The Rise of Human Chromosome 2: Beyond the Deme

Perhaps this is a really stupid question, but I've sometimes heard the argument from Creationists that the fusion event happened after God created man in the last 6,000 years, and quite simply man used to have the same number of chromosomes as Apes and it looked similar because we are relatively similar animals.
I'm pretty sure that the mutational erosion on the telomeres basically proves this fusion happened millions of years ago, but can you properly/scientifically address this claim? I hate seeing Creationists throw it around without a complete answer.

The finding that the probability of fixation in the whole population is roughly equal to the probability of fixation in one deme does not seem intuitively obvious. Indeed, it seems counter intuitive.

If there is no advantage to having the fused chromosome over having two separate ones, and if only one deme out of a meta population of several demes has fixed the fused chromosome, then it seems to me the probability of fixation of the fused form in the whole population from that point on (i.e., once it became fixed in one deme) would be proportional to the 1/(# of demes).

Am I missing something?

Many thanks also to the ID proponent ‘Ilion’ (wherever he may be) for getting me mad enough to actually put it all together.

I’m pretty sure that the mutational erosion on the telomeres basically proves this fusion happened millions of years ago, but can you properly/scientifically address this claim? I hate seeing Creationists throw it around without a complete answer.

— Ken

They pointed out that the process of colonization often involves small groups of individuals, so genetic drift in the form of the “founder effect” plays an important role.

Furthermore, the individuals in these founder groups may be closely related. So, if a chromosome rearrangement becomes established in a deme, then any founder groups derived from it will already have the rearrangement at a very high frequency to start with.

If the group establishes itself in an unoccupied area, fixation would be instantaneous for that deme.

If the group joins another existing group, given that most demes are small, the newcomers may compose a significant percentage of the combined deme.

Therefore, the initial frequency of the rearrangement could already be high enough to exceed the unstable equilibrium frequency (see “Fixation Within a Deme” for discussion of this) and thus drive the rearrangement to fixation there as well.

I'm thinking that this is all well and good, but of course IDers and out-and-out creationists are not really making scientific arguments, and will not be (at least for the vast majority) swayed by your discussion. They aren't really arguing that this is a problem, they are just looking for anything that could possibly cast doubt on the science and reinforce their preconceptions.

Remember, they have already made up their minds. Their arguments are not really intended to start a dialogue (as would be the case if they actually did science). They are intended for the rubes to fall back on, and for them to point out later that they had (of course) devastatingly demolished the evolutionists' arguments (even if their own arguments have been proven false).

Reprod Biol. 2007 Jul;7(2):143-62.(pdf) Links Gonadal expression of aromatase and estrogen receptor alpha genes in two races of Tunisian mice and their hypofertile hybrids.Saïd L, Delalande C, Britton-Davidian J, Saïd K, Saad A, Carreau S. Biochemistry Laboratory, University, Caen, France. House mice (Mus musculus domesticus) in Tunisia consists of two races, one carries the 40-acrocentric standard karyotypes and the other one is a robertsonian race (2n=22) homozygous for nine centric fusions (Rb). The F1 hybrids between the two chromosomal races showed a significant decrease in reproductive success and litter size. Such results can be related to the formation of meiotic trivalent in the hybrids leading to the production of viable aneuploid gametes and post-zygotic elimination of embryos due to chromosomal non disjunction events at meiosis. Moreover, testicular histology of F1 and backcross males showed in some cases a breakdown in spermatogenesis. In both females and males, androgens but also estrogens play an important role in gametogenesis. In this study, we have studied aromatase and estrogen receptor alpha (ERalpha) gene expression in the gonads of the two parental races and their chromosomal hybrids. The results showed that aromatase and ERalpha mRNAs are expressed in hybrid males of inter-racial crosses (female22Rb x male40Std and female40Std x male22Rb) and in hybrid females of inter-racial crosses (female22Rb x male40Std) as in the two parental races. However, in hybrid females of inter-racial crosses (female40Std x male22Rb) the amount of aromatase transcripts decreased sharply suggesting that this gene is involved in the breakdown of hybrid fertility in females, but not in males. However, in hybrid males, a putative post-translational modification of this enzyme, in terms of activity, should be verified.

They aren’t really arguing that this is a problem, they are just looking for anything that could possibly cast doubt on the science and reinforce their preconceptions.

