Conservation Biology

Friday, July 28, 2006

"WHY" - CHROMOSOMAL ADAM?


The documentary “Journey of Man” is an ambiguous title, which is suggestive of the journey as outlined in the previously viewed documentary “The Real Eve,” as “Mankind,” but also suggests the journey of the male sex literally. The title in itself is a micro-summary of the entire theory of the journey of the human race through the tracking of the male Y- chromosome.

Staying with romanticisms, “Adam” fits in perfectly as the politically correct candidate to lobby the plight of future male offspring…but here is the interesting thing, if there is race to the finish between the genes, who is the most successful, is it man or woman? Can mitochondrial DNA outlast Y-chromosomal DNA in remaining relatively unchanged through generations in evolutionary time, or, is mitochondrial DNA dominant over Y-chromosomal DNA, which is “submissive” because of all the changes which it faces in the same length of time…maybe this explains why stubbornness is a common and unresolved trait amongst so many women today (your comments ladies?). Is it just written in their genes? And it looks as if us males have genes, which just cannot commit…

Lets look at some of the facts again.

Y-chromosomal Adam represents the most recent common ancestor from whom all male sex chromosome are descended [1], and lived approximately 60 000 to 90 000 years ago [1]. The Y-chromosomal DNA (deoxyribonucleic acid) is unique to males because females have two X-chromosomes. The sex chromosomes have two variants, namely male denoted as XY and female XX. The Y-chromosomal DNA, because it is passed from one generation to another, can indicate a purely male historical line of descent [1]. So apart from the sex difference, what else is different in Y-chromosomal DNA and mitochondrial DNA? Y-chromosomal DNA is found in the nucleus, unlike the mitochondrial DNA.

As I have mentioned previously, the chromosomes are macromolucules containing genetic information. This genetic information is supplied in a sequence of codes called alleles, which code for a specific gene [2] like hair colour, eye colour etc. When you put a series of theses alleles together seen on specific locations on the chromosome, this is known as a haplotype, or haploid genotype [3]. Large groups of haploid genotypes form haplogroups [3]. Differences in the Y-chromosomal DNA of people determines the haplogroups [3]. The variation patterns often seen in human DNA is generally accepted as resulting from both neutral processes [4], where mixing of genetic material creates new re-combinations of shared genetic material from mother and father, mutation, and the migration of a group of people to expand their genetic “diversity,” and natural selection [4]. Natural selection is survival of the fittest, and can be seen as “purifying selection,” where useless variants or mutations are removed [4], “balancing selection,” where the most successful variant remains constant [4], or “directional selection,” where trends form in the variants [4]. Directional selection is indicated as rare in human genetics [4], but a reflection of this is the ability of generations of people living in malaria areas having acquired immunity to the parasite for example [4]. Interestingly, looking at this example, Directional selection must therefore be reliant on not only balancing selection, but purifying selection as well since not all progeny toward the successful variant will be successful, and, only the strongest will survive. These directionally selected variants display a signature on the genome, indicated as an increase in the frequency of the selected allele (coding for this gene) and all its subsequent results from other links, which form a haplotype that is found more often than what can be expected normally [4]. These signatures are now also thought to be produced by the results of human activities, since we have to adapt to our new surroundings, particularly during migration, where food items change, diseases are encountered, and changes in climate etc. [4]. If the changes in the variations or mutations can be recognised and mapped, with time-frames given, tracing the migration routes through different geographical areas is possible. What is needed to be more accurate though is the time it takes for normal variations and these accelerated variations to take place, and, how do accelerated variations play a role in swaying time-result-assumptions of migratory processes in humans? A possible answer to this question is the study of population-specific Y-chromosome haplotypes that can act as markers of founder events which happen in the population [6]. This research was sparked by the fact that there is actually reduced variation in the Y-chromosome, less than in the X-chromosome [6].

While digging even further, I was interested to find an echo of what is suggested in “Journey of Man,” that the Khoisan people from Southern Africa genetically may well be the closest living relatives to Y-chromosomal Adam [5]. This is explained by the finding and recording of the types of variations or polymorphisms on the Y-chromosome. A primitive variation “A” is found in 15% of the Khoisan men sampled [5], while “A” is found in 5 – 10% of Sudanese men sampled [5]. All people found living outside Africa have the “T” variation on the Y-chromosome, as do most Africans [5]. It is thought that the “A – T” mutation occurred very early on in human evolution after humans split from Apes [5], with the majority of modern humans now having the “T” variation [5]. This supports the idea of an African origin, but with some differences to that of Mitochondrial Eve.

Also of interest is the Y-chromosomal tool being used to determine the ancestral origins of those African Americans whose ancestors were taken as slaves during the slave trade during the 18th century [7]. From this study, in support of the suggestion of a difference in the mutation variance in the Y-Chromosome of men in Africa, those with an African origin in America have been shown to have a significantly different lineage [7].

