The Nature of Mutations

Here are three referencesEvolution of paired domains: isolation and sequencing of jellyfish and
hydra Pax genes related to Pax-5 and Pax-6.Sun H, Rodin A, Zhou Y, Dickinson DP, Harper DE, Hewett-Emmett D, Li WH.Proc Natl Acad Sci USA 1997 May 13;94(10):5156-61.Pax proteins are a family of transcription factors with a highly conserved paired domain; many members also contain a paired-type homeodomain and/or an octapeptide. Nine mammalian Pax genes are known and classified into four subgroups: Pax-1/9, Pax-2/5/8, Pax-3/7, and Pax-4/6. Most of these genes are involved in nervous system development. In particular, Pax-6 is a key regulator that controls eye development in vertebrates and Drosophila. Although the Pax-4/6 subgroup seems to be more closely related to Pax-2/5/8 than to Pax-3/7 or Pax-1/9, its evolutionary origin is unknown. We therefore searched for a Pax-6 homolog and related genes in Cnidaria, which is the lowest phylum of animals that possess a nervous system and eyes. A sea nettle (a jellyfish) genomic library was constructed and two pax genes (Pax-A and -B) were isolated and partially sequenced. Surprisingly, unlike most known Pax genes, the paired box in these two genes contains no intron. In addition, the complete cDNA sequences of hydra Pax-A and -B were obtained. Hydra Pax-B contains both the homeodomain and the octapeptide, whereas hydra Pax-A contains neither. DNA binding assays showed that sea nettle Pax-A and -B and hydra Pax-A paired domains bound to a Pax-5/6 site and a Pax-5 site, although hydra Pax-B paired domain bound neither. An alignment of all available paired domain sequences revealed two highly conserved regions, which cover the DNA binding contact positions. Phylogenetic analysis showed that Pax-A and especially Pax-B were more closely related to Pax-2/5/8 and Pax-4/6 than to Pax-1/9 or Pax-3/7 and that the Pax genes can be classified into two supergroups: Pax-A/Pax-B/Pax-2/5/8/4/6 and Pax-1/9/3/7. From this analysis and the gene structure, we propose that modern Pax-4/6 and Pax-2/5/8 genes evolved from an ancestral gene similar to cnidarian Pax-B, having both the homeodomain and the octapeptide.Pax-6 origins--implications from the structure of two coral pax genes.Catmull J, Hayward DC, McIntyre NE, Reece-Hoyes JS, Mastro R, Callaerts P, Ball EE, Miller DJ.Dev Genes Evol 1998 Aug;208(6):352-6Vertebrate Pax-6 and its Drosophila homolog eyeless play central roles in eye specification, although it is not clear if this represents the ancestral role ofmthis gene class. As the most "primitive" animals with true nervous systems, the,Cnidaria may be informative in terms of the evolution of the Pax gene family. For this reason we surveyed the Pax gene complement of a representative of the basal cnidarian class (the Anthozoa), the coral Acropora millepora. cDNAs encoding two coral Pax proteins were isolated. Pax-Aam encoded a protein containing only a paired domain, whereas Pax-Cam also contained a homeodomain clearly related to those in the Pax-6 family. The paired domains in both proteins most resembled the vertebrate Pax-2/5/8 class, but shared several distinctive substitutions. As in most Pax-6 homologs and orthologs, an intron was present in the Pax-Cam locus at a position corresponding to residues 46/47 in the homeodomain. We propose a model for evolution of the Pax family, in which the ancestor of all of the vertebrate Pax genes most resembled Pax-6, and arose via fusion of a Pax-Aam-like gene (encoding only a paired domain) with an anteriorly-expressed homeobox gene resembling the paired-like class.Pax gene diversity in the basal cnidarian Acropora millepora (Cnidaria,
Anthozoa): implications for the evolution of the Pax gene family.Miller DJ, Hayward DC, Reece-Hoyes JS, Scholten I, Catmull J, Gehring WJ, Callaerts P, Larsen JE, Ball EE.Proc Natl Acad Sci U S A 2000 Apr 25;97(9):4475-80Pax genes encode a family of transcription factors, many of which play key roles in animal embryonic development but whose evolutionary relationships and ancestral functions are unclear. To address these issues, we are characterizing
the Pax gene complement of the coral Acropora millepora, an anthozoan cnidarian. As the simplest animals at the tissue level of organization, cnidarians occupy a key position in animal evolution, and the Anthozoa are the basal class within this diverse phylum. We have identified four Pax genes in Acropora: two (Pax-Aam and Pax-Bam) are orthologs of genes identified in other cnidarians; the others (Pax-Cam and Pax-Dam) are unique to Acropora. Pax-Aam may be orthologous with
Drosophila Pox neuro, and Pax-Bam clearly belongs to the Pax-2/5/8 class. The Pax-Bam Paired domain binds specifically and preferentially to Pax-2/5/8 binding sites. The recently identified Acropora gene Pax-Dam belongs to the Pax-3/7 class. Clearly, substantial diversification of the Pax family occurred before the Cnidaria/higher Metazoa split. The fourth Acropora Pax gene, Pax-Cam, may correspond to the ancestral vertebrate Pax gene and most closely resembles Pax-6. The expression pattern of Pax-Cam, in putative neurons, is consistent with an ancestral role of the Pax family in neural differentiation and
patterning. We have determined the genomic structure of each Acropora Pax gene and show that some splice sites are shared both between the coral genes and between these and Pax genes in triploblastic metazoans. Together, these data support the monophyly of the Pax family and indicate ancient origins of several introns.The PNAS references should be available free online.