— GvlGeologist, FCD

Remember, they have already made up their minds. Their arguments are not really intended to start a dialogue (as would be the case if they actually did science). They are intended for the rubes to fall back on, and for them to point out later that they had (of course) devastatingly demolished the evolutionists’ arguments (even if their own arguments have been proven false).

GvlGeologist, FCD said: Their arguments...are intended for the rubes to fall back on, and for them to point out later that they had (of course) devastatingly demolished the evolutionists' arguments (even if their own arguments have been proven false).

Great timing with this post as I've been debating Chromosome 2 with someone over at UD and this information is very helpful.

I have just one question you might be able to answer. If a hominid with 48 chromosomes mated with a hominid with only 46 chromosomes because two were fused, wouldn't the two separate chromosomes from the first parent recombine with the fused chromosome of the second parent leaving the offspring with only 46 chromosomes? Would this lead to the change being fixed in the deme even faster than with other mutations?

I have a question similar to that of Camanintx but related to Equus.

Przewalski's Horse (Equus ferus przewalskii), a.k.a. Wild Horses, have 66 chromosomes.

The Tarpan or Eurasian Wild Horse (Equus ferus ferus) have 64 Chromosomes.

The Domestic horse (Equus ferus caballus) has 64 chromosomes.

The donkey (Equus asinus) has 62 chromosomes.

The cross of a domestic horse and a donkey produces a mule or hinney with 63 chromosomes. Crossing a wild horse with a domestic horse produces a horse with 65 chromosomes.

Have the Equus genomes been studied in the same manner than human genomes have been studied in order to determine whether or not there are extra centromeres and/or telomeres?

Thanks,

Ed

Sorry if this is a duplicate, but my last comment seems to have not been posted.

Wild Horses (Equus ferus przewalskii) have 66 chromosomes. Domestic horses (Equus caballus) and have 64 chromosomes, and Donkeys (Equues asinus) have 62 chromosomes. The cross of a domestic horse and a donkey produces a mule or hinney with 63 chromosomes. Crossing a wild horse with a domestic horse produces a horse with 65 chromosomes.

Have any scientists studied the Equus genome in the same manner that scientists have studied the human and ape genome? Do we know whether or not there are extra centromeres and telomeres in the Equus species of lower chromosome number due to fusion of chromosome pairs?

camanintx said: Great timing with this post as I've been debating Chromosome 2 with someone over at UD and this information is very helpful. I have just one question you might be able to answer. If a hominid with 48 chromosomes mated with a hominid with only 46 chromosomes because two were fused, wouldn't the two separate chromosomes from the first parent recombine with the fused chromosome of the second parent leaving the offspring with only 46 chromosomes? Would this lead to the change being fixed in the deme even faster than with other mutations?

INTELLIGENT DESIGN. YOU ARE STUPID IF YOU THINK THAT NATURE IS NOT INTELLIGENT.

Harold, I don't think you see the problem. The statement "The overall fixation probability turned out to be the probability of fixation within that first deme ..." implies (if I am interpreting it correctly) that once a new allele arises in one deme, then it is virtually certain to become fixed in the global population of all demes (since if the probability of A *then* B occurring is the same as the probability of A occurring, then the probability of B occurring once A has occurred is 1.0).

But if there is no advantage to having either form of the chromosome(s) (i.e., fused or separate), then this is not really different from the case of two equivalent alleles, and the deme aspect of it really doesn't change the basic process.

All of the things you noted (the deme with the new allele could split and form a new deme by colonization, or a lot of them could migrate into an existing deme with few members, etc) would be just as likely to occur for demes with the old allele; and there are many more of them. Why couldn't you look at any one (of the many) demes that have the old allele and use the same logic to say that it's allele is virtually certain to become fixed in the population?

Divalent said: Harold, I don't think you see the problem. The statement "The overall fixation probability turned out to be the probability of fixation within that first deme ..." implies (if I am interpreting it correctly) that once a new allele arises in one deme, then it is virtually certain to become fixed in the global population of all demes (since if the probability of A *then* B occurring is the same as the probability of A occurring, then the probability of B occurring once A has occurred is 1.0). But if there is no advantage to having either form of the chromosome(s) (i.e., fused or separate), then this is not really different from the case of two equivalent alleles, and the deme aspect of it really doesn't change the basic process. All of the things you noted (the deme with the new allele could split and form a new deme by colonization, or a lot of them could migrate into an existing deme with few members, etc) would be just as likely to occur for demes with the old allele; and there are many more of them. Why couldn't you look at any one (of the many) demes that have the old allele and use the same logic to say that it's allele is virtually certain to become fixed in the population?

