 8218 chimpanzee loci were identified, and they yielded 5537 unique human homologues.
So they identified 5537 microsattelites uniquely homologues to human microsatellite regions, and these were initially identified by homology in a region covering a considerably larger region than that of the microsatellite or its region of 'influence'.
I don't know to what extent this corresponds to chromosomal synteny.
2) The proportion of mutations that occur within "rnage" of the microsatellites.
This depends rather upon the model of mutation you are looking at. Certainly it is highly unlikely that a protein coding region is going to be within the range of influence of a microsatellite, except perhaps a small (N)2 dinucleotide repeat, but it is not totally impossible that a regulatory element could be near to a substantial microsatellite.
One of the aims of this paper was to investigate whether the rate of mutation was higher or lower than expected in sequences flanking the microsatellites, what was found was that both were the case, but at different positions relative to the microsatellite.
Part of the paper estimates that around 30% of the genome will be under the range of effect of an 'ACAC' repeat. Taking into account other lengths of repeat and dinucleotide sequences the number is likely to be much haigher than that. It is worth bearing in mind however how small a proportion of the genome is actually protein coding.
The best way to get real answers to your questions aboutthe number and nature of mutations would be to read the paper.
TTFN,
WK

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 Message 251 by pink sasquatch, posted 06-23-2005 1:54 PM Wounded King has replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 259 of 306 (219051)
06-23-2005 3:12 PM
Reply to: Message 251 by pink sasquatch
06-23-2005 1:54 PM


Re: highly unlikely? really?
As I was going home I did think that I was overstating things, especially given the small size of the repeats, the length with the greatest effect was (AC)9 and 18 bps isn't really too much to fit into a region near a gene, or even within a gene itself, its only 6 amino acids after all. So on reflection I was definitely overstating this.
The Amos and Vowles paper does draw a distinction between the phenomena they observe and that of repeat expansion/slippage but the Dog paper certainly shows that the microsatellites are ther within the regions containing protein coding genes.
TTFN,
WK

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