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I got into trouble with someone yesterday for poo-pooing this idea as it smelled of apples and oranges to me.

The specific statistic was that genetically there is a 5% difference between men and women, while there is only a 2% difference between men and (I assume) male chimpanzees.

Googling briefly brought up this (hardly authoritative) quote.

So, is this even true? And if it is, what gives?

EDIT I chose a bad example, as vartec points out below. I actually heard this in French, here's an example, which (roughly) says:

"Genetically, there is only a 2% difference between men and male chimpanzees, whereas there is a 5% difference between men and women: thus there are twice as many differences between men and women than between men and male chimpanzees"

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The Y chromosome doesn't contain many genes, so this figure sounds highly suspicious! Another problem with any genetic difference statistic is how it is defined. Is it based on nucleotide similarity at the exon level? What about when different genes have different copy numbers in different species? –  Nick Aug 23 '12 at 10:06
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Article states, that there is more difference between men and male chimps, than women and female chimps, not that the difference is more than the one between man and women. –  vartec Aug 23 '12 at 10:07
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Just quick calculation, the Y chromosome is 59Mbase long, and the whole genome is 3194Mbase. (en.wikipedia.org/wiki/Human_genes). This means the Y is 1.8% of the genome. Women and men cannot therefore differ by more than this, as this is assuming the Y is completely different to anything in the X chromosome, while there could be overlap. Therefore 5% difference between men and women is completely wrong. –  Nick Aug 23 '12 at 12:20
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@Nick, what I suspect is the following 'reasoning': human/chimp DNA difference ≈ 2%, male/female chromosome difference is 1/22 ≈ 5%. So, apples and oranges, but I would like some confirmation... –  Benjol Aug 23 '12 at 13:19
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@Nick: Why is the difference determined by the length of Y chromosome rather than the longer length of the second/missing X chromosome? Colour blindness / haemophilia / similar X-chromosome recessive features are predominately expressed in males because of this genetic difference. –  Henry Aug 24 '12 at 17:06

2 Answers 2

The only genetic difference between men and women is that men have 1 Y chromosome and 1 X chromosome on their sex determinative chromosome.

The Human Genome

The human (Homo sapiens) genome is stored on 23 chromosome pairs and in the small mitochondrial DNA. Twenty-two of the 23 chromosomes belong to autosomal chromosome pairs, while the remaining pair is sex determinative.

So there are a total of 46 chromosomes on the normal human. Any 45 of them can be shared by men and women and only 1 belongs to men only. Simple math (1/46) says that the difference is < 2.2% if 100% of the Y chromosome is unique to the Y chromosome and the number of genes on each is roughly equal.

However the Chromosomes are not equal.

The human chromosomes that determine sex, the X and Y, are a bizarre pair. The other 22 sets of chromosomes in our cells consist of wellmatched partners, as alike as twin candlesticks. One chromosome in each duo comes from the mother and one from the father, but both are normally the same size and carry the same genes. (Genes are the DNA blueprints for proteins, which do most of the work in the body.) In stark contrast, the Y chromosome is much smaller than the X; in fact, it is positively puny. It harbors no more than several dozen genes, far fewer than the 2,000 to 3,000 on the X. A number of the Y genes have no kin at all on the X. And the Y is riddled with unusually high amounts of "junk" DNA: sequences of code letters, or nucleotides, that contain no instructions for making useful molecules.

The human genome is estimated to contain 20,000-25,000 genes. The Y chromosome has 231. Other than those 231 sequences that do not exist in the female all of the genes are shared. So the math says (231/20000) so < 1.2% difference.

So the numbers in the quote are wrong. But is there more difference between Men and Women than humans and Chimps? For that I found this research which found:

Humans and chimps can have 95% or >98.5% similar DNA depending on which nucleotides are counted and which are excluded.

So even using best case Men vs Women < 1.2% : Man vs Chimp > 1.5%

Clearly this is false.

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Having two X chromosomes is different than having one X chromosome. Women that have only one X chromosome look a lot more manly than normal women that have two X. –  Christian Aug 26 '12 at 21:25
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@Christian - Agreed but this question is about the genetic difference between normal humans. A chimp looks completely different than a human despite being as much 98% similar in DNA. Even a human missing or with extra sex chromosomes. –  Chad Aug 29 '12 at 12:18
    
I don't see how that justifies your 1.2% difference for Men vs. Women. The 1.2% is XY Men vs. X Women, when the question is more about XY vs. XX. –  Christian Aug 29 '12 at 18:19
    
@Christian actually the math works out the same. There are 231 genes that are different between men and women. a Single X woman has the same genes as a XX woman. She just can not recombine to express them differently. –  Chad Aug 29 '12 at 18:47
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@Christian - This question is about the statistics not the expression though. You are not wrong but in this case you are wanting to fight about the color of the grass when we are just counting the number of blades. –  Chad Aug 30 '12 at 13:44

See "Relatedness" article on "The Tech Museum of Innovation" site, part of "Stanford at The Tech Understanding Genetics" where this question is answered by a Geneticist. Here's the pertinent excerpt from the article:

So is the bottom line that men and male chimps have more in common than men and women? Of course not. If we take a closer look, we see some of the dangers of looking at raw percentages instead of individual changes.

source

Another way to think about this is the 55 million or so differences between men and women are all concentrated on one chromosome and 78 genes. For chimps, the 42-150 million differences are spread out all over the chromosomes over many, many more genes.

In other words, while the quantity of changes may be the same, the quality is different. Even though we share most of our genes with a chimpanzee, lots of the chimp's genes have changed in ways not seen in people. These changes make a chimp a chimp and a human a human."*

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Welcome to Skeptics! Please provide some more authoritative references to support your claims. –  Sklivvz Jan 10 '13 at 21:47

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