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If the history of science has taught you anything, surely you know that science has been wrong on many occassions, and maintained that error ONLY because there was a vast number of scientists in that day and age who - based upon nothing more than emotional attatchment - kept the theory and ideals alive for their own agenda. Phlegistron (?) for example.

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Adaptation is not due to mutation.

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I notice that you are evading the point that your argument rested on misreading the article you referred to. And you do not even identify the supposed error in the science.

Your final point is a strawman. Adaption is explained mutation AND natural selection. Without a source of variation natural selection is powerless. Without natural selection there could not even be such a thing as a beneficial mutation. However a beneficial mutation is - by definition - an adaption.

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I am not a supporter of anyone's "ideas", I am a supporter of the facts. And the facts dictate what is and what is not. A genetic change is not a mutation if it is mediated by the organism. Period.

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I am not aware of any reason to think that that is anything other than your idiosyncratic idea. Why would a heritbable genetic change not be a mutation ?

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A mutation (I have not yet looked over the entire site so I do not yet know what we have decided that your definition of a mutation is, so I will stick with mine until I get that far) is only a random copying error made during replication that mutation correcting enzymes failed to fix. Period.

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That is not my definition, that is the facts.

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So it is your definition, but it is not your definition. If you can't even keep that straight in the course of a single paragraph then I am not about to accept your assertion that it is a fact.

A mutation (I have not yet looked over the entire site so I do not yet know what we have decided that your definition of a mutation is, so I will stick with mine until I get that far) is only a random copying error made during replication that mutation correcting enzymes failed to fix. Period.Ok, ok, let's not keep arguing about the definition of a word.
Let's try this:
There are heritable changes to a genome of an organism. Is this correct?
Some of these heritable changes are purely "random" whatever the word is taken to mean. Is that right?
Other heritable changes are formed by different mechanisms than what you call "mutations". We'll call those HC's.These things (HC's + mutations) supply variation. Is that correct?

So its being proposed that only point mutations be considered 'mutations' and that we call everything else 'heritable changes'? But many mutations, sorry 'heritable changes', other than point mutations are, well lets say stochastic since random is such a controverial concept for some people. I could see a point in distinguishing between sequence rearrangements, chromosome rearrangements and heritable epigenetic changes, but this current idea seems to be based on nothing except trying to make point mutations somehow unique.

The goal was to create a simple definition. Let's stick with the simple definition where any difference in DNA between parent and offspring is a mutation. Then there can be different types of mutations. I'm not the best person to create a list of different mutation types, but a few I can think of are:

• Single nucleotide substitution
  
• Single nucleotide deletion
  
• Single nucleotide addition
  
• Sequence duplication
  
• Sequence deletion
  
• Transposon
  
• Organism mediated (isn't there a better term for this?)
  

--Percy

Percy,Is recombination mutation? I would say so. Not trying to make a point here, but it seems in the broadest sense, that genetic material is being altered, that recombination is mutation too.Mark

Hi Mark,I can't answer your question. As I said, I'm not the best person to list different types of mutation. Someone else take over, please!

The only strong feelings I have about this is that mutation should be defined broadly and simply, and that there definitely should not be a list exceptions of things that are genetic changes but aren't mutations. While you could set up the definitions to work for the exception approach, it would no longer be simple, and I don't think it would be consistent with the definitions in biology textbooks. For example, see the definition of mutation in this site's glossary.

--Percy

hi
the answer to your question is NO
recombination doesnot result in altered function of the gene it merely reshuffles the genes around

maverick,

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recombination doesnot result in altered function of the gene it merely reshuffles the genes around

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Well, it can if the genes are chopped up during recombination, but that really is missing the point. Do chiasma always occur between genes, rather than amongst them? If expressed genetic material is altered during recombination, this is a mutation, surely. Your sperm may contain a geno/pheno type not seen in any human ever-ever-ever, due to recombination, yet it is not a mutation? This is inconsistent with all genetic definitions I've read or understood.

Regardless, a genes function does not have to be altered for a mutation to have occurred, hence the term, "neutral mutation".

Mark

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Occam's razor is not for shaving with.

[This message has been edited by mark24, 05-25-2003][This message has been edited by mark24, 05-25-2003]

Percy,How about; mutation is a change in genetic material that is passed on from one cell to another via mitosis, meiosis, or recombination?This covers both point mutations, chromosomal, & everything inbetween, germ line & somatic?Mark

Mark writes: How about; mutation is a change in genetic material that is passed on from one cell to another via mitosis, meiosis, or recombination?

Maybe this could be covered by adding the word "heritable"?

--Percy

>Percy,But if you want a broad & simple a definition as possible, you'll need to include somatic mutations in the same definition, which of course, are not heritable. In fact, I'd drop the "via mitosis, meiosis, or recombination" from the definition, it's unnecessary.

Mutation is a change in genetic material that is passed on from one cell to another.

Mark

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Occam's razor is not for shaving with.

I think your phrasing here makes it sound like the mutations are transmissable between cells. The maintenance of a mutation in the daughter cells of a somatic cell is still an example of a heritable change, simply one within the cell population rather than that of the organismal population.

Wounded,You're right, how about:

Mutation is a change of genetic material?

Perhaps this too broad, since it allows human tinkering with the genetic material of a cell to come under the umbrella of "mutation" too.

Mark

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Occam's razor is not for shaving with.

Hi Mark,How about, "Mutation is a heritable change of genetic material."

--Percy