Non-mendelian genetics/ non-darwinian evolution

I just saw an interesting article about horizontal gene transfer (HGT) on the new scientist website. The article describes a study in which soil bacteria exposed to artificial lightning were found to have taken up exogenous DNA from their environment. The suggestion from the article was that a similar sort of naturally ocurring electroporation could partly account for the apparent high frequency of HGT.This, as well as Salty's recent drive-by, put me to wondering to what extent new discoveries of various non-mendelian genetic systems or exceptions to the generally recieved Darwinian inheritance are being fully integrated into peoples general understanding of evolution.I know that one of the bugbears for many of us is that creationists frequently represent all proponents of evolution as being strict literal adherents to Darwin's writings as if they were some sort of religious doctrine, as some indeed claim they are, but while the inertia in the field of evolutionary biology is clearly not that bad is there not some truth that as more and more exceptions to the various basic foundations of the modern synthesis accrue not enough is being done to give the whole field the sort of radical overhaul it may soon need?Perhaps this is being done outside of the scientific literature, I read very little popular science texts now but more and more people seem to prefer to produce new syntheses of current thinking in the form of saleable popular books rather than as peer reviewed literature, a trend which has allowed the ID movement to make a lot of headway with a surface appearance of scholarly parity.Are there new synthses of evolutionary thinking out there which are accomodating the more recent findings of epigenetics, and other unusual forms of inheritance/gene transfer?TTFN,WK

Not previous or subsequent inheritance perhaps but the initial introduction into the genome is itself an inheritance, albeit from an exogenous source, and therefore distinct from de novo mutations of the genome based on changes or rearrangements of that genome in isolation as it were. No I wouldn't consider transposable elements moving around within a genome to be a form of non mendelian inheritance. I would consider retroviral insertions of exogenous genetic material to be.I have to point out that I am not saying that any of these processes must be both non-mendelian and non-darwinian, just that examples which can be charactised as either of these have arisen and may not as yet have been properly integrated into modern evolutionary thought.I was thinking along the lines of epigenetic effects such as DNA methylation, which is not only responsible for your imprinting but for other heritable changes, or heritable histone alterations of chromosome structure. Many of these epigenetic factors may not be heritable in the long term, at the moment it is not clear to what extent epigenetic factors are generally heritable or how stable those factors are. Also the existence of genetic elements which affect segregation and work to skew population ratios of certain traits, i.e. the Sex-ratio drive gene in Drosophila simulans. I don't think it violates the modern synthesis, but I feel that if you broaden things to the point where 'mutation' covers every concievable route for the introduction of changes in the genome, either genetic or affecting expression epigenetically, then you are making the term meaningless for the purposes of molecular genetics. Distinctions need to be made as to the operation and subsequent effects of these various mechanisms. Certainly they can all act to produce variation within a population and if you are only looking at the level of the phenotypic traits an organism presents then it may not matter what the source of that variation is, but I think that it is still important to distinguish between these various mechanisms as they pertain to the reshaping of a genome if we want to be able to reconstruct an organism or species genetic history as accurately as we can.TTFN,WK

I would consider endosymbiotic acquisition of genetic material, compartmentalised or not, to be non-mendelian, yes.TTFN,WK

It occurred to me that we really need a working definition of what might be considered 'non-mendelian' and 'non-darwinian'. I'll try a couple of definitions first and see what the rest of you think.Or that was what I planned to do, but between my difficulty in framing a really useful definition of either term, having started writing this post at around 10 this morning and only managed about half a paragraph on non-mendelian genetics by 5 in the afternoon, and actually having to do some work today I have totally failed to come up with any as yet, rest assured I shall give it some more thought and get back to you. If anyone else has any definitions they are partial to then all donations are gratefully accepted.TTFN,WKP.S. Here is what I did so far, any critiques or comments are welcome, unless you disagree with me in which case I shall have a hissy fit. This message has been edited by Wounded King, 10-20-2004 12:09 PM

Genotypes would be my preference.TTFN,WKP.S. I'm still thinking, unforunately I actually have to do some work today, anyone reccommend a good method of searching for specific transcription factor binding sites in a sequence almost a megabase long?

It makes mutation meaningless for molecular biology because it covers such a broad spectrum. It may still be useful for organismal and population genetics levels, but if a mutation covers anything from a synonymous point mutation to a large scale rearrangement of the chromosomes themselves then the term 'mutation' without any qualification is fairly meaningless.As to the difference between new retroviral insertions and transposons, I agree that there is no functional difference on the genome between the two, the difference comes in terms of our ability to reconstruct the history of the genome and in terms of whether insertions were the result of jumping around within the genome or a novel insertion, as far as that relates to arguments on informational content of a genome, a line of argument I have never had the neccessary understanding of definitions of information to be really certain of following.This relates to something Mammuthus said in the HERV thread. TTFN,WKP.S. Thanks to mammuthus for that genomatix link, the Matinspector program itself wasn't much use but the Bibliosphere program is very interesting, considerably superior to the other literature mining programs I have tried.

