I attended the American Society of Human Genetics 2012 meeting last week. The following work presented by a Berkeley lab at the meeting shows that the whole Y chr is under strong purifying natural selection and shows extremely low diversity. Thus the markers on Y chr are not neutral and should not be used for phylogeny inferences. If two different human populations share some hypolotypes in Y chr, it does not indicate shared ancestry but rather some sort of common selection. We have been saying in recent years that nearly all human genome variations are not neutral and are under natural selection. There are essentially no junks. To date human evolution history, one must use slow evolving neutral sequences as we have been advocating. All existing literature on human history using Y chr or mtDNA or any other sequences are mistaken.
There are only one scientific theory known so far that advocates no junk DNAs, i.e., the MGD hypothesis. Much work in recent years have essentially killed the junk DNA concept, most recently by the ENCODE finding of at least 80% human genome being functional. But the theory that predicts the neutral and junk DNA concept still remains to be overthrown. The MGD represents the best chance to explain nearly 100% functional genome and to supercede the neutral theory.
Abundant selection explains low diversity on human Y chromosomes. M. Wilson Sayres1,2, K. Lohmueller1,2, R. Nielsen1,2 1) Integrative Biology, University of California, Berkeley, Berkeley, CA; 2) Statistics, University of California, Berkeley, Berkeley, CA.
The human Y chromosome exhibits levels of diversity that are significantly lower than expected under neutral population genetic theory. Variance in male reproductive success (reducing the effective population size of males relative to females) has recently been proposed as an alternative neutral model to explain reduced diversity on the Y relative to mtDNA. Generally Y chromosomes are not included in whole genome analyses, so explicit tests of this hypothesis have yet to be conducted. Here we show that neutral models with unequal male and female effective population sizes are not consistent with observed genome-wide diversity on autosomes, X, Y and mtDNA across completely sequenced males. Instead, a model including selection is needed to explain the departure of observed Y diversity from expectations. We found that models with similar estimates of the strength of background selection can explain diversity for both the Y chromosome and mitochondrial genomes. Our results suggest that strong selection is necessary for explaining the evolutionary history of the human Y chromosome, and argue against the concept of the "junk" Y chromosome .
There are only one scientific theory known so far that advocates no junk DNAs, i.e., the MGD hypothesis. Much work in recent years have essentially killed the junk DNA concept, most recently by the ENCODE finding of at least 80% human genome being functional. But the theory that predicts the neutral and junk DNA concept still remains to be overthrown. The MGD represents the best chance to explain nearly 100% functional genome and to supercede the neutral theory.
Abundant selection explains low diversity on human Y chromosomes. M. Wilson Sayres1,2, K. Lohmueller1,2, R. Nielsen1,2 1) Integrative Biology, University of California, Berkeley, Berkeley, CA; 2) Statistics, University of California, Berkeley, Berkeley, CA.
The human Y chromosome exhibits levels of diversity that are significantly lower than expected under neutral population genetic theory. Variance in male reproductive success (reducing the effective population size of males relative to females) has recently been proposed as an alternative neutral model to explain reduced diversity on the Y relative to mtDNA. Generally Y chromosomes are not included in whole genome analyses, so explicit tests of this hypothesis have yet to be conducted. Here we show that neutral models with unequal male and female effective population sizes are not consistent with observed genome-wide diversity on autosomes, X, Y and mtDNA across completely sequenced males. Instead, a model including selection is needed to explain the departure of observed Y diversity from expectations. We found that models with similar estimates of the strength of background selection can explain diversity for both the Y chromosome and mitochondrial genomes. Our results suggest that strong selection is necessary for explaining the evolutionary history of the human Y chromosome, and argue against the concept of the "junk" Y chromosome .
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