That's why it's important to emphasize to creationists that the "Signature In The Cell" that they claim proves intelligent design creationism cannot be proven to be solely that of Jehovah/Yahweh but can equally be "proven" to be the "signature" of Wotan/Odin, Jupiter/Zeus Pater, Amun-Ra, Brahma, Ometecuhtli, Chthulhu or the Flying Spaghetti Monster.

— Paul Burnett

John Dingleberry said: INTELLIGENT DESIGN. YOU ARE STUPID IF YOU THINK THAT NATURE IS NOT INTELLIGENT.

harold said: No-one is arguing with Dembski or Luskin to convince Dembski or Luskin. Indeed, it's debatable that words like "evidence", "reasoning", or "convince" even have meaning in the context of minds that biased by various factors. The point is to prevent them from being the only voice that third parties hear.

All of the things you noted (the deme with the new allele could split and form a new deme by colonization, or a lot of them could migrate into an existing deme with few members, etc) would be just as likely to occur for demes with the old allele;

and there are many more of them. Why couldn’t you look at any one (of the many) demes that have the old allele and use the same logic to say that it’s allele is virtually certain to become fixed in the population?

INTELLIGENT DESIGN. YOU ARE STUPID IF YOU THINK THAT NATURE IS NOT INTELLIGENT.

Harold, I don’t think you see the problem. The statement “The overall fixation probability turned out to be the probability of fixation within that first deme …” implies (if I am interpreting it correctly) that once a new allele arises in one deme, then it is virtually certain to become fixed in the global population of all demes (since if the probability of A *then* B occurring is the same as the probability of A occurring, then the probability of B occurring once A has occurred is 1.0).

Nature 403, 158 (13 January 2000) | doi:10.1038/35003116 Janice Britton-Davidian1, Josette Catalan1, Maria da Graça Ramalhinho2, Guila Ganem1, Jean-Christophe Auffray1, Ruben Capela3, Manuel Biscoito4, Jeremy B. Searle5 & Maria da Luz Mathias6 AbstractMadeira is a small volcanic island in the Atlantic Ocean with steep mountains separating narrow valleys that are the only areas habitable by humans and their commensals. Here we show that house mice (Mus musculus domesticus ) on Madeira have an unexpected chromosomal diversity, the evolution of which is independent of adaptive processes, relying instead on geographic isolation and genetic drift.

Dave Wisker -

Thank you, by the way.

Raven -

It's unbelievable how much we learn from mice.

actually the punishment for blasphemy is DEATH...

http://www.facebook.com/topic.php?topic=14976&uid=21080812784

see you deluded, fuc*....

I am sending this via email to the entire university - faculty and stuff. Your blaspheming head will serve as example and warning to the whole place...

Sorry if this is a dumb question. I don't have any experience in studying biology, so a lot of the "demes" and "negatively heterotic chromosome" terms are whizzing over my head. I'm having a tough time wrapping my head around this one. I get the notion that point mutations, even frame shifts can occur frequently. These seem like "easy" mutations. I get that these can potentially be passed on. But in order to get "fixed" in a population, unless for some reason the mutation is "dominant" (in some sense?) don't such mutations have to occur more than once? Or, is it sufficient in a sufficiently small population that such a mutation only has to occur once, and with enough inbreeding you eventually get a pair with the right recessive mutation to pass on the full blown mutation?

But the merging or splitting of whole genes? That sounds too "difficult" in some sense to successfully occur very often. Even if a merge or split were to occur again, wouldn't it have to occur at the same point in the same gene(s) in order to "match" in some sense? This difficulty in getting "matching" mutations (if my intuition is anywhere near accurate) would suggest that a given merge or split must have happened only a single (successful) time. This single mutation was then passed on, and through fortuitous inbreeding became "fixed" in some isolated lineage.

Without the jargon, am I on the right track here? And this essay is (perhaps) pointing out that the probabilities of "single" mutations (even "difficult" ones like gene fusion) getting "fixed" in a population are better than earlier predicted or popularly appreciated?

This really isn't a troll question. I was hoping for some edification (I've been following PT for quite some time with great enjoyment), but I'm afraid I got bogged down in the jargon on this one, and didn't get as much out of this essay as I had hoped to.

Thanks for your help and patience.

Scott said: Sorry if this is a dumb question. I don't have any experience in studying biology, so a lot of the "demes" and "negatively heterotic chromosome" terms are whizzing over my head. I'm having a tough time wrapping my head around this one.