Of utmost importance, and something that comes through from most sources is the fact that through Y-chromosome tracking of evolutionary past, the routes of our actions as humans determines not only how we adapted to our new environment physically, but also how we adapted to each other as different populations with different cultures and language, and the spreading of the idea of farming and trade. Our ecological footprint began with us, and is written in our genes. We initially impacted ourselves by changing the environment around us, but look at us now. Presently our ecological footprint has “evolved” from an indication of human presence and ingenuity to ecological erosion!

Thought-provoking!

References

[1] Wikipedia contributors. Y-chromosomal Adam [Internet]. Wikipedia, The Free Encyclopedia; 2006 Jun 29, 09:22 UTC [cited 2006 Jul 28]. Available from: http://en.wikipedia.org/w/index.php?title=Y-chromosomal_Adam&oldid=61169096.

[2] Wikipedia contributors. Allele [Internet]. Wikipedia, The Free Encyclopedia; 2006 Jul 18, 23:25 UTC [cited 2006 Jul 28]. Available from: http://en.wikipedia.org/w/index.php?title=Allele&oldid=64560556.

[3] Wikipedia contributors. Haplogroup [Internet]. Wikipedia, The Free Encyclopedia; 2006 Jul 23, 12:46 UTC [cited 2006 Jul 28]. Available from: http://en.wikipedia.org/w/index.php?title=Haplogroup&oldid=65369165

[4] Zerjal T., Xue Y., Bertorello G., Spencer Wells R., Bao W., Zhu S., Qamar R., Ayub Q., Mohyuddin A., Fu S., Li P., Yuldasheva N., Ruzibakiev R., Xu J., Shu Q., Du R., Yang H., Hurles M. E., Robinson E., Gerelsaikhan T., Dashnyam B., Mehdi Q., and Tyler-Smith C. 2003. The Genetic Legacy of the Mongols. American Journal of Human Genetics 72 (Report. pages not given).

[5] Nelson D. Lecture Notes For Evolution (2) [Internet] 2001 Dec 19. 8:15 [cited 2006 Jul 28] 23:02. Available from: http://drnelson.utmem.edu/evolution2.html

[6] Poloni E. S., Semino O., Passarino G., Santachiara-Benerecetti A. S., Dupanloup I., Langaney A., and Excoffier L. 1997. Human Genetic Affinities for Y-Chromosome P49a,f/Taql Haplotypes Show Strong Correspondence with Linguistics. American Journal of Human Genetics 61: 1015 – 1035.

[7] Parra E. J., Marcini A., Akey J., Martinson J., Batzer M. A., Cooper R., Forrester T., Allison D. B., Deka R., Ferrell R. E., and Shriver M. D. 1998. Estimating African American Admixture Proportions by Use of Population-Specific Alleles. American Journal of Human Genetics 63: 1839 – 1851.

David Vaughan
Senior aquarist, Quarantine
Two Oceans Aquarium
Cape Town, South Africa
dvaughan@aquarium.co.za
davidvaughan.b-logging.com

8 Comments:

  • Hi David
    So, what you are saying is that the y-chromosome mutations are more frequent than the muations seen in the mitochondrial DNA? About the lack of commitment... (has your girlfriend read this??) and stubborness... maybe that's exactly why the mitochondrial lineage goes so much further back in time!

    By Blogger Karen Marais, at July 30, 2006 4:47 PM  

  • Guess it's up to me to be nitpicky again...

    Okay, first off I like that you covered a lot of the important concepts necessary to understand Y-chromosome Adam. And it's all very interesting stuff, and nicely handled.

    However, you need to be more careful about how you phrase things, though. For example, you say that "the Khoisan people from Southern Africa genetically may well be the closest living relatives to Y-chromosomal Adam". What, exactly, does this mean?

    I was also a bit confused by the pragraph about the struggle for dominance between the Y-chromosome DNA and mtDNA.Sexual conflict is indeed a subject worthy of discussion, but mtDNA doesn't really contribute to it (it is, after all, found in both sexes).

    Some other minor issues, but not worth mentioning...Quick question: when mtDNA and Y-DNA disagree about specifics about our ancestry (as with the videos you reviewed), what does it mean? A post on this would be particularly useful, both for me and, I believe, for you...

    Cheers
    Nick

    By Blogger NcK, at July 30, 2006 4:57 PM  

  • Nicks's last point is exactly what I haven't been able to figure out yet! What makes the one better genetic material to work with?? Can someone out there enlighten me? From everything I have read so far, I just dont seem to get the point...

    By Blogger Karen Marais, at July 31, 2006 9:11 AM  

  • Nick, about mtDNA being found in both sexes. That is true, but remember that it is only the female that passes her mitochondrial DNA on to the next generation. Therefore even if her sons inherit her mtDNA, they cannot pass it on as the mtDNA of their sperm cells get discarded after fertilization. The daughters however pass it on to their offspring, where the males again form a mtDNA dead-end, but the females pass it on again to their offspring. So, mtDNA can be used to trace back ONLY the female lineage.

    By Blogger Karen Marais, at July 31, 2006 10:01 AM  

  • Hello everyone!

    Karen, a bit of humour regarding the way we seem to be today and what our genes do...and no, no ex-girlfriends reading this post, ha ha.

    Nick once again thanks for your comment, though I fail to see how my statement is not straight forward. The Khoisan's genes are by far the oldest and therefore the closest living remnants of the genes from Africa. Have a look at the reference: Nelson D. Lecture Notes For Evolution. "May well be" suggests that there is no concrete proof, though evidence is strongest in support of this. Please clarify what is not understood regarding this statement and I will do my best to explain further.

    Cheers

    David

    By Blogger davidvaughan, at July 31, 2006 10:16 AM  

  • Another bloated comment from me, it seems...

    Karen:
    My bad, I misunderstood the point of the paragraph. I thought David was trying to work sexual conflict and sex linkage into the Y-DNA/mtDNA mix. Upon re-reading, I find that the issue of dominance was only to do with which type of DNA is more useful as a tool for tracing our ancestry. Sorry David, I was otherwise occupied on my first reading, and, not being blessed with two X chromosomes, I'm not very good at multi-tasking...

    Given that, I think these are the wrong questions. It's not about which one is "dominant", but rather which is more useful for a particular purpose (if one mutated a lot faster, it would tell us something about recent history and prehistory, while the slower one would allow us to dig further back into time). Both do the same thing - find the ancestral bearer of a particular haplotype.

    Hopefully this will make sense towards the end of the post...


    David:
    I actually did have a look at the reference before I commented. And I'm pretty sure I understand what you (and the source) meant by it - that their Y-DNA is most like that of Y-Adam. But they're only as related to Y-Adam - the actual individual man - as everyone else is, a point which I wasn't sure you understood. The only region of DNA in which that doesn't hold true is, as you know, in the Y-DNA. (Yes, there are other factors that complicate matters, but basically what I've just said is sound)

    It's actually the distinction that's behind most of my comments. Basically, I'm just trying to call your attention to the difference between gene trees and genealogies. It's all got to do with the way sex mixes genes around in a population, destorying any simple notion of linear inheritance.

    You very probably already know this, but maybe you'll want to transform my ramblings into a coherent post that'll put to rest all my doubts and incidentally help you meet your word quota...

    The reason we employ mtDNA and Y-DNA in ancestral reconstruction is that they are far easier to handle than autosomal DNA - they don't have the pitfall of sexual mixing to bring them down, so it's easy to track down ancestors - for that PARTICULAR GENE.

    The reason mtDNA and Y-DNA may tell different stories is that tracing them back is only tracing gene (or haplotype) trees. It's the same reason that two random genes from any of the other chromosomes might tell contrasting tales. Any particular gene may have come from pretty much any member of the ancestral population - sex allows genes from different lineages to combine. Gene ancestors are not the same as the ancestors you'll find in a proper genealogy, which is concerned with INDIVIDUAL ORGANISMS, not individual genes. Genealogies are essentially averages of all the gene trees that could be drawn for an individual.

    Odd point that might illustrate it: it's probable that I'm more closely related to a chimpanzee in one or more of my genes than I am to you.

    All that was a hopeless mess, but I'm sure one of you guys can make sense of it, given the way you've handled technical matters so far (props to you in particular for the massive but well-handled paragraph five, btw).

    If all that sounded like the utterances of a crackhead, feel free to lemme know!

    Cheers
    Nick

    By Blogger NcK, at July 31, 2006 1:13 PM  

  • Nick raises some good points:

    Firstly, the concept of a genetic Adam or Eve can be a bit confusing and we should be careful how we word things. The Khoisan may share a certain genetic mutation with the hypothesised Adam - this does not mean that they are any more closely related to our human ancestors that anyone else on the planet.

    Secondly, (and this also relates to what Karen said earlier) I don't think that either the mtDNA or the Y-chromosome approach is better than the other. They are simply two different methods of tackling the same question and as neither method is perfect, we might expect that they give slightly different answers. For example, there is evidence to suggest that mtDNA might be inherited from fathers on rare occasions. These kinds of small flaws in methodology on both sides (mtDNA and Y-chromosome) might have an influence on the results of the genetic tests and lead to some discrepancies. Which method is more accurate? ... Hard to say.

    Cheers,
    Vanessa.

    By Blogger Vanessa Couldridge, at July 31, 2006 2:51 PM  

  • I asked Prof Channing about this, but he said that you needed to do the test on the same populations and they should give identical results. Unfortunately it is a case of comparing apples with pears. Wikipedia had the following to account for 30 000 years differences is due "to a larger statistical dispersion of the probability distribution for a paleolithic man to have living descendants compared to that of a paleolithic woman. While fertile women had more or less equally distributed chances of giving birth to a certain number of fertile descendants, chances for fertile men varied more widely, with some fathering no children and others fathering many, with multiple women."

    Hope this helps

    Rich

    By Blogger Rich Knight, at July 31, 2006 7:02 PM  

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