Dear Percy,
I have some comments on the human ZFY region:
It was very surprising that within the samples obtained from human subpopulations NO polymorphisms were detected whatsoever. On the contrary, inspection of the corresponding homologous intron region in the primates reveals that several variable sites are distributed throughout the intron and include at least 39 substitutions (21 transitions and 14 transversions) and 4 insertion/deletion (indel) mutations. Thus, at least 5% variation in this region is observed between human and primates.
The complete absence of variation in the ZFY region in humans is very awkward, and, according to the authors, cannot be ascribed to a chance alone (= random mechanism).
Introns are thought to be subject to neutral evolution, and variation within the human population is predicted on neutral positions. Confronted with the peculiar situation of the absence of variation, the authors must apply statistics to define an era when the common ancestor of all males lived. They estimate that ‘Y-chromosome Adam’ lived around 270.000 (range 0-800.000) years before present.
It should be noted that the non-variant intron sequences in the ZFY region provides a severe problem for evolution biologists, since molecular rules demand some neutral evolution: variation on silent positions. But, he authors state that "the invariance likely may results from a selective sweep, a recent origin of modern Homo sapiens, or a historically small effective male population sizes". Let us have a look what this evolutionary jargon means.
Humans have 46 chromosomes. One set of 23 chromosomes is inherited from the mother, including the sex-determining chromosome X. The other set of 23 chromosomes is obtained from the father, and may include either an X- or a Y chromosome. Females have two 22 pairs of autosomal and one pair of X chromosomes. Therefore, all genes are backed up by an additional copy. In contrast, males have one X chromosome and a Y chromosome. Genetic information on these chromosomes is present as single non-allelic genes, meaning that these genes are not backed up by genes present on other chromosomes.
Because the X and Y chromosome have little sequence homology there is no recombination possible between the major part of these chromosomes, and most of the genes on the Y chromosome will behave as one linked genetic group. Hence, if an advantageous mutation occurs in a gene on the Y chromosome it will drag with it all the non-recombining parts of the chromosome. A rapid, natural selection driven fixation of any advantageous gene on the Y chromosome would therefore result in loss of variance throughout the entire Y chromosome (Svante Paabo in Nature). Because all non-recombining DNA sequences of the Y chromosome are replaced in a single sweep, this vision predicts that variability should be absent in all linked non-recombining Y chromosome genes.
A recent study in mice on the non-coding region flanking the SRY gene, which is directly responsible for inducing maleness, is revealing in this matter. The study compared the amount of variation within the species and related it to the amount of variation among species. Then, the authors compared this ratio to the ratio for a rapidly changing region in the mitochondrial DNA obtained in the same way.
If any of the two regions were subject to a selective sweep, it would be demonstrated by a reduced variation within species. It was found, however, that the non-coding region of the SRY gene changed at a neutral rate. It implicates that, because of linkage of the major part of the Y chromosomal genes, the entire non-recombining part of the Y chromosome changes at a neutral rate. Therefore, it is unlikely that natural selection acts upon the Y chromosome. More recently, similar findings were observed in human.
But if natural selection did not act upon the Y chromosome the high degree of variability of the Y chromosome between primates apparently defies the theory of evolution, since the coding region of the SRY gene is very stable within a species, whereas considerable variation is observed between distinct species (again!).
"Some part of the SRY protein show such high degree of variability between distinct primate species that one must conclude that part of the protein has no function at all, or that the gene is subject to directional selection (!)", says evolution biologist Svante Pbo in Nature. However, directional selection is only demonstrated in cases involving intergenomic conflict, such as occur between host and pathogen, but is has never been observed for non-immune system related protein coding genes.
The only remaining scientific explanation of the variability in the Y chromosome between species is by the mechanism of NEUTRAL EVOLUTION. Yet, the observation that more replacement substitutions than synonymous substitutions are present between species suggests that a neutral mechanism is not likely to be responsible for variation among species. The ultimate hypothesis evolutionists propose is that "these regions have been retained throughout the primate lineage without any requirement for sequence conservation, implying that the SRY protein is [] the HMG box alone".
But that doesn't solve the problem. It would still imply that the SRY protein is expected to evolve at a neutral rate! The peculiar thing about the SRY proteins was, however, that they are much more variable than predicted by neutral evolution. To properly understand this one has to assume selection on neutral positions (= neutral selection!!). (OR: a NON-RANDOM mechanism of mutations).
I can imagine that evolutionary biologists really get frustrated solving the riddles around the SRY region. Despite several ad hoc hypotheses it all ends in a paradox. Apparently, there is no explanation for the high degree of dissimilarity of SRY region between distinct primates within the current evolutionary paradigm.
Best wishes,
Peter
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