Without the jargon, am I on the right track here? And this essay is (perhaps) pointing out that the probabilities of "single" mutations (even "difficult" ones like gene fusion) getting "fixed" in a population are better than earlier predicted or popularly appreciated?

scott: But the merging or splitting of whole genes? That sounds too “difficult” in some sense to successfully occur very often.

I would add is, the probability of fixation is far better than ID’s simplistic claim that it was practically impossible.

Sorry if this is a dumb question. I don’t have any experience in studying biology, so a lot of the “demes” and “negatively heterotic chromosome” terms are whizzing over my head. I’m having a tough time wrapping my head around this one.

I get the notion that point mutations, even frame shifts can occur frequently.

These seem like “easy” mutations.

I get that these can potentially be passed on. But in order to get “fixed” in a population, unless for some reason the mutation is “dominant” (in some sense?) don’t such mutations have to occur more than once?

Or, is it sufficient in a sufficiently small population that such a mutation only has to occur once, and with enough inbreeding you eventually get a pair with the right recessive mutation to pass on the full blown mutation?

But the merging or splitting of whole genes? That sounds too “difficult” in some sense to successfully occur very often.

Even if a merge or split were to occur again, wouldn’t it have to occur at the same point in the same gene(s) in order to “match” in some sense?

This difficulty in getting “matching” mutations (if my intuition is anywhere near accurate) would suggest that a given merge or split must have happened only a single (successful) time. This single mutation was then passed on, and through fortuitous inbreeding became “fixed” in some isolated lineage.

Without the jargon, am I on the right track here? And this essay is (perhaps) pointing out that the probabilities of “single” mutations (even “difficult” ones like gene fusion) getting “fixed” in a population are better than earlier predicted or popularly appreciated?

This really isn’t a troll question. I was hoping for some edification (I’ve been following PT for quite some time with great enjoyment), but I’m afraid I got bogged down in the jargon on this one, and didn’t get as much out of this essay as I had hoped to.

I would also add that there are living species (which I believe Dave knows about more than I) that maintain karyotypic polymorphism within their populations. The reproductive barrier that IDCs like to tos out is not what it is made out to be.

Make that 'toss' out...

The cartoon in your first post is wrong as it shows a Robertsonian fusion in which one arm of the centromere is lost. This happens in cancer cells but is not viable. The fusion of chromoosome 2 is a tandem telemere to telemere fusion in which no coding dna was lost. Robertson studied insects (grasshoppers) and insects don't to my knowledge have these tandem fusions. Also, mice have acentric chromosome fusions since all their chromosome are acentric or acentric fusions. This confusion stems from many biology texts and several papers. Tandem fusions have been found in other mammals, especially mujac deer.

Looking at the dead centromere of chromosome 2 in a genome browser you see two things. One, is that it is very small. the other is that it contains 3 VSA primate retrotransposons of which two are human specific. As centromeres are very dynamic and retrotransposons can be very disruptive one could speculate on perhaps a single cause for the fusion. Just speculation.

The fusion event is currently said to be between 1 and 6 million years ago. Not very accurate. I don't know of any method to date rearrangements as yet. Fusion seems to have stopped the active repeats, inserts and rearrangements of the fused telemeres because in chimps the regions are larger in one of the chromosomes.

Bill Beaver -

Your basic point seems to be correct.

However, Robertsonian translocations can also be germline in humans, and can be compatible with normal phenotype, except that descendants are at risk of chromosome imbalance. Without meaning to offend Wikipedia haters, Wikipedia does have a somewhat decent summary of this, with a small but good quality reference section.

It is certainly true that they can also be seen in cancer cells, which often have many somatic mutations and chromosome abnormalities.

Bill Beaver said: The cartoon in your first post is wrong as it shows a Robertsonian fusion in which one arm of the centromere is lost.

Unrelated but just wondering if anyone has read/heard about this book:
http://www.amazon.com/When-Faith-Science-Collide-Creationism/dp/0982048602/ref=sr_1_1?ie=UTF8&s=books&qid=1253154904&sr=1-1#reader

It was written by a professor in my Geology department (University of Mississippi). He is really adamant about his faith (He doesn't preach in class or anything but he does say up front what he believes). I was thinking of getting it but then I read the 'Tenets' in the first chapter. Any comments/opinions would be appreciated.