Hi Ooook,There are really two distinct but related concepts of epigenetics being discussed here. Initially epigenetics was used to cover short term alterations to a cell lineage leading to differring cell phenotypes from genetically identical cells, many of the inputs for which are environmental. More recently the inheritance of epigenetically modified DNA, modifications not affecting the primary sequence of the DNA, has become a hot area of research.Both of these share common mechanisms for modifying the genome, such as methylation and chromatin remodelling.What you seem to be describing is a rather loose form of the 1st type, where you suggest that phenotypic plasticity is itself a desirable heritable trait. What you are describing seems to be rather a normal genetic system but one which allows for phenotypic plasticity followed by a restriction of that plasticity, say through the mutation of sites required for the expression of a no longer required phenotype.Clearly this relates to the developmental basis of phenotypic plasticity and therefore epigenetics in the sense of the environmental factors affecting development of the disparate phenotypes. It does not seem to be either a non-mendelian nor a non-darwinian mechanism in the way that the 2nd form of epigenetics may be considered to be.To me you seem to be discussing something along the lines of 'evolvability', I just came across a paper I read some time ago when I was first getting interesed in Evo-Devo, which Mammuthus mentioned previously, which discusses both 'evolvability' and the possible role of Evo-Devo as the source of a major updating of the modern synthesis. For an example of epigenetic inheritance I shall give the address of a full-text article on a heritable methylation based trait in mice. TTFN,WK

Do you mean that it is unclear whether imprinting is simply a parental effect, similar in operation to maternal effect genes setting up initial conditions for the embryos development, or if it is a pattern which is heritable transgenerationally?TTFN,WKP.S. Surely something does not have to contradict mendelian-genetics to be non-mendelian.

Can you clarify this a bit. Do you mean that if an imprinted gene was hypermethylated in the gametes and that methylation was maintained so as to never be expressed then it would be considered some sort of null allele? Even if the actual gene itself was fully functional?On further reflection I see what you mean about the representation in the paper, that mendelian genetics is base on an assumption of equal expression of the 2 inherited alleles. I don't think this is unreasonable in the context of changes within the protein coding regions of a gene, but it obviously falls down somewhat when the source of the allelic variation is within a regulatory region and causes differences in levels of expression itself.I'm not sure if this equivalence of expression levels is really a neccessary feature for menedelian inheritance, although I can see how it works as a simplifying assumption. Ceratinly I can see a distinction between a difference in expression based upon a change in the primary sequence of DNA in a regulatory region and one based upon the hypermethylation of the gene in question.TTFN,WKThis message has been edited by Wounded King, 10-26-2004 08:20 AM

I just had my attention drawn to a new paper in 'Genes & Development' on an apparent induction of stable epigenetic inheritance in flies. It isn't totally clear how distinct this mechanism is from other previously noted epigenetic modifications localised to chromatin restructuring or methylation but it has been induced in a novel way.TTFN,WK

I'm a bad lazy person and I never got around to properly writing up my thoughts on this topic. Nevertheless I thought I might bump this thread since a new and interesting 'non-mendelian' paper has come up. The paper is being discussed in the 'Mendel wasn't entirely right' thread, whose originator seems to be under the impression that Mendelian genetics is both the be all and end all of genetics and some sort of keystone of all evolution, so I thought a little reminder of the other factors known to mediate inherited characteristics would be worthwhile.TTFN,WK

More epigenetic inheritance research, this time from Science. So this methylation based male infertility has been heritable over 4 generations.TTFN,WK

Another non-mendelian example probably related to epigenetic factors. In mice again and this time associated with tail colour (Rassoulzadegan, et al., 2006). TTFN,WK

I'd be inclined to count this as a form of cytoplasmic inheritance if the bacteria aren't actually enclosed in the bacteriocyte.Actually looking at some of the literature it seems that rather than an organelle, unless you are using this in an unusual way, the bacteriocytes are actually specialised cells (Braendle, et al., 2003).It sounds quite similar to the maternal transmission of acquired immunity to me. I'd definitely tend to consider this a valid example of epigentic inheritance, akin to mitochondrial inheritance but on an organismal rather than cellular level.TTFN,WKEdited by Wounded King, : for comprehensibility