Case in point: okapis routinely have either 44, 45 or 46 chromosomes. Most of them are heterozygous (I'm probably misusing the term?) with one fused chromosome (I looked it up, it's rob(4;26)) matched to two unfused chromosomes.

Bring this up when creationists claim that chromosomes can't fuse.

The fusion event is currently said to be between 1 and 6 million years ago. Not very accurate. I don’t know of any method to date rearrangements as yet. Fusion seems to have stopped the active repeats, inserts and rearrangements of the fused telemeres because in chimps the regions are larger in one of the chromosomes.

— Bill Beaver

Y. Fan, E. Linardopoulou, C. Friedman, E. Williams, and B. J. Trask

Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14.1 and Paralogous Regions on Other Human Chromosomes
Genome Res 2002 12:1651-1662

This and it's companion are good papers and about all I've found so far that deals vaguely with timing. It does give a good idea of the complexity of the issue.

Just found another source from UC Davis using biased substitutions dated 2007:

2.94 - .74 million years

www.soe.ucsc.edu/research/compbio/ubcs/ubcs-supp1c.pdf

Thanks Bill!

Let me guess that you have not found any similar publications from the anti-evolution community. I don't mean armchair "critiques" of the hard work of "evolutionists," but papers describing their own hard work and supporting their alternate explanation independently of any problems they might have with evolution.

but papers describing their own hard work

Dave, Harold, Raven: I appreciate your responses. It does sound like my understanding of the essay was on the right track.

1) I'm afraid that stats was one class I didn't do very well in. And re-taking that doesn't sound like fun. :-) One thing that I did learn was that, like quantum mechanics, statistics often runs counter to "intuition".

2) I was at first surprised that changes in the shape or number of chromosomes (which I did confuse with "genes") would allow for successful matings to pass on the change. Thinking further, it only makes sense that some such matings should still be possible, otherwise certain observed speciations (or differences in DNA) would not have been possible.

3) And yes, to be "certain", rather than just speculating, I should run the experiments myself. However, I have neither the time (to change careers again), the expertise, nor the equipment to do such. I'm more than happy to defer to (and learn from) the expertise of those who know better, if I can understand what they're saying. :-)

4) Upon further reflection, it also seems that changes in the shape or number of chromosomes may not be all that "difficult" for successful matings, in that such changes only effect how the genes within them are packaged, rather than in how they are expressed. (Except for any side effects produced by changing the proximity of certain stretches of DNA.) If the gene duplication mechanisms are sufficiently flexible, they should be able to "patch up" differences between the parents' chromosome packaging, to some extent.

Thanks for the clarifications!

And, yes, #4 is still an oversimplification. There are other complications with changes in the shape or number of chromosomes, such as changes in how much of a particular gene product gets expressed. But, certain kinds of changes to the mere morphology of chromosomes should not be as "difficult" to pass on as I first supposed.

Dave Wisker said:

Bill Beaver said: The cartoon in your first post is wrong as it shows a Robertsonian fusion in which one arm of the centromere is lost.

The cartoon was merely an illustration of how a dicentric chromsome could form. That is why I said it was a 'similar' situation, not an exact replica of the fusion itself.

Scott said: I'm afraid that stats was one class I didn't do very well in. And re-taking that doesn't sound like fun. :-) One thing that I did learn was that, like quantum mechanics, statistics often runs counter to "intuition".

Steve P. said:

Dave Wisker said:

Bill Beaver said: The cartoon in your first post is wrong as it shows a Robertsonian fusion in which one arm of the centromere is lost.

The cartoon was merely an illustration of how a dicentric chromsome could form. That is why I said it was a 'similar' situation, not an exact replica of the fusion itself.

Mr. Wisker, I dunno, but its looks like you may be having a Dawkins' moment. Tell me it isn't so. Don't thing the general public needs to be subjected to more 'Weasel'expositions to defend your 'merely an illustration of how a decentric chromosome 'could' form'.

Steve P. said: Don't thing the general public needs to be subjected to more 'Weasel'expositions to defend your 'merely an illustration of how a decentric chromosome 'could' form'.

Steve P. said: Don't think the general public needs to be subjected to ...

Surely Steve P wasn't being serious.

Bob O'H said:

Many thanks also to the ID proponent ‘Ilion’ (wherever he may be) for getting me mad enough to actually put it all together.

Sure Ilion wasn't a 'ras sock?

derwood said: Pretty Sure ...

The difference between God and a programmer is that God does not think he is a